{ "exit_code": null, "summary": { "num_errors": 0, "num_failures": 0, "num_skips": 0, "num_tests": 1 }, "tests": [ { "data": { "end_datetime": "2026-09-18T00:37:24.385162", "execution_problem": null, "inputs": { "reads_paired_collection": { "class": "Collection", "collection_type": "list:paired", "elements": [ { "class": "Collection", "collection_type": "paired", "elements": [ { "class": "File", "identifier": "forward", "path": "test-data/SRR5085167_forward.fastqsanger.gz" }, { "class": "File", "identifier": "reverse", "path": "test-data/SRR5085167_reverse.fastqsanger.gz" } ], "identifier": "SRR5085167" }, { "class": "Collection", "collection_type": "paired", "elements": [ { "class": "File", "identifier": "forward", "path": "test-data/SRR5085168_forward.fastqsanger.gz" }, { "class": "File", "identifier": "reverse", "path": "test-data/SRR5085168_reverse.fastqsanger.gz" } ], "identifier": "SRR5085168" }, { "class": "Collection", "collection_type": "paired", "elements": [ { "class": "File", "identifier": "forward", "path": "test-data/SRR5085169_forward.fastqsanger.gz" }, { "class": "File", "identifier": "reverse", "path": "test-data/SRR5085169_reverse.fastqsanger.gz" } ], "identifier": "SRR5085169" }, { "class": "Collection", "collection_type": "paired", "elements": [ { "class": "File", "identifier": "forward", "path": "test-data/SRR5085170_forward.fastqsanger.gz" }, { "class": "File", "identifier": "reverse", "path": "test-data/SRR5085170_reverse.fastqsanger.gz" } ], "identifier": "SRR5085170" } ] }, "salmon_index": { "class": "File", "filetype": "fasta", "path": "test-data/transcriptome.fasta" }, "sample_metadata": { "class": "File", "filetype": "tabular", "path": "test-data/sample_metadata.tabular" }, "tx2gene_map": { "class": "File", "filetype": "tabular", "path": "test-data/tx2gene.tabular" } }, "invocation_details": { "details": { "error_message": null, "history_id": "ab426e56a688ed95", "history_state": "ok", "invocation_id": "ab426e56a688ed95", "invocation_state": "scheduled", "messages": [], "workflow_id": "ab426e56a688ed95" }, "steps": { "0. reads_paired_collection": { "action": null, "id": "ab426e56a688ed95", "implicit_collection_jobs_id": null, "job_id": null, "jobs": [], "model_class": "WorkflowInvocationStep", "order_index": 0, "output_collections": { "output": { "id": "ab426e56a688ed95", "src": "hdca" } }, "outputs": {}, "state": "scheduled", "subworkflow": null, "subworkflow_invocation_id": null, "update_time": "2026-09-17T22:35:57.519266", "workflow_step_id": "2cb54babe410fc94", "workflow_step_label": "reads_paired_collection", "workflow_step_uuid": "7d56b955-14ad-4a46-a725-fdfd61132d27" }, "1. salmon_index": { "action": null, "id": "d67aa88f27cf1ce3", "implicit_collection_jobs_id": null, "job_id": null, "jobs": [], "model_class": "WorkflowInvocationStep", "order_index": 1, "output_collections": {}, "outputs": { "output": { "id": "9dfa17f44c905ecf", "src": "hda", "uuid": "92fd78af-c743-4925-9063-bddbc393e415" } }, "state": "scheduled", "subworkflow": null, "subworkflow_invocation_id": null, "update_time": "2026-09-17T22:35:57.519267", "workflow_step_id": "4e0ba31121077773", "workflow_step_label": "salmon_index", "workflow_step_uuid": "693bf0c6-9be0-4add-aae6-c384899e73f9" }, "2. sample_metadata": { "action": null, "id": "2cb54babe410fc94", "implicit_collection_jobs_id": null, "job_id": null, "jobs": [], "model_class": "WorkflowInvocationStep", "order_index": 2, "output_collections": {}, "outputs": { "output": { "id": "4e5a7135364a358a", "src": "hda", "uuid": "780cf916-4908-4afe-b6d2-33585818cad7" } }, "state": "scheduled", "subworkflow": null, "subworkflow_invocation_id": null, "update_time": "2026-09-17T22:35:57.519268", "workflow_step_id": "1c80d65d322b105c", "workflow_step_label": "sample_metadata", "workflow_step_uuid": "99186d21-c196-4c06-bf8b-ad297086bef1" }, "3. tx2gene_map": { "action": null, "id": "4e0ba31121077773", "implicit_collection_jobs_id": null, "job_id": null, "jobs": [], "model_class": "WorkflowInvocationStep", "order_index": 3, "output_collections": {}, "outputs": { "output": { "id": "ee96573fcbe71150", "src": "hda", "uuid": "1c5a4296-cbb5-4821-bdb7-ba0e4a0034ef" } }, "state": "scheduled", "subworkflow": null, "subworkflow_invocation_id": null, "update_time": "2026-09-17T22:35:57.519269", "workflow_step_id": "99bd1f66aad6c7b5", "workflow_step_label": "tx2gene_map", "workflow_step_uuid": "98bb30a2-507f-4f97-b443-e803d04e9975" }, "4. salmon_quant": { "action": null, "id": "1c80d65d322b105c", "implicit_collection_jobs_id": null, "job_id": null, "jobs": [ { "command_line": "SLOTS=$(( ${GALAXY_SLOTS:-4} > 1 ? ${GALAXY_SLOTS:-4} - 1 : 1 )); mkdir ./index && mkdir ./output && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/9/2/f/dataset_92fd78af-c743-4925-9063-bddbc393e415.dat' 'input_index.fasta' && salmon --no-version-check index -i ./index --kmerLen '31' --gencode --threads \"$SLOTS\" --transcripts 'input_index.fasta' && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/1/0/1/dataset_10154cd9-fadd-4b3c-8eda-c980273d7660.dat' ./mate1.fastq && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/e/0/2/dataset_e0200b37-84c3-4836-a919-72b9416f9613.dat' ./mate2.fastq && salmon --no-version-check quant --index './index' --libType A --mates1 <(zcat < ./mate1.fastq) --mates2 <(zcat < ./mate2.fastq) --threads \"$SLOTS\" --consensusSlack '0.349999994' --incompatPrior '0.0' --minAssignedFrags '10' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '200' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --rangeFactorizationBins '4' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '0.01' -o ./output", "command_version": "1.10.1", "copied_from_job_id": null, "create_time": "2026-09-17T22:35:57.555000", "dependencies": [], "exit_code": 0, "external_id": "33599", "galaxy_version": "26.1", "handler": null, "history_id": "ab426e56a688ed95", "id": "32d9dd6ff07d88c9", "inputs": { "quant_type|input|single_or_paired|input_11": { "id": "ab426e56a688ed95", "src": "hda", "uuid": "10154cd9-fadd-4b3c-8eda-c980273d7660" }, "quant_type|input|single_or_paired|input_12": { "id": "d67aa88f27cf1ce3", "src": "hda", "uuid": "e0200b37-84c3-4836-a919-72b9416f9613" }, "quant_type|refTranscriptSource|s_index|fasta": { "id": "9dfa17f44c905ecf", "src": "hda", "uuid": "92fd78af-c743-4925-9063-bddbc393e415" } }, "job_messages": [], "job_metrics": [ { "name": "container_id", "plugin": "core", "raw_value": "quay.io/biocontainers/mulled-v2-1db50f99443206288f90b902e1044e9932611944:15d91f5dbe07eb894f2e2f01d20c25d30301434b-0", "title": "Container ID", "value": "quay.io/biocontainers/mulled-v2-1db50f99443206288f90b902e1044e9932611944:15d91f5dbe07eb894f2e2f01d20c25d30301434b-0" }, { "name": "container_type", "plugin": "core", "raw_value": "docker", "title": "Container Type", "value": "docker" }, { "name": "galaxy_slots", "plugin": "core", "raw_value": "1.0000000", "title": "Cores Allocated", "value": "1" }, { "name": "start_epoch", "plugin": "core", "raw_value": "1789684558.0000000", "title": "Job Start Time", "value": "2026-09-18 00:35:58" }, { "name": "end_epoch", "plugin": "core", "raw_value": "1789684563.0000000", "title": "Job End Time", "value": "2026-09-18 00:36:03" }, { "name": "runtime_seconds", "plugin": "core", "raw_value": "5.0000000", "title": "Job Runtime (Wall Clock)", "value": "5 seconds" } ], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "output_quant": { "id": "d67aa88f27cf1ce3", "src": "hdca" } }, "outputs": { "output_quant": { "id": "32d9dd6ff07d88c9", "src": "hda", "uuid": "f041bf5b-d266-4bbf-99ba-d158ecf8144a" } }, "params": { "__input_ext": "\"input\"", "__workflow_invocation_uuid__": "\"26835a54b2e811f1a764e6fd7feff8e8\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"200\", \"minAssignedFrags\": \"10\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"4\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"0.01\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "chromInfo": "\"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "gcBias": "false", "geneMap": null, "generate_aux": "false", "incompatPrior": "\"0.0\"", "meta": "false", "quant_type": "{\"__current_case__\": 0, \"bam_options\": {\"__current_case__\": 1, \"writeMappings\": \"\"}, \"consensusSlack\": \"0.349999994\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": false, \"input\": {\"single_or_paired\": {\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 1, \"src\": \"dce\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"single_or_paired_opts\": \"paired_collection\"}}, \"qtype\": \"reads\", \"recoverOrphans\": false, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 9, \"src\": \"hda\"}]}, \"genome\": null, \"kmer\": \"31\"}}, \"validmap\": {\"__current_case__\": 1, \"validateMappings\": \"\"}}", "seqBias": "false" }, "state": "ok", "stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\n[2026-09-17 22:35:59.502] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2026-09-17 22:35:59.504] [jLog] [info] building index\nout : ./index\n[2026-09-17 22:35:59.505] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2026-09-17 22:35:59.525] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2026-09-17 22:35:59.525] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 24 cleaned references\n[2026-09-17 22:35:59.530] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2026-09-17 22:35:59.531] [puff::index::jointLog] [info] ntHll estimated 48842 distinct k-mers, setting filter size to 2^20\nTwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.\nTwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);\nallowedIn: 5\nMax Junction ID: 89\nseen.size():721 kmerInfo.size():90\napproximateContigTotalLength: 4056\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 25 element count: 4800 complex nodes: 0\n# of ones in rank vector: 24\n[2026-09-17 22:35:59.564] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2026-09-17 22:35:59.565] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 4800\n-----------------------------------------\n| Loading contigs | Time = 371.71 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading contig boundaries | Time = 348.88 us\n-----------------------------------------\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n24\n[2026-09-17 22:35:59.568] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2026-09-17 22:35:59.568] [puff::index::jointLog] [info] contig count for validation: 24\n[2026-09-17 22:35:59.569] [puff::index::jointLog] [info] Total # of Contigs : 24\n[2026-09-17 22:35:59.569] [puff::index::jointLog] [info] Total # of numerical Contigs : 24\n[2026-09-17 22:35:59.569] [puff::index::jointLog] [info] Total # of contig vec entries: 24\n[2026-09-17 22:35:59.569] [puff::index::jointLog] [info] bits per offset entry 5\n[2026-09-17 22:35:59.570] [puff::index::jointLog] [info] Done constructing the contig vector. 25\n[2026-09-17 22:35:59.571] [puff::index::jointLog] [info] # segments = 24\n[2026-09-17 22:35:59.571] [puff::index::jointLog] [info] total length = 4800\n[2026-09-17 22:35:59.574] [puff::index::jointLog] [info] Reading the reference files ...\n[2026-09-17 22:35:59.576] [puff::index::jointLog] [info] positional integer width = 13\n[2026-09-17 22:35:59.576] [puff::index::jointLog] [info] seqSize = 4800\n[2026-09-17 22:35:59.576] [puff::index::jointLog] [info] rankSize = 4800\n[2026-09-17 22:35:59.576] [puff::index::jointLog] [info] edgeVecSize = 0\n[2026-09-17 22:35:59.576] [puff::index::jointLog] [info] num keys = 4080\n\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2026-09-17 22:35:59.598] [puff::index::jointLog] [info] mphf size = 0.00328064 MB\n[2026-09-17 22:35:59.598] [puff::index::jointLog] [info] chunk size = 4800\n[2026-09-17 22:35:59.599] [puff::index::jointLog] [info] chunk 0 = [0, 4770)\n[2026-09-17 22:35:59.599] [puff::index::jointLog] [info] finished populating pos vector\n[2026-09-17 22:35:59.599] [puff::index::jointLog] [info] writing index components\n[2026-09-17 22:35:59.604] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2026-09-17 22:35:59.606] [jLog] [info] done building index\n### salmon (selective-alignment-based) v1.10.1\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { A }\n### [ mates1 ] => { /dev/fd/63 }\n### [ mates2 ] => { /dev/fd/62 }\n### [ threads ] => { 1 }\n### [ consensusSlack ] => { 0.349999994 }\n### [ incompatPrior ] => { 0.0 }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 200 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ rangeFactorizationBins ] => { 4 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 0.01 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n-----------------------------------------\n| Loading contig table | Time = 850.71 us\n-----------------------------------------\nsize = 25\n-----------------------------------------\n| Loading contig offsets | Time = 637 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 289.12 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 714.54 us\n-----------------------------------------\nsize = 4800\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 966.38 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading sequence | Time = 380.25 us\n-----------------------------------------\nsize = 4080\n-----------------------------------------\n| Loading positions | Time = 316.5 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading reference sequence | Time = 378 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 137.38 us\n-----------------------------------------\n[2026-09-17 22:35:59.738] [jointLog] [info] setting maxHashResizeThreads to 1\n[2026-09-17 22:35:59.738] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2026-09-17 22:35:59.738] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2026-09-17 22:35:59.739] [jointLog] [info] parsing read library format\n[2026-09-17 22:35:59.740] [jointLog] [info] There is 1 library.\n[2026-09-17 22:35:59.743] [jointLog] [info] Loading pufferfish index\n[2026-09-17 22:35:59.744] [jointLog] [info] Loading dense pufferfish index.\n[2026-09-17 22:35:59.752] [jointLog] [info] done\n[2026-09-17 22:35:59.822] [jointLog] [info] Index contained 24 targets\n[2026-09-17 22:35:59.822] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2026-09-17 22:35:59.889] [jointLog] [info] Computed 24 rich equivalence classes for further processing\n[2026-09-17 22:35:59.889] [jointLog] [info] Counted 593 total reads in the equivalence classes \n[2026-09-17 22:35:59.889] [jointLog] [info] Number of mappings discarded because of alignment score : 0\n[2026-09-17 22:35:59.889] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2026-09-17 22:35:59.889] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2026-09-17 22:35:59.889] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2026-09-17 22:35:59.890] [jointLog] [warning] Only 593 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2026-09-17 22:35:59.890] [jointLog] [info] Mapping rate = 100%\n\n[2026-09-17 22:35:59.890] [jointLog] [info] finished quantifyLibrary()\n[2026-09-17 22:35:59.891] [jointLog] [info] Starting optimizer\n[2026-09-17 22:35:59.898] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2026-09-17 22:35:59.899] [jointLog] [info] iteration = 0 | max rel diff. = 3.11802\n[2026-09-17 22:35:59.903] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2026-09-17 22:35:59.903] [jointLog] [info] Finished optimizer\n[2026-09-17 22:35:59.903] [jointLog] [info] writing output \n\n[2026-09-17 22:35:59.906] [jointLog] [warning] NOTE: Read Lib [[ /dev/fd/63, /dev/fd/62]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "stdout": "Threads = 1\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 0\nFalse junctions count = 48\nHash table size = 48\nCandidate marks count = 48\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 48\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 0\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 27520 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy5", "tool_stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\n[2026-09-17 22:35:59.502] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2026-09-17 22:35:59.504] [jLog] [info] building index\nout : ./index\n[2026-09-17 22:35:59.505] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2026-09-17 22:35:59.525] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2026-09-17 22:35:59.525] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 24 cleaned references\n[2026-09-17 22:35:59.530] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2026-09-17 22:35:59.531] [puff::index::jointLog] [info] ntHll estimated 48842 distinct k-mers, setting filter size to 2^20\nTwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.\nTwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);\nallowedIn: 5\nMax Junction ID: 89\nseen.size():721 kmerInfo.size():90\napproximateContigTotalLength: 4056\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 25 element count: 4800 complex nodes: 0\n# of ones in rank vector: 24\n[2026-09-17 22:35:59.564] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2026-09-17 22:35:59.565] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 4800\n-----------------------------------------\n| Loading contigs | Time = 371.71 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading contig boundaries | Time = 348.88 us\n-----------------------------------------\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n24\n[2026-09-17 22:35:59.568] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2026-09-17 22:35:59.568] [puff::index::jointLog] [info] contig count for validation: 24\n[2026-09-17 22:35:59.569] [puff::index::jointLog] [info] Total # of Contigs : 24\n[2026-09-17 22:35:59.569] [puff::index::jointLog] [info] Total # of numerical Contigs : 24\n[2026-09-17 22:35:59.569] [puff::index::jointLog] [info] Total # of contig vec entries: 24\n[2026-09-17 22:35:59.569] [puff::index::jointLog] [info] bits per offset entry 5\n[2026-09-17 22:35:59.570] [puff::index::jointLog] [info] Done constructing the contig vector. 25\n[2026-09-17 22:35:59.571] [puff::index::jointLog] [info] # segments = 24\n[2026-09-17 22:35:59.571] [puff::index::jointLog] [info] total length = 4800\n[2026-09-17 22:35:59.574] [puff::index::jointLog] [info] Reading the reference files ...\n[2026-09-17 22:35:59.576] [puff::index::jointLog] [info] positional integer width = 13\n[2026-09-17 22:35:59.576] [puff::index::jointLog] [info] seqSize = 4800\n[2026-09-17 22:35:59.576] [puff::index::jointLog] 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2026-09-17 22:35:59.598] [puff::index::jointLog] [info] mphf size = 0.00328064 MB\n[2026-09-17 22:35:59.598] [puff::index::jointLog] [info] chunk size = 4800\n[2026-09-17 22:35:59.599] [puff::index::jointLog] [info] chunk 0 = [0, 4770)\n[2026-09-17 22:35:59.599] [puff::index::jointLog] [info] finished populating pos vector\n[2026-09-17 22:35:59.599] [puff::index::jointLog] [info] writing index components\n[2026-09-17 22:35:59.604] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2026-09-17 22:35:59.606] [jLog] [info] done building index\n### salmon (selective-alignment-based) v1.10.1\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { A }\n### [ mates1 ] => { /dev/fd/63 }\n### [ mates2 ] => { /dev/fd/62 }\n### [ threads ] => { 1 }\n### [ consensusSlack ] => { 0.349999994 }\n### [ incompatPrior ] => { 0.0 }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 200 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ rangeFactorizationBins ] => { 4 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 0.01 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n-----------------------------------------\n| Loading contig table | Time = 850.71 us\n-----------------------------------------\nsize = 25\n-----------------------------------------\n| Loading contig offsets | Time = 637 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 289.12 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 714.54 us\n-----------------------------------------\nsize = 4800\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 966.38 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading sequence | Time = 380.25 us\n-----------------------------------------\nsize = 4080\n-----------------------------------------\n| Loading positions | Time = 316.5 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading reference sequence | Time = 378 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 137.38 us\n-----------------------------------------\n[2026-09-17 22:35:59.738] [jointLog] [info] setting maxHashResizeThreads to 1\n[2026-09-17 22:35:59.738] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2026-09-17 22:35:59.738] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2026-09-17 22:35:59.739] [jointLog] [info] parsing read library format\n[2026-09-17 22:35:59.740] [jointLog] [info] There is 1 library.\n[2026-09-17 22:35:59.743] [jointLog] [info] Loading pufferfish index\n[2026-09-17 22:35:59.744] [jointLog] [info] Loading dense pufferfish index.\n[2026-09-17 22:35:59.752] [jointLog] [info] done\n[2026-09-17 22:35:59.822] [jointLog] [info] Index contained 24 targets\n[2026-09-17 22:35:59.822] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2026-09-17 22:35:59.889] [jointLog] [info] Computed 24 rich equivalence classes for further processing\n[2026-09-17 22:35:59.889] [jointLog] [info] Counted 593 total reads in the equivalence classes \n[2026-09-17 22:35:59.889] [jointLog] [info] Number of mappings discarded because of alignment score : 0\n[2026-09-17 22:35:59.889] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2026-09-17 22:35:59.889] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2026-09-17 22:35:59.889] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2026-09-17 22:35:59.890] [jointLog] [warning] Only 593 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2026-09-17 22:35:59.890] [jointLog] [info] Mapping rate = 100%\n\n[2026-09-17 22:35:59.890] [jointLog] [info] finished quantifyLibrary()\n[2026-09-17 22:35:59.891] [jointLog] [info] Starting optimizer\n[2026-09-17 22:35:59.898] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2026-09-17 22:35:59.899] [jointLog] [info] iteration = 0 | max rel diff. = 3.11802\n[2026-09-17 22:35:59.903] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2026-09-17 22:35:59.903] [jointLog] [info] Finished optimizer\n[2026-09-17 22:35:59.903] [jointLog] [info] writing output \n\n[2026-09-17 22:35:59.906] [jointLog] [warning] NOTE: Read Lib [[ /dev/fd/63, /dev/fd/62]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "tool_stdout": "Threads = 1\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 0\nFalse junctions count = 48\nHash table size = 48\nCandidate marks count = 48\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 48\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 0\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 27520 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "update_time": "2026-09-17T22:36:03.996746", "user_email": "planemo@galaxyproject.org", "user_id": "ab426e56a688ed95" }, { "command_line": "SLOTS=$(( ${GALAXY_SLOTS:-4} > 1 ? ${GALAXY_SLOTS:-4} - 1 : 1 )); mkdir ./index && mkdir ./output && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/9/2/f/dataset_92fd78af-c743-4925-9063-bddbc393e415.dat' 'input_index.fasta' && salmon --no-version-check index -i ./index --kmerLen '31' --gencode --threads \"$SLOTS\" --transcripts 'input_index.fasta' && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/c/2/e/dataset_c2e8c51a-e868-4846-bbfa-0ea50c3b46e7.dat' ./mate1.fastq && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/6/d/8/dataset_6d8e9a44-4c63-4a3c-8f12-444a74147d8e.dat' ./mate2.fastq && salmon --no-version-check quant --index './index' --libType A --mates1 <(zcat < ./mate1.fastq) --mates2 <(zcat < ./mate2.fastq) --threads \"$SLOTS\" --consensusSlack '0.349999994' --incompatPrior '0.0' --minAssignedFrags '10' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '200' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --rangeFactorizationBins '4' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '0.01' -o ./output", "command_version": "1.10.1", "copied_from_job_id": null, "create_time": "2026-09-17T22:35:57.555002", "dependencies": [], "exit_code": 0, "external_id": "33637", "galaxy_version": "26.1", "handler": null, "history_id": "ab426e56a688ed95", "id": "53558844794bf923", "inputs": { "quant_type|input|single_or_paired|input_11": { "id": "2cb54babe410fc94", "src": "hda", "uuid": "c2e8c51a-e868-4846-bbfa-0ea50c3b46e7" }, "quant_type|input|single_or_paired|input_12": { "id": "4e0ba31121077773", "src": "hda", "uuid": "6d8e9a44-4c63-4a3c-8f12-444a74147d8e" }, "quant_type|refTranscriptSource|s_index|fasta": { "id": "9dfa17f44c905ecf", "src": "hda", "uuid": "92fd78af-c743-4925-9063-bddbc393e415" } }, "job_messages": [], "job_metrics": [ { "name": "container_id", "plugin": "core", "raw_value": "quay.io/biocontainers/mulled-v2-1db50f99443206288f90b902e1044e9932611944:15d91f5dbe07eb894f2e2f01d20c25d30301434b-0", "title": "Container ID", "value": "quay.io/biocontainers/mulled-v2-1db50f99443206288f90b902e1044e9932611944:15d91f5dbe07eb894f2e2f01d20c25d30301434b-0" }, { "name": "container_type", "plugin": "core", "raw_value": "docker", "title": "Container Type", "value": "docker" }, { "name": "galaxy_slots", "plugin": "core", "raw_value": "1.0000000", "title": "Cores Allocated", "value": "1" }, { "name": "start_epoch", "plugin": "core", "raw_value": "1789684564.0000000", "title": "Job Start Time", "value": "2026-09-18 00:36:04" }, { "name": "end_epoch", "plugin": "core", "raw_value": "1789684568.0000000", "title": "Job End Time", "value": "2026-09-18 00:36:08" }, { "name": "runtime_seconds", "plugin": "core", "raw_value": "4.0000000", "title": "Job Runtime (Wall Clock)", "value": "4 seconds" } ], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "output_quant": { "id": "d67aa88f27cf1ce3", "src": "hdca" } }, "outputs": { "output_quant": { "id": "53558844794bf923", "src": "hda", "uuid": "b57aec04-bb88-49dc-9393-4de578624e7e" } }, "params": { "__input_ext": "\"input\"", "__workflow_invocation_uuid__": "\"26835a54b2e811f1a764e6fd7feff8e8\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"200\", \"minAssignedFrags\": \"10\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"4\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"0.01\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "chromInfo": "\"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "gcBias": "false", "geneMap": null, "generate_aux": "false", "incompatPrior": "\"0.0\"", "meta": "false", "quant_type": "{\"__current_case__\": 0, \"bam_options\": {\"__current_case__\": 1, \"writeMappings\": \"\"}, \"consensusSlack\": \"0.349999994\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": false, \"input\": {\"single_or_paired\": {\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 4, \"src\": \"dce\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"single_or_paired_opts\": \"paired_collection\"}}, \"qtype\": \"reads\", \"recoverOrphans\": false, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 9, \"src\": \"hda\"}]}, \"genome\": null, \"kmer\": \"31\"}}, \"validmap\": {\"__current_case__\": 1, \"validateMappings\": \"\"}}", "seqBias": "false" }, "state": "ok", "stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\n[2026-09-17 22:36:05.107] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2026-09-17 22:36:05.109] [jLog] [info] building index\nout : ./index\n[2026-09-17 22:36:05.111] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2026-09-17 22:36:05.129] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2026-09-17 22:36:05.130] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 24 cleaned references\n[2026-09-17 22:36:05.134] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2026-09-17 22:36:05.136] [puff::index::jointLog] [info] ntHll estimated 48842 distinct k-mers, setting filter size to 2^20\nTwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.\nTwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);\nallowedIn: 5\nMax Junction ID: 89\nseen.size():721 kmerInfo.size():90\napproximateContigTotalLength: 4056\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 25 element count: 4800 complex nodes: 0\n# of ones in rank vector: 24\n[2026-09-17 22:36:05.165] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2026-09-17 22:36:05.166] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 4800\n-----------------------------------------\n| Loading contigs | Time = 278.12 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading contig boundaries | Time = 283.67 us\n-----------------------------------------\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n24\n[2026-09-17 22:36:05.168] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2026-09-17 22:36:05.169] [puff::index::jointLog] [info] contig count for validation: 24\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] Total # of Contigs : 24\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] Total # of numerical Contigs : 24\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] Total # of contig vec entries: 24\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] bits per offset entry 5\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] Done constructing the contig vector. 25\n[2026-09-17 22:36:05.172] [puff::index::jointLog] [info] # segments = 24\n[2026-09-17 22:36:05.172] [puff::index::jointLog] [info] total length = 4800\n[2026-09-17 22:36:05.173] [puff::index::jointLog] [info] Reading the reference files ...\n[2026-09-17 22:36:05.174] [puff::index::jointLog] [info] positional integer width = 13\n[2026-09-17 22:36:05.174] [puff::index::jointLog] [info] seqSize = 4800\n[2026-09-17 22:36:05.174] [puff::index::jointLog] 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2026-09-17 22:36:05.196] [puff::index::jointLog] [info] mphf size = 0.00328064 MB\n[2026-09-17 22:36:05.197] [puff::index::jointLog] [info] chunk size = 4800\n[2026-09-17 22:36:05.197] [puff::index::jointLog] [info] chunk 0 = [0, 4770)\n[2026-09-17 22:36:05.198] [puff::index::jointLog] [info] finished populating pos vector\n[2026-09-17 22:36:05.198] [puff::index::jointLog] [info] writing index components\n[2026-09-17 22:36:05.201] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2026-09-17 22:36:05.202] [jLog] [info] done building index\n### salmon (selective-alignment-based) v1.10.1\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { A }\n### [ mates1 ] => { /dev/fd/63 }\n### [ mates2 ] => { /dev/fd/62 }\n### [ threads ] => { 1 }\n### [ consensusSlack ] => { 0.349999994 }\n### [ incompatPrior ] => { 0.0 }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 200 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ rangeFactorizationBins ] => { 4 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 0.01 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n-----------------------------------------\n| Loading contig table | Time = 939.04 us\n-----------------------------------------\nsize = 25\n-----------------------------------------\n| Loading contig offsets | Time = 645.58 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 312.79 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 796.33 us\n-----------------------------------------\nsize = 4800\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 932.25 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading sequence | Time = 341.08 us\n-----------------------------------------\nsize = 4080\n-----------------------------------------\n| Loading positions | Time = 352.62 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading reference sequence | Time = 369.29 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 122.38 us\n-----------------------------------------\n[2026-09-17 22:36:05.289] [jointLog] [info] setting maxHashResizeThreads to 1\n[2026-09-17 22:36:05.289] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2026-09-17 22:36:05.289] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2026-09-17 22:36:05.290] [jointLog] [info] parsing read library format\n[2026-09-17 22:36:05.291] [jointLog] [info] There is 1 library.\n[2026-09-17 22:36:05.294] [jointLog] [info] Loading pufferfish index\n[2026-09-17 22:36:05.295] [jointLog] [info] Loading dense pufferfish index.\n[2026-09-17 22:36:05.304] [jointLog] [info] done\n[2026-09-17 22:36:05.349] [jointLog] [info] Index contained 24 targets\n[2026-09-17 22:36:05.349] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2026-09-17 22:36:05.416] [jointLog] [info] Computed 24 rich equivalence classes for further processing\n[2026-09-17 22:36:05.416] [jointLog] [info] Counted 741 total reads in the equivalence classes \n[2026-09-17 22:36:05.417] [jointLog] [info] Number of mappings discarded because of alignment score : 0\n[2026-09-17 22:36:05.417] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2026-09-17 22:36:05.417] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2026-09-17 22:36:05.417] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2026-09-17 22:36:05.417] [jointLog] [warning] Only 741 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2026-09-17 22:36:05.417] [jointLog] [info] Mapping rate = 100%\n\n[2026-09-17 22:36:05.417] [jointLog] [info] finished quantifyLibrary()\n[2026-09-17 22:36:05.419] [jointLog] [info] Starting optimizer\n[2026-09-17 22:36:05.426] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2026-09-17 22:36:05.427] [jointLog] [info] iteration = 0 | max rel diff. = 4.14577\n[2026-09-17 22:36:05.431] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2026-09-17 22:36:05.432] [jointLog] [info] Finished optimizer\n[2026-09-17 22:36:05.432] [jointLog] [info] writing output \n\n[2026-09-17 22:36:05.434] [jointLog] [warning] NOTE: Read Lib [[ /dev/fd/63, /dev/fd/62]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "stdout": "Threads = 1\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 0\nFalse junctions count = 48\nHash table size = 48\nCandidate marks count = 48\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 48\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 0\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 27520 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy5", "tool_stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\n[2026-09-17 22:36:05.107] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2026-09-17 22:36:05.109] [jLog] [info] building index\nout : ./index\n[2026-09-17 22:36:05.111] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2026-09-17 22:36:05.129] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2026-09-17 22:36:05.130] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 24 cleaned references\n[2026-09-17 22:36:05.134] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2026-09-17 22:36:05.136] [puff::index::jointLog] [info] ntHll estimated 48842 distinct k-mers, setting filter size to 2^20\nTwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.\nTwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);\nallowedIn: 5\nMax Junction ID: 89\nseen.size():721 kmerInfo.size():90\napproximateContigTotalLength: 4056\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 25 element count: 4800 complex nodes: 0\n# of ones in rank vector: 24\n[2026-09-17 22:36:05.165] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2026-09-17 22:36:05.166] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 4800\n-----------------------------------------\n| Loading contigs | Time = 278.12 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading contig boundaries | Time = 283.67 us\n-----------------------------------------\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n24\n[2026-09-17 22:36:05.168] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2026-09-17 22:36:05.169] [puff::index::jointLog] [info] contig count for validation: 24\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] Total # of Contigs : 24\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] Total # of numerical Contigs : 24\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] Total # of contig vec entries: 24\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] bits per offset entry 5\n[2026-09-17 22:36:05.170] [puff::index::jointLog] [info] Done constructing the contig vector. 25\n[2026-09-17 22:36:05.172] [puff::index::jointLog] [info] # segments = 24\n[2026-09-17 22:36:05.172] [puff::index::jointLog] [info] total length = 4800\n[2026-09-17 22:36:05.173] [puff::index::jointLog] [info] Reading the reference files ...\n[2026-09-17 22:36:05.174] [puff::index::jointLog] [info] positional integer width = 13\n[2026-09-17 22:36:05.174] [puff::index::jointLog] [info] seqSize = 4800\n[2026-09-17 22:36:05.174] [puff::index::jointLog] 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2026-09-17 22:36:05.196] [puff::index::jointLog] [info] mphf size = 0.00328064 MB\n[2026-09-17 22:36:05.197] [puff::index::jointLog] [info] chunk size = 4800\n[2026-09-17 22:36:05.197] [puff::index::jointLog] [info] chunk 0 = [0, 4770)\n[2026-09-17 22:36:05.198] [puff::index::jointLog] [info] finished populating pos vector\n[2026-09-17 22:36:05.198] [puff::index::jointLog] [info] writing index components\n[2026-09-17 22:36:05.201] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2026-09-17 22:36:05.202] [jLog] [info] done building index\n### salmon (selective-alignment-based) v1.10.1\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { A }\n### [ mates1 ] => { /dev/fd/63 }\n### [ mates2 ] => { /dev/fd/62 }\n### [ threads ] => { 1 }\n### [ consensusSlack ] => { 0.349999994 }\n### [ incompatPrior ] => { 0.0 }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 200 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ rangeFactorizationBins ] => { 4 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 0.01 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n-----------------------------------------\n| Loading contig table | Time = 939.04 us\n-----------------------------------------\nsize = 25\n-----------------------------------------\n| Loading contig offsets | Time = 645.58 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 312.79 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 796.33 us\n-----------------------------------------\nsize = 4800\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 932.25 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading sequence | Time = 341.08 us\n-----------------------------------------\nsize = 4080\n-----------------------------------------\n| Loading positions | Time = 352.62 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading reference sequence | Time = 369.29 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 122.38 us\n-----------------------------------------\n[2026-09-17 22:36:05.289] [jointLog] [info] setting maxHashResizeThreads to 1\n[2026-09-17 22:36:05.289] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2026-09-17 22:36:05.289] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2026-09-17 22:36:05.290] [jointLog] [info] parsing read library format\n[2026-09-17 22:36:05.291] [jointLog] [info] There is 1 library.\n[2026-09-17 22:36:05.294] [jointLog] [info] Loading pufferfish index\n[2026-09-17 22:36:05.295] [jointLog] [info] Loading dense pufferfish index.\n[2026-09-17 22:36:05.304] [jointLog] [info] done\n[2026-09-17 22:36:05.349] [jointLog] [info] Index contained 24 targets\n[2026-09-17 22:36:05.349] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2026-09-17 22:36:05.416] [jointLog] [info] Computed 24 rich equivalence classes for further processing\n[2026-09-17 22:36:05.416] [jointLog] [info] Counted 741 total reads in the equivalence classes \n[2026-09-17 22:36:05.417] [jointLog] [info] Number of mappings discarded because of alignment score : 0\n[2026-09-17 22:36:05.417] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2026-09-17 22:36:05.417] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2026-09-17 22:36:05.417] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2026-09-17 22:36:05.417] [jointLog] [warning] Only 741 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2026-09-17 22:36:05.417] [jointLog] [info] Mapping rate = 100%\n\n[2026-09-17 22:36:05.417] [jointLog] [info] finished quantifyLibrary()\n[2026-09-17 22:36:05.419] [jointLog] [info] Starting optimizer\n[2026-09-17 22:36:05.426] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2026-09-17 22:36:05.427] [jointLog] [info] iteration = 0 | max rel diff. = 4.14577\n[2026-09-17 22:36:05.431] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2026-09-17 22:36:05.432] [jointLog] [info] Finished optimizer\n[2026-09-17 22:36:05.432] [jointLog] [info] writing output \n\n[2026-09-17 22:36:05.434] [jointLog] [warning] NOTE: Read Lib [[ /dev/fd/63, /dev/fd/62]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "tool_stdout": "Threads = 1\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 0\nFalse junctions count = 48\nHash table size = 48\nCandidate marks count = 48\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 48\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 0\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 27520 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "update_time": "2026-09-17T22:36:08.840186", "user_email": "planemo@galaxyproject.org", "user_id": "ab426e56a688ed95" }, { "command_line": "SLOTS=$(( ${GALAXY_SLOTS:-4} > 1 ? ${GALAXY_SLOTS:-4} - 1 : 1 )); mkdir ./index && mkdir ./output && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/9/2/f/dataset_92fd78af-c743-4925-9063-bddbc393e415.dat' 'input_index.fasta' && salmon --no-version-check index -i ./index --kmerLen '31' --gencode --threads \"$SLOTS\" --transcripts 'input_index.fasta' && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/b/e/6/dataset_be6e434a-5cfd-4572-976e-540558021743.dat' ./mate1.fastq && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/0/4/9/dataset_04956493-9ef8-4169-a6f7-26235a410e1e.dat' ./mate2.fastq && salmon --no-version-check quant --index './index' --libType A --mates1 <(zcat < ./mate1.fastq) --mates2 <(zcat < ./mate2.fastq) --threads \"$SLOTS\" --consensusSlack '0.349999994' --incompatPrior '0.0' --minAssignedFrags '10' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '200' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --rangeFactorizationBins '4' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '0.01' -o ./output", "command_version": "1.10.1", "copied_from_job_id": null, "create_time": "2026-09-17T22:35:57.555002", "dependencies": [], "exit_code": 0, "external_id": "33671", "galaxy_version": "26.1", "handler": null, "history_id": "ab426e56a688ed95", "id": "8a599077f39a97c7", "inputs": { "quant_type|input|single_or_paired|input_11": { "id": "1c80d65d322b105c", "src": "hda", "uuid": "be6e434a-5cfd-4572-976e-540558021743" }, "quant_type|input|single_or_paired|input_12": { "id": "99bd1f66aad6c7b5", "src": "hda", "uuid": "04956493-9ef8-4169-a6f7-26235a410e1e" }, "quant_type|refTranscriptSource|s_index|fasta": { "id": "9dfa17f44c905ecf", "src": "hda", "uuid": "92fd78af-c743-4925-9063-bddbc393e415" } }, "job_messages": [], "job_metrics": [ { "name": "container_id", "plugin": "core", "raw_value": "quay.io/biocontainers/mulled-v2-1db50f99443206288f90b902e1044e9932611944:15d91f5dbe07eb894f2e2f01d20c25d30301434b-0", "title": "Container ID", "value": "quay.io/biocontainers/mulled-v2-1db50f99443206288f90b902e1044e9932611944:15d91f5dbe07eb894f2e2f01d20c25d30301434b-0" }, { "name": "container_type", "plugin": "core", "raw_value": "docker", "title": "Container Type", "value": "docker" }, { "name": "galaxy_slots", "plugin": "core", "raw_value": "1.0000000", "title": "Cores Allocated", "value": "1" }, { "name": "start_epoch", "plugin": "core", "raw_value": "1789684569.0000000", "title": "Job Start Time", "value": "2026-09-18 00:36:09" }, { "name": "end_epoch", "plugin": "core", "raw_value": "1789684573.0000000", "title": "Job End Time", "value": "2026-09-18 00:36:13" }, { "name": "runtime_seconds", "plugin": "core", "raw_value": "4.0000000", "title": "Job Runtime (Wall Clock)", "value": "4 seconds" } ], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "output_quant": { "id": "d67aa88f27cf1ce3", "src": "hdca" } }, "outputs": { "output_quant": { "id": "8a599077f39a97c7", "src": "hda", "uuid": "b0353697-eb59-4c42-9f29-ef4a42e3439d" } }, "params": { "__input_ext": "\"input\"", "__workflow_invocation_uuid__": "\"26835a54b2e811f1a764e6fd7feff8e8\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"200\", \"minAssignedFrags\": \"10\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"4\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"0.01\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "chromInfo": "\"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "gcBias": "false", "geneMap": null, "generate_aux": "false", "incompatPrior": "\"0.0\"", "meta": "false", "quant_type": "{\"__current_case__\": 0, \"bam_options\": {\"__current_case__\": 1, \"writeMappings\": \"\"}, \"consensusSlack\": \"0.349999994\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": false, \"input\": {\"single_or_paired\": {\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 7, \"src\": \"dce\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"single_or_paired_opts\": \"paired_collection\"}}, \"qtype\": \"reads\", \"recoverOrphans\": false, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 9, \"src\": \"hda\"}]}, \"genome\": null, \"kmer\": \"31\"}}, \"validmap\": {\"__current_case__\": 1, \"validateMappings\": \"\"}}", "seqBias": "false" }, "state": "ok", "stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\n[2026-09-17 22:36:09.973] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2026-09-17 22:36:09.975] [jLog] [info] building index\nout : ./index\n[2026-09-17 22:36:09.977] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2026-09-17 22:36:09.996] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2026-09-17 22:36:09.996] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 24 cleaned references\n[2026-09-17 22:36:10.001] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2026-09-17 22:36:10.002] [puff::index::jointLog] [info] ntHll estimated 48842 distinct k-mers, setting filter size to 2^20\nTwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.\nTwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);\nallowedIn: 5\nMax Junction ID: 89\nseen.size():721 kmerInfo.size():90\napproximateContigTotalLength: 4056\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 25 element count: 4800 complex nodes: 0\n# of ones in rank vector: 24\n[2026-09-17 22:36:10.040] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2026-09-17 22:36:10.041] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 4800\n-----------------------------------------\n| Loading contigs | Time = 426.54 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading contig boundaries | Time = 302.17 us\n-----------------------------------------\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n24\n[2026-09-17 22:36:10.044] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2026-09-17 22:36:10.044] [puff::index::jointLog] [info] contig count for validation: 24\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] Total # of Contigs : 24\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] Total # of numerical Contigs : 24\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] Total # of contig vec entries: 24\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] bits per offset entry 5\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] Done constructing the contig vector. 25\n[2026-09-17 22:36:10.047] [puff::index::jointLog] [info] # segments = 24\n[2026-09-17 22:36:10.047] [puff::index::jointLog] [info] total length = 4800\n[2026-09-17 22:36:10.048] [puff::index::jointLog] [info] Reading the reference files ...\n[2026-09-17 22:36:10.049] [puff::index::jointLog] [info] positional integer width = 13\n[2026-09-17 22:36:10.049] [puff::index::jointLog] [info] seqSize = 4800\n[2026-09-17 22:36:10.049] [puff::index::jointLog] [info] rankSize = 4800\n[2026-09-17 22:36:10.049] [puff::index::jointLog] [info] edgeVecSize = 0\n[2026-09-17 22:36:10.049] [puff::index::jointLog] [info] num keys = 4080\n\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec\r[Building BooPHF] 10.8 % elapsed: 0 min 0 sec remaining: 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2026-09-17 22:36:10.069] [puff::index::jointLog] [info] mphf size = 0.00328064 MB\n[2026-09-17 22:36:10.070] [puff::index::jointLog] [info] chunk size = 4800\n[2026-09-17 22:36:10.070] [puff::index::jointLog] [info] chunk 0 = [0, 4770)\n[2026-09-17 22:36:10.071] [puff::index::jointLog] [info] finished populating pos vector\n[2026-09-17 22:36:10.071] [puff::index::jointLog] [info] writing index components\n[2026-09-17 22:36:10.075] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2026-09-17 22:36:10.076] [jLog] [info] done building index\n### salmon (selective-alignment-based) v1.10.1\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { A }\n### [ mates1 ] => { /dev/fd/63 }\n### [ mates2 ] => { /dev/fd/62 }\n### [ threads ] => { 1 }\n### [ consensusSlack ] => { 0.349999994 }\n### [ incompatPrior ] => { 0.0 }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 200 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ rangeFactorizationBins ] => { 4 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 0.01 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n-----------------------------------------\n| Loading contig table | Time = 903.38 us\n-----------------------------------------\nsize = 25\n-----------------------------------------\n| Loading contig offsets | Time = 539.38 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 294 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 774.79 us\n-----------------------------------------\nsize = 4800\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 966.92 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading sequence | Time = 345.92 us\n-----------------------------------------\nsize = 4080\n-----------------------------------------\n| Loading positions | Time = 304.75 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading reference sequence | Time = 329.96 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 173.83 us\n-----------------------------------------\n[2026-09-17 22:36:10.164] [jointLog] [info] setting maxHashResizeThreads to 1\n[2026-09-17 22:36:10.164] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2026-09-17 22:36:10.164] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2026-09-17 22:36:10.165] [jointLog] [info] parsing read library format\n[2026-09-17 22:36:10.166] [jointLog] [info] There is 1 library.\n[2026-09-17 22:36:10.169] [jointLog] [info] Loading pufferfish index\n[2026-09-17 22:36:10.170] [jointLog] [info] Loading dense pufferfish index.\n[2026-09-17 22:36:10.178] [jointLog] [info] done\n[2026-09-17 22:36:10.195] [jointLog] [info] Index contained 24 targets\n[2026-09-17 22:36:10.196] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2026-09-17 22:36:10.265] [jointLog] [info] Computed 24 rich equivalence classes for further processing\n[2026-09-17 22:36:10.265] [jointLog] [info] Counted 1143 total reads in the equivalence classes \n[2026-09-17 22:36:10.266] [jointLog] [info] Number of mappings discarded because of alignment score : 0\n[2026-09-17 22:36:10.266] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2026-09-17 22:36:10.266] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2026-09-17 22:36:10.266] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2026-09-17 22:36:10.266] [jointLog] [warning] Only 1143 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2026-09-17 22:36:10.266] [jointLog] [info] Mapping rate = 100%\n\n[2026-09-17 22:36:10.266] [jointLog] [info] finished quantifyLibrary()\n[2026-09-17 22:36:10.268] [jointLog] [info] Starting optimizer\n[2026-09-17 22:36:10.275] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2026-09-17 22:36:10.276] [jointLog] [info] iteration = 0 | max rel diff. = 6.93734\n[2026-09-17 22:36:10.280] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2026-09-17 22:36:10.280] [jointLog] [info] Finished optimizer\n[2026-09-17 22:36:10.280] [jointLog] [info] writing output \n\n[2026-09-17 22:36:10.283] [jointLog] [warning] NOTE: Read Lib [[ /dev/fd/63, /dev/fd/62]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "stdout": "Threads = 1\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 0\nFalse junctions count = 48\nHash table size = 48\nCandidate marks count = 48\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 48\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 0\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 27520 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy5", "tool_stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\n[2026-09-17 22:36:09.973] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2026-09-17 22:36:09.975] [jLog] [info] building index\nout : ./index\n[2026-09-17 22:36:09.977] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2026-09-17 22:36:09.996] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2026-09-17 22:36:09.996] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 24 cleaned references\n[2026-09-17 22:36:10.001] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2026-09-17 22:36:10.002] [puff::index::jointLog] [info] ntHll estimated 48842 distinct k-mers, setting filter size to 2^20\nTwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.\nTwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);\nallowedIn: 5\nMax Junction ID: 89\nseen.size():721 kmerInfo.size():90\napproximateContigTotalLength: 4056\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 25 element count: 4800 complex nodes: 0\n# of ones in rank vector: 24\n[2026-09-17 22:36:10.040] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2026-09-17 22:36:10.041] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 4800\n-----------------------------------------\n| Loading contigs | Time = 426.54 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading contig boundaries | Time = 302.17 us\n-----------------------------------------\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n24\n[2026-09-17 22:36:10.044] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2026-09-17 22:36:10.044] [puff::index::jointLog] [info] contig count for validation: 24\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] Total # of Contigs : 24\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] Total # of numerical Contigs : 24\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] Total # of contig vec entries: 24\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] bits per offset entry 5\n[2026-09-17 22:36:10.045] [puff::index::jointLog] [info] Done constructing the contig vector. 25\n[2026-09-17 22:36:10.047] [puff::index::jointLog] [info] # segments = 24\n[2026-09-17 22:36:10.047] [puff::index::jointLog] [info] total length = 4800\n[2026-09-17 22:36:10.048] [puff::index::jointLog] [info] Reading the reference files ...\n[2026-09-17 22:36:10.049] [puff::index::jointLog] [info] positional integer width = 13\n[2026-09-17 22:36:10.049] [puff::index::jointLog] [info] seqSize = 4800\n[2026-09-17 22:36:10.049] [puff::index::jointLog] 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2026-09-17 22:36:10.069] [puff::index::jointLog] [info] mphf size = 0.00328064 MB\n[2026-09-17 22:36:10.070] [puff::index::jointLog] [info] chunk size = 4800\n[2026-09-17 22:36:10.070] [puff::index::jointLog] [info] chunk 0 = [0, 4770)\n[2026-09-17 22:36:10.071] [puff::index::jointLog] [info] finished populating pos vector\n[2026-09-17 22:36:10.071] [puff::index::jointLog] [info] writing index components\n[2026-09-17 22:36:10.075] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2026-09-17 22:36:10.076] [jLog] [info] done building index\n### salmon (selective-alignment-based) v1.10.1\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { A }\n### [ mates1 ] => { /dev/fd/63 }\n### [ mates2 ] => { /dev/fd/62 }\n### [ threads ] => { 1 }\n### [ consensusSlack ] => { 0.349999994 }\n### [ incompatPrior ] => { 0.0 }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 200 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ rangeFactorizationBins ] => { 4 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 0.01 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n-----------------------------------------\n| Loading contig table | Time = 903.38 us\n-----------------------------------------\nsize = 25\n-----------------------------------------\n| Loading contig offsets | Time = 539.38 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 294 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 774.79 us\n-----------------------------------------\nsize = 4800\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 966.92 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading sequence | Time = 345.92 us\n-----------------------------------------\nsize = 4080\n-----------------------------------------\n| Loading positions | Time = 304.75 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading reference sequence | Time = 329.96 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 173.83 us\n-----------------------------------------\n[2026-09-17 22:36:10.164] [jointLog] [info] setting maxHashResizeThreads to 1\n[2026-09-17 22:36:10.164] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2026-09-17 22:36:10.164] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2026-09-17 22:36:10.165] [jointLog] [info] parsing read library format\n[2026-09-17 22:36:10.166] [jointLog] [info] There is 1 library.\n[2026-09-17 22:36:10.169] [jointLog] [info] Loading pufferfish index\n[2026-09-17 22:36:10.170] [jointLog] [info] Loading dense pufferfish index.\n[2026-09-17 22:36:10.178] [jointLog] [info] done\n[2026-09-17 22:36:10.195] [jointLog] [info] Index contained 24 targets\n[2026-09-17 22:36:10.196] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2026-09-17 22:36:10.265] [jointLog] [info] Computed 24 rich equivalence classes for further processing\n[2026-09-17 22:36:10.265] [jointLog] [info] Counted 1143 total reads in the equivalence classes \n[2026-09-17 22:36:10.266] [jointLog] [info] Number of mappings discarded because of alignment score : 0\n[2026-09-17 22:36:10.266] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2026-09-17 22:36:10.266] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2026-09-17 22:36:10.266] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2026-09-17 22:36:10.266] [jointLog] [warning] Only 1143 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2026-09-17 22:36:10.266] [jointLog] [info] Mapping rate = 100%\n\n[2026-09-17 22:36:10.266] [jointLog] [info] finished quantifyLibrary()\n[2026-09-17 22:36:10.268] [jointLog] [info] Starting optimizer\n[2026-09-17 22:36:10.275] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2026-09-17 22:36:10.276] [jointLog] [info] iteration = 0 | max rel diff. = 6.93734\n[2026-09-17 22:36:10.280] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2026-09-17 22:36:10.280] [jointLog] [info] Finished optimizer\n[2026-09-17 22:36:10.280] [jointLog] [info] writing output \n\n[2026-09-17 22:36:10.283] [jointLog] [warning] NOTE: Read Lib [[ /dev/fd/63, /dev/fd/62]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "tool_stdout": "Threads = 1\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 0\nFalse junctions count = 48\nHash table size = 48\nCandidate marks count = 48\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 48\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 0\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 27520 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "update_time": "2026-09-17T22:36:13.689696", "user_email": "planemo@galaxyproject.org", "user_id": "ab426e56a688ed95" }, { "command_line": "SLOTS=$(( ${GALAXY_SLOTS:-4} > 1 ? ${GALAXY_SLOTS:-4} - 1 : 1 )); mkdir ./index && mkdir ./output && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/9/2/f/dataset_92fd78af-c743-4925-9063-bddbc393e415.dat' 'input_index.fasta' && salmon --no-version-check index -i ./index --kmerLen '31' --gencode --threads \"$SLOTS\" --transcripts 'input_index.fasta' && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/6/e/3/dataset_6e39692e-9cf2-4bb9-a40e-c4fee4b16d4c.dat' ./mate1.fastq && ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/6/e/f/dataset_6efd6e94-b2e8-4ebf-aae6-0919e9a1c674.dat' ./mate2.fastq && salmon --no-version-check quant --index './index' --libType A --mates1 <(zcat < ./mate1.fastq) --mates2 <(zcat < ./mate2.fastq) --threads \"$SLOTS\" --consensusSlack '0.349999994' --incompatPrior '0.0' --minAssignedFrags '10' --biasSpeedSamp '5' --fldMax '1000' --fldMean '250' --fldSD '25' --forgettingFactor '0.65' --maxReadOcc '200' --numBiasSamples '2000000' --numAuxModelSamples '5000000' --numPreAuxModelSamples '5000' --rangeFactorizationBins '4' --numGibbsSamples '0' --numBootstraps '0' --thinningFactor '16' --sigDigits '3' --vbPrior '0.01' -o ./output", "command_version": "1.10.1", "copied_from_job_id": null, "create_time": "2026-09-17T22:35:57.555003", "dependencies": [], "exit_code": 0, "external_id": "33705", "galaxy_version": "26.1", "handler": null, "history_id": "ab426e56a688ed95", "id": "624b1fd4c0b6fdf6", "inputs": { "quant_type|input|single_or_paired|input_11": { "id": "3e4592b97329669a", "src": "hda", "uuid": "6e39692e-9cf2-4bb9-a40e-c4fee4b16d4c" }, "quant_type|input|single_or_paired|input_12": { "id": "fceaa9d00d78e49d", "src": "hda", "uuid": "6efd6e94-b2e8-4ebf-aae6-0919e9a1c674" }, "quant_type|refTranscriptSource|s_index|fasta": { "id": "9dfa17f44c905ecf", "src": "hda", "uuid": "92fd78af-c743-4925-9063-bddbc393e415" } }, "job_messages": [], "job_metrics": [ { "name": "container_id", "plugin": "core", "raw_value": "quay.io/biocontainers/mulled-v2-1db50f99443206288f90b902e1044e9932611944:15d91f5dbe07eb894f2e2f01d20c25d30301434b-0", "title": "Container ID", "value": "quay.io/biocontainers/mulled-v2-1db50f99443206288f90b902e1044e9932611944:15d91f5dbe07eb894f2e2f01d20c25d30301434b-0" }, { "name": "container_type", "plugin": "core", "raw_value": "docker", "title": "Container Type", "value": "docker" }, { "name": "galaxy_slots", "plugin": "core", "raw_value": "1.0000000", "title": "Cores Allocated", "value": "1" }, { "name": "start_epoch", "plugin": "core", "raw_value": "1789684574.0000000", "title": "Job Start Time", "value": "2026-09-18 00:36:14" }, { "name": "end_epoch", "plugin": "core", "raw_value": "1789684578.0000000", "title": "Job End Time", "value": "2026-09-18 00:36:18" }, { "name": "runtime_seconds", "plugin": "core", "raw_value": "4.0000000", "title": "Job Runtime (Wall Clock)", "value": "4 seconds" } ], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": { "output_quant": { "id": "d67aa88f27cf1ce3", "src": "hdca" } }, "outputs": { "output_quant": { "id": "624b1fd4c0b6fdf6", "src": "hda", "uuid": "35098e74-4003-4f04-abd5-54848a0d4b7c" } }, "params": { "__input_ext": "\"input\"", "__workflow_invocation_uuid__": "\"26835a54b2e811f1a764e6fd7feff8e8\"", "adv": "{\"biasSpeedSamp\": \"5\", \"bootstrapReproject\": false, \"dumpEq\": false, \"dumpEqWeights\": false, \"fldMax\": \"1000\", \"fldMean\": \"250\", \"fldSD\": \"25\", \"forgettingFactor\": \"0.65\", \"initUniform\": false, \"maxReadOcc\": \"200\", \"minAssignedFrags\": \"10\", \"noBiasLengthThreshold\": false, \"noEffectiveLengthCorrection\": false, \"noFragLengthDist\": false, \"noGammaDraw\": false, \"noLengthCorrection\": false, \"numAuxModelSamples\": \"5000000\", \"numBiasSamples\": \"2000000\", \"numBootstraps\": \"0\", \"numGibbsSamples\": \"0\", \"numPreAuxModelSamples\": \"5000\", \"perTranscriptPrior\": false, \"rangeFactorizationBins\": \"4\", \"sigDigits\": \"3\", \"skipQuant\": false, \"thinningFactor\": \"16\", \"useEM\": false, \"vbPrior\": \"0.01\", \"writeOrphanLinks\": false, \"writeUnmappedNames\": false}", "chromInfo": "\"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "gcBias": "false", "geneMap": null, "generate_aux": "false", "incompatPrior": "\"0.0\"", "meta": "false", "quant_type": "{\"__current_case__\": 0, \"bam_options\": {\"__current_case__\": 1, \"writeMappings\": \"\"}, \"consensusSlack\": \"0.349999994\", \"consistentHits\": false, \"discardOrphansQuasi\": false, \"dovetail\": false, \"input\": {\"single_or_paired\": {\"__current_case__\": 1, \"input_1\": {\"values\": [{\"id\": 10, \"src\": \"dce\"}]}, \"libtype\": {\"__current_case__\": 0, \"strandedness\": \"A\"}, \"single_or_paired_opts\": \"paired_collection\"}}, \"qtype\": \"reads\", \"recoverOrphans\": false, \"refTranscriptSource\": {\"TranscriptSource\": \"history\", \"__current_case__\": 1, \"s_index\": {\"fasta\": {\"values\": [{\"id\": 9, \"src\": \"hda\"}]}, \"genome\": null, \"kmer\": \"31\"}}, \"validmap\": {\"__current_case__\": 1, \"validateMappings\": \"\"}}", "seqBias": "false" }, "state": "ok", "stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\n[2026-09-17 22:36:14.789] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2026-09-17 22:36:14.790] [jLog] [info] building index\nout : ./index\n[2026-09-17 22:36:14.792] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2026-09-17 22:36:14.812] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2026-09-17 22:36:14.812] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 24 cleaned references\n[2026-09-17 22:36:14.817] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2026-09-17 22:36:14.818] [puff::index::jointLog] [info] ntHll estimated 48842 distinct k-mers, setting filter size to 2^20\nTwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.\nTwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);\nallowedIn: 5\nMax Junction ID: 89\nseen.size():721 kmerInfo.size():90\napproximateContigTotalLength: 4056\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 25 element count: 4800 complex nodes: 0\n# of ones in rank vector: 24\n[2026-09-17 22:36:14.849] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2026-09-17 22:36:14.849] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 4800\n-----------------------------------------\n| Loading contigs | Time = 351.88 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading contig boundaries | Time = 307.67 us\n-----------------------------------------\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n24\n[2026-09-17 22:36:14.852] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2026-09-17 22:36:14.852] [puff::index::jointLog] [info] contig count for validation: 24\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] Total # of Contigs : 24\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] Total # of numerical Contigs : 24\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] Total # of contig vec entries: 24\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] bits per offset entry 5\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] Done constructing the contig vector. 25\n[2026-09-17 22:36:14.855] [puff::index::jointLog] [info] # segments = 24\n[2026-09-17 22:36:14.855] [puff::index::jointLog] [info] total length = 4800\n[2026-09-17 22:36:14.856] [puff::index::jointLog] [info] Reading the reference files ...\n[2026-09-17 22:36:14.859] [puff::index::jointLog] [info] positional integer width = 13\n[2026-09-17 22:36:14.859] [puff::index::jointLog] [info] seqSize = 4800\n[2026-09-17 22:36:14.859] [puff::index::jointLog] 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2026-09-17 22:36:14.879] [puff::index::jointLog] [info] mphf size = 0.00328064 MB\n[2026-09-17 22:36:14.879] [puff::index::jointLog] [info] chunk size = 4800\n[2026-09-17 22:36:14.879] [puff::index::jointLog] [info] chunk 0 = [0, 4770)\n[2026-09-17 22:36:14.880] [puff::index::jointLog] [info] finished populating pos vector\n[2026-09-17 22:36:14.880] [puff::index::jointLog] [info] writing index components\n[2026-09-17 22:36:14.883] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2026-09-17 22:36:14.885] [jLog] [info] done building index\n### salmon (selective-alignment-based) v1.10.1\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { A }\n### [ mates1 ] => { /dev/fd/63 }\n### [ mates2 ] => { /dev/fd/62 }\n### [ threads ] => { 1 }\n### [ consensusSlack ] => { 0.349999994 }\n### [ incompatPrior ] => { 0.0 }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 200 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ rangeFactorizationBins ] => { 4 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 0.01 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n-----------------------------------------\n| Loading contig table | Time = 926.58 us\n-----------------------------------------\nsize = 25\n-----------------------------------------\n| Loading contig offsets | Time = 484.92 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 307.75 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 698.29 us\n-----------------------------------------\nsize = 4800\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 1.0172 ms\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading sequence | Time = 351.29 us\n-----------------------------------------\nsize = 4080\n-----------------------------------------\n| Loading positions | Time = 350.08 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading reference sequence | Time = 258.33 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 104.83 us\n-----------------------------------------\n[2026-09-17 22:36:14.989] [jointLog] [info] setting maxHashResizeThreads to 1\n[2026-09-17 22:36:14.989] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2026-09-17 22:36:14.989] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2026-09-17 22:36:14.990] [jointLog] [info] parsing read library format\n[2026-09-17 22:36:14.991] [jointLog] [info] There is 1 library.\n[2026-09-17 22:36:14.995] [jointLog] [info] Loading pufferfish index\n[2026-09-17 22:36:14.996] [jointLog] [info] Loading dense pufferfish index.\n[2026-09-17 22:36:15.004] [jointLog] [info] done\n[2026-09-17 22:36:15.022] [jointLog] [info] Index contained 24 targets\n[2026-09-17 22:36:15.022] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2026-09-17 22:36:15.097] [jointLog] [info] Computed 24 rich equivalence classes for further processing\n[2026-09-17 22:36:15.097] [jointLog] [info] Counted 1523 total reads in the equivalence classes \n[2026-09-17 22:36:15.097] [jointLog] [info] Number of mappings discarded because of alignment score : 0\n[2026-09-17 22:36:15.097] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2026-09-17 22:36:15.097] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2026-09-17 22:36:15.097] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2026-09-17 22:36:15.098] [jointLog] [warning] Only 1523 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2026-09-17 22:36:15.098] [jointLog] [info] Mapping rate = 100%\n\n[2026-09-17 22:36:15.098] [jointLog] [info] finished quantifyLibrary()\n[2026-09-17 22:36:15.099] [jointLog] [info] Starting optimizer\n[2026-09-17 22:36:15.106] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2026-09-17 22:36:15.107] [jointLog] [info] iteration = 0 | max rel diff. = 6.05074\n[2026-09-17 22:36:15.111] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2026-09-17 22:36:15.112] [jointLog] [info] Finished optimizer\n[2026-09-17 22:36:15.112] [jointLog] [info] writing output \n\n[2026-09-17 22:36:15.114] [jointLog] [warning] NOTE: Read Lib [[ /dev/fd/63, /dev/fd/62]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "stdout": "Threads = 1\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 0\nFalse junctions count = 48\nHash table size = 48\nCandidate marks count = 48\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 48\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 0\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 27520 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/1.10.1+galaxy5", "tool_stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\n[2026-09-17 22:36:14.789] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode.\n[2026-09-17 22:36:14.790] [jLog] [info] building index\nout : ./index\n[2026-09-17 22:36:14.792] [puff::index::jointLog] [info] Running fixFasta\n\n[Step 1 of 4] : counting k-mers\n\n[2026-09-17 22:36:14.812] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides\n[2026-09-17 22:36:14.812] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts\nwrote 24 cleaned references\n[2026-09-17 22:36:14.817] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers\n[2026-09-17 22:36:14.818] [puff::index::jointLog] [info] ntHll estimated 48842 distinct k-mers, setting filter size to 2^20\nTwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.\nTwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);\nallowedIn: 5\nMax Junction ID: 89\nseen.size():721 kmerInfo.size():90\napproximateContigTotalLength: 4056\ncounters for complex kmers:\n(prec>1 & succ>1)=0 | (succ>1 & isStart)=0 | (prec>1 & isEnd)=0 | (isStart & isEnd)=0\ncontig count: 25 element count: 4800 complex nodes: 0\n# of ones in rank vector: 24\n[2026-09-17 22:36:14.849] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file.\n[2026-09-17 22:36:14.849] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory ./index\nsize = 4800\n-----------------------------------------\n| Loading contigs | Time = 351.88 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading contig boundaries | Time = 307.67 us\n-----------------------------------------\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n24\n[2026-09-17 22:36:14.852] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure.\n[2026-09-17 22:36:14.852] [puff::index::jointLog] [info] contig count for validation: 24\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] Total # of Contigs : 24\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] Total # of numerical Contigs : 24\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] Total # of contig vec entries: 24\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] bits per offset entry 5\n[2026-09-17 22:36:14.854] [puff::index::jointLog] [info] Done constructing the contig vector. 25\n[2026-09-17 22:36:14.855] [puff::index::jointLog] [info] # segments = 24\n[2026-09-17 22:36:14.855] [puff::index::jointLog] [info] total length = 4800\n[2026-09-17 22:36:14.856] [puff::index::jointLog] [info] Reading the reference files ...\n[2026-09-17 22:36:14.859] [puff::index::jointLog] [info] positional integer width = 13\n[2026-09-17 22:36:14.859] [puff::index::jointLog] [info] seqSize = 4800\n[2026-09-17 22:36:14.859] [puff::index::jointLog] 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elapsed: 0 min 0 sec remaining: 0 min 0 sec\n[2026-09-17 22:36:14.879] [puff::index::jointLog] [info] mphf size = 0.00328064 MB\n[2026-09-17 22:36:14.879] [puff::index::jointLog] [info] chunk size = 4800\n[2026-09-17 22:36:14.879] [puff::index::jointLog] [info] chunk 0 = [0, 4770)\n[2026-09-17 22:36:14.880] [puff::index::jointLog] [info] finished populating pos vector\n[2026-09-17 22:36:14.880] [puff::index::jointLog] [info] writing index components\n[2026-09-17 22:36:14.883] [puff::index::jointLog] [info] finished writing dense pufferfish index\n[2026-09-17 22:36:14.885] [jLog] [info] done building index\n### salmon (selective-alignment-based) v1.10.1\n### [ program ] => salmon \n### [ command ] => quant \n### [ index ] => { ./index }\n### [ libType ] => { A }\n### [ mates1 ] => { /dev/fd/63 }\n### [ mates2 ] => { /dev/fd/62 }\n### [ threads ] => { 1 }\n### [ consensusSlack ] => { 0.349999994 }\n### [ incompatPrior ] => { 0.0 }\n### [ minAssignedFrags ] => { 10 }\n### [ biasSpeedSamp ] => { 5 }\n### [ fldMax ] => { 1000 }\n### [ fldMean ] => { 250 }\n### [ fldSD ] => { 25 }\n### [ forgettingFactor ] => { 0.65 }\n### [ maxReadOcc ] => { 200 }\n### [ numBiasSamples ] => { 2000000 }\n### [ numAuxModelSamples ] => { 5000000 }\n### [ numPreAuxModelSamples ] => { 5000 }\n### [ rangeFactorizationBins ] => { 4 }\n### [ numGibbsSamples ] => { 0 }\n### [ numBootstraps ] => { 0 }\n### [ thinningFactor ] => { 16 }\n### [ sigDigits ] => { 3 }\n### [ vbPrior ] => { 0.01 }\n### [ output ] => { ./output }\nLogs will be written to ./output/logs\n-----------------------------------------\n| Loading contig table | Time = 926.58 us\n-----------------------------------------\nsize = 25\n-----------------------------------------\n| Loading contig offsets | Time = 484.92 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference lengths | Time = 307.75 us\n-----------------------------------------\n-----------------------------------------\n| Loading mphf table | Time = 698.29 us\n-----------------------------------------\nsize = 4800\nNumber of ones: 24\nNumber of ones per inventory item: 512\nInventory entries filled: 1\n-----------------------------------------\n| Loading contig boundaries | Time = 1.0172 ms\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading sequence | Time = 351.29 us\n-----------------------------------------\nsize = 4080\n-----------------------------------------\n| Loading positions | Time = 350.08 us\n-----------------------------------------\nsize = 4800\n-----------------------------------------\n| Loading reference sequence | Time = 258.33 us\n-----------------------------------------\n-----------------------------------------\n| Loading reference accumulative lengths | Time = 104.83 us\n-----------------------------------------\n[2026-09-17 22:36:14.989] [jointLog] [info] setting maxHashResizeThreads to 1\n[2026-09-17 22:36:14.989] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored.\n[2026-09-17 22:36:14.989] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65\n[2026-09-17 22:36:14.990] [jointLog] [info] parsing read library format\n[2026-09-17 22:36:14.991] [jointLog] [info] There is 1 library.\n[2026-09-17 22:36:14.995] [jointLog] [info] Loading pufferfish index\n[2026-09-17 22:36:14.996] [jointLog] [info] Loading dense pufferfish index.\n[2026-09-17 22:36:15.004] [jointLog] [info] done\n[2026-09-17 22:36:15.022] [jointLog] [info] Index contained 24 targets\n[2026-09-17 22:36:15.022] [jointLog] [info] Number of decoys : 0\n\n\n\n\n\n\n\n\n\n\n\n\n[2026-09-17 22:36:15.097] [jointLog] [info] Computed 24 rich equivalence classes for further processing\n[2026-09-17 22:36:15.097] [jointLog] [info] Counted 1523 total reads in the equivalence classes \n[2026-09-17 22:36:15.097] [jointLog] [info] Number of mappings discarded because of alignment score : 0\n[2026-09-17 22:36:15.097] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 0\n[2026-09-17 22:36:15.097] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0\n[2026-09-17 22:36:15.097] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 0\n[2026-09-17 22:36:15.098] [jointLog] [warning] Only 1523 fragments were mapped, but the number of burn-in fragments was set to 5000000.\nThe effective lengths have been computed using the observed mappings.\n\n[2026-09-17 22:36:15.098] [jointLog] [info] Mapping rate = 100%\n\n[2026-09-17 22:36:15.098] [jointLog] [info] finished quantifyLibrary()\n[2026-09-17 22:36:15.099] [jointLog] [info] Starting optimizer\n[2026-09-17 22:36:15.106] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\n[2026-09-17 22:36:15.107] [jointLog] [info] iteration = 0 | max rel diff. = 6.05074\n[2026-09-17 22:36:15.111] [jointLog] [info] iteration = 100 | max rel diff. = 0\n[2026-09-17 22:36:15.112] [jointLog] [info] Finished optimizer\n[2026-09-17 22:36:15.112] [jointLog] [info] writing output \n\n[2026-09-17 22:36:15.114] [jointLog] [warning] NOTE: Read Lib [[ /dev/fd/63, /dev/fd/62]] :\n\nDetected a *potential* strand bias > 1% in an unstranded protocol check the file: ./output/lib_format_counts.json for details\n\n", "tool_stdout": "Threads = 1\nVertex length = 31\nHash functions = 5\nFilter size = 1048576\nCapacity = 2\nFiles: \n./index/ref_k31_fixed.fa\n--------------------------------------------------------------------------------\nRound 0, 0:1048576\nPass\tFilling\tFiltering\n1\t0\t0\t\n2\t0\t0\nTrue junctions count = 0\nFalse junctions count = 48\nHash table size = 48\nCandidate marks count = 48\n--------------------------------------------------------------------------------\nReallocating bifurcations time: 0\nTrue marks count: 48\nEdges construction time: 0\n--------------------------------------------------------------------------------\nDistinct junctions = 0\n\nfor info, total work write each : 2.331 total work inram from level 3 : 4.322 total work raw : 25.000 \nBitarray 27520 bits (100.00 %) (array + ranks )\nfinal hash 0 bits (0.00 %) (nb in final hash 0)\n", "update_time": "2026-09-17T22:36:18.473921", "user_email": "planemo@galaxyproject.org", "user_id": "ab426e56a688ed95" } ], "model_class": "WorkflowInvocationStep", "order_index": 4, "output_collections": { "output_quant": { "id": "d67aa88f27cf1ce3", "src": "hdca" } }, "outputs": {}, "state": "scheduled", "subworkflow": null, "subworkflow_invocation_id": null, "update_time": "2026-09-17T22:35:57.602256", "workflow_step_id": "ab426e56a688ed95", "workflow_step_label": "salmon_quant", "workflow_step_uuid": "19a21d4b-4799-4ddf-989c-db7fa6142201" }, "5. deseq2": { "action": null, "id": "99bd1f66aad6c7b5", "implicit_collection_jobs_id": null, "job_id": "1c570cff87abc172", "jobs": [ { "command_line": "ln -s '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/1/c/5/dataset_1c5a4296-cbb5-4821-bdb7-ba0e4a0034ef.dat' mapping.txt && cat '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/deseq2/b060944b3989/deseq2/get_deseq_dataset.R' > /dev/null && Rscript '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/deseq2/b060944b3989/deseq2/deseq2.R' --cores ${GALAXY_SLOTS:-1} -o '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/16/outputs/dataset_46ba9a21-7a67-4893-84ef-a6d45b9be978.dat' -p '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/16/outputs/dataset_d53e7a31-9620-47fa-9e6e-2b10101e67b0.dat' -A 0.1 -n '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/16/outputs/dataset_9c3d28d4-6168-4a18-8839-ba6d3e31ad83.dat' --sample_sheet_mode --sample_sheet '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/7/8/0/dataset_780cf916-4908-4afe-b6d2-33585818cad7.dat' --collection_files '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/f/0/4/dataset_f041bf5b-d266-4bbf-99ba-d158ecf8144a.dat,/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/b/5/7/dataset_b57aec04-bb88-49dc-9393-4de578624e7e.dat,/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/b/0/3/dataset_b0353697-eb59-4c42-9f29-ef4a42e3439d.dat,/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/3/5/0/dataset_35098e74-4003-4f04-abd5-54848a0d4b7c.dat' --custom_design_formula --design_formula '~ Condition' -H -l 'eyJkYXRhc2V0X2YwNDFiZjViLWQyNjYtNGJiZi05OWJhLWQxNThlY2Y4MTQ0YS5kYXQiOiAiU1JSNTA4NTE2NyIsICJkYXRhc2V0X2I1N2FlYzA0LWJiODgtNDlkYy05MzkzLTRkZTU3ODYyNGU3ZS5kYXQiOiAiU1JSNTA4NTE2OCIsICJkYXRhc2V0X2IwMzUzNjk3LWViNTktNGM0Mi05ZjI5LWVmNGE0MmUzNDM5ZC5kYXQiOiAiU1JSNTA4NTE2OSIsICJkYXRhc2V0XzM1MDk4ZTc0LTQwMDMtNGYwNC1hYmQ1LTU0ODQ4YTBkNGI3Yy5kYXQiOiAiU1JSNTA4NTE3MCJ9' -t 1 --lfc_shrinkage_type 'none' -i -y salmon -x mapping.txt", "command_version": "R version 4.3.3 (2024-02-29) -- \"Angel Food Cake\", DESeq2 version 1.40.2", "copied_from_job_id": null, "create_time": "2026-09-17T22:35:57.599417", "dependencies": [], "exit_code": 0, "external_id": "33739", "galaxy_version": "26.1", "handler": null, "history_id": "ab426e56a688ed95", "id": "1c570cff87abc172", "inputs": { "select_data|countsFile1": { "id": "32d9dd6ff07d88c9", "src": "hda", "uuid": "f041bf5b-d266-4bbf-99ba-d158ecf8144a" }, "select_data|countsFile2": { "id": "53558844794bf923", "src": "hda", "uuid": "b57aec04-bb88-49dc-9393-4de578624e7e" }, "select_data|countsFile3": { "id": "8a599077f39a97c7", "src": "hda", "uuid": "b0353697-eb59-4c42-9f29-ef4a42e3439d" }, "select_data|countsFile4": { "id": "624b1fd4c0b6fdf6", "src": "hda", "uuid": "35098e74-4003-4f04-abd5-54848a0d4b7c" }, "select_data|sample_sheet": { "id": "4e5a7135364a358a", "src": "hda", "uuid": "780cf916-4908-4afe-b6d2-33585818cad7" }, "tximport|mapping_format|tabular_file": { "id": "ee96573fcbe71150", "src": "hda", "uuid": "1c5a4296-cbb5-4821-bdb7-ba0e4a0034ef" } }, "job_messages": [], "job_metrics": [ { "name": "container_id", "plugin": "core", "raw_value": "quay.io/biocontainers/mulled-v2-7659558cb19fdc912d0cd19e19bf435130b46160:87a8bb04f733cb6f18f6b98efe33ef26ee46e137-0", "title": "Container ID", "value": "quay.io/biocontainers/mulled-v2-7659558cb19fdc912d0cd19e19bf435130b46160:87a8bb04f733cb6f18f6b98efe33ef26ee46e137-0" }, { "name": "container_type", "plugin": "core", "raw_value": "docker", "title": "Container Type", "value": "docker" }, { "name": "galaxy_slots", "plugin": "core", "raw_value": "1.0000000", "title": "Cores Allocated", "value": "1" }, { "name": "start_epoch", "plugin": "core", "raw_value": "1789684580.0000000", "title": "Job Start Time", "value": "2026-09-18 00:36:20" }, { "name": "end_epoch", "plugin": "core", "raw_value": "1789684644.0000000", "title": "Job End Time", "value": "2026-09-18 00:37:24" }, { "name": "runtime_seconds", "plugin": "core", "raw_value": "64.0000000", "title": "Job Runtime (Wall Clock)", "value": "1 minute" } ], "job_runner_name": null, "job_stderr": "", "job_stdout": "", "model_class": "Job", "output_collections": {}, "outputs": { "counts_out": { "id": "cb5e47673389f186", "src": "hda", "uuid": "9c3d28d4-6168-4a18-8839-ba6d3e31ad83" }, "deseq_out": { "id": "1c570cff87abc172", "src": "hda", "uuid": "46ba9a21-7a67-4893-84ef-a6d45b9be978" }, "plots": { "id": "ade146db41b533bb", "src": "hda", "uuid": "d53e7a31-9620-47fa-9e6e-2b10101e67b0" } }, "params": { "__input_ext": "\"input\"", "__workflow_invocation_uuid__": "\"26835a54b2e811f1a764e6fd7feff8e8\"", "advanced_options": "{\"auto_mean_filter_off\": false, \"esf_cond\": {\"__current_case__\": 0, \"esf\": \"\"}, \"fit_type\": \"1\", \"lfc_shrinkage_type\": \"none\", \"outlier_filter_off\": false, \"outlier_replace_off\": false, \"prefilter_conditional\": {\"__current_case__\": 1, \"prefilter\": \"\"}, \"use_beta_priors\": false}", "batch_factors": null, "chromInfo": "\"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", "header": "true", "output_options": "{\"alpha_ma\": \"0.1\", \"output_selector\": [\"pdf\", \"normCounts\"]}", "select_data": "{\"__current_case__\": 2, \"countsFile\": {\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}, \"design_formula_mode\": {\"__current_case__\": 1, \"design_formula\": \"~ Condition\", \"mode\": \"custom\", \"reference_level\": null, \"target_level\": null}, \"how\": \"sample_sheet_contrasts\", \"sample_sheet\": {\"values\": [{\"id\": 10, \"src\": \"hda\"}]}}", "tximport": "{\"__current_case__\": 0, \"mapping_format\": {\"__current_case__\": 1, \"mapping_format_selector\": \"tabular\", \"tabular_file\": {\"values\": [{\"id\": 11, \"src\": \"hda\"}]}}, \"tximport_selector\": \"tximport\", \"txtype\": \"salmon\"}" }, "state": "ok", "stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\nreading in files with read.delim (install 'readr' package for speed up)\n1 2 3 4 \ntranscripts missing from tx2gene: 1\nsummarizing abundance\nsummarizing counts\nsummarizing length\nusing counts and average transcript lengths from tximport\nestimating size factors\nusing 'avgTxLength' from assays(dds), correcting for library size\nestimating dispersions\ngene-wise dispersion estimates\nmean-dispersion relationship\n-- note: fitType='parametric', but the dispersion trend was not well captured by the\n function: y = a/x + b, and a local regression fit was automatically substituted.\n specify fitType='local' or 'mean' to avoid this message next time.\nfinal dispersion estimates\nfitting model and testing\n-- note: fitType='parametric', but the dispersion trend was not well captured by the\n function: y = a/x + b, and a local regression fit was automatically substituted.\n specify fitType='local' or 'mean' to avoid this message next time.\nWarning message:\n`aes_string()` was deprecated in ggplot2 3.0.0.\n\u2139 Please use tidy evaluation idioms with `aes()`.\n\u2139 See also `vignette(\"ggplot2-in-packages\")` for more information. \nWarning: Your system is mis-configured: '/var/db/timezone/localtime' is not a symlink\nWarning: '/var/db/timezone/localtime' is not identical to any known timezone file\n", "stdout": "primary factor: Condition \n\n---------------------\nNo size factor was used\nDESeq2 run information\n\nsample table:\n Condition\nSRR5085167 Mock\nSRR5085168 Mock\nSRR5085169 Ebola\nSRR5085170 Ebola\n\ndesign formula:\n~Condition\n\n\n4 samples with counts over 23 genes\nApplied default - beta prior off\n[1] \"use_beta_prior is set to FALSE\"\nusing disperion fit type: parametric \ncreating plots\nsummary of results\nCondition: Ebola vs Mock\n\nout of 23 with nonzero total read count\nadjusted p-value < 0.1\nLFC > 0 (up) : 0, 0%\nLFC < 0 (down) : 0, 0%\noutliers [1] : 0, 0%\nlow counts [2] : 0, 0%\n(mean count < 20)\n[1] see 'cooksCutoff' argument of ?results\n[2] see 'independentFiltering' argument of ?results\n\nNULL\nclosing plot device\nnull device \n 1 \nSession information:\n\nR version 4.3.3 (2024-02-29)\nPlatform: x86_64-conda-linux-gnu (64-bit)\nRunning under: Debian GNU/Linux 12 (bookworm)\n\nMatrix products: default\nBLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.33.so; LAPACK version 3.12.0\n\nlocale:\n [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 \n [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 \n [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C \n[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C \n\ntime zone: NA\ntzcode source: system (glibc)\n\nattached base packages:\n[1] stats4 tools stats graphics grDevices utils datasets \n[8] methods base \n\nother attached packages:\n [1] pheatmap_1.0.12 ggrepel_0.9.3 \n [3] ggplot2_3.5.2 tximport_1.28.0 \n [5] rjson_0.2.21 gplots_3.1.3.1 \n [7] RColorBrewer_1.1-3 DESeq2_1.40.2 \n [9] SummarizedExperiment_1.30.2 Biobase_2.60.0 \n[11] MatrixGenerics_1.12.2 matrixStats_1.5.0 \n[13] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1 \n[15] IRanges_2.34.1 S4Vectors_0.38.1 \n[17] BiocGenerics_0.46.0 getopt_1.20.3 \n\nloaded via a namespace (and not attached):\n [1] generics_0.1.4 bitops_1.0-9 KernSmooth_2.23-26 \n [4] gtools_3.9.5 lattice_0.22-7 magrittr_2.0.3 \n [7] caTools_1.18.3 grid_4.3.3 jsonlite_2.0.0 \n[10] Matrix_1.6-5 scales_1.4.0 codetools_0.2-20 \n[13] cli_3.6.5 rlang_1.1.6 crayon_1.5.3 \n[16] XVector_0.40.0 withr_3.0.2 base64enc_0.1-3 \n[19] DelayedArray_0.26.6 S4Arrays_1.0.4 parallel_4.3.3 \n[22] BiocParallel_1.34.2 dplyr_1.1.4 colorspace_2.1-1 \n[25] locfit_1.5-9.12 GenomeInfoDbData_1.2.11 vctrs_0.6.5 \n[28] R6_2.6.1 lifecycle_1.0.4 zlibbioc_1.46.0 \n[31] pkgconfig_2.0.3 pillar_1.11.0 gtable_0.3.6 \n[34] glue_1.8.0 Rcpp_1.1.0 tibble_3.3.0 \n[37] tidyselect_1.2.1 farver_2.1.2 labeling_0.4.3 \n[40] compiler_4.3.3 RCurl_1.98-1.17 \n", "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy3", "tool_stderr": "WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested\nreading in files with read.delim (install 'readr' package for speed up)\n1 2 3 4 \ntranscripts missing from tx2gene: 1\nsummarizing abundance\nsummarizing counts\nsummarizing length\nusing counts and average transcript lengths from tximport\nestimating size factors\nusing 'avgTxLength' from assays(dds), correcting for library size\nestimating dispersions\ngene-wise dispersion estimates\nmean-dispersion relationship\n-- note: fitType='parametric', but the dispersion trend was not well captured by the\n function: y = a/x + b, and a local regression fit was automatically substituted.\n specify fitType='local' or 'mean' to avoid this message next time.\nfinal dispersion estimates\nfitting model and testing\n-- note: fitType='parametric', but the dispersion trend was not well captured by the\n function: y = a/x + b, and a local regression fit was automatically substituted.\n specify fitType='local' or 'mean' to avoid this message next time.\nWarning message:\n`aes_string()` was deprecated in ggplot2 3.0.0.\n\u2139 Please use tidy evaluation idioms with `aes()`.\n\u2139 See also `vignette(\"ggplot2-in-packages\")` for more information. \nWarning: Your system is mis-configured: '/var/db/timezone/localtime' is not a symlink\nWarning: '/var/db/timezone/localtime' is not identical to any known timezone file\n", "tool_stdout": "primary factor: Condition \n\n---------------------\nNo size factor was used\nDESeq2 run information\n\nsample table:\n Condition\nSRR5085167 Mock\nSRR5085168 Mock\nSRR5085169 Ebola\nSRR5085170 Ebola\n\ndesign formula:\n~Condition\n\n\n4 samples with counts over 23 genes\nApplied default - beta prior off\n[1] \"use_beta_prior is set to FALSE\"\nusing disperion fit type: parametric \ncreating plots\nsummary of results\nCondition: Ebola vs Mock\n\nout of 23 with nonzero total read count\nadjusted p-value < 0.1\nLFC > 0 (up) : 0, 0%\nLFC < 0 (down) : 0, 0%\noutliers [1] : 0, 0%\nlow counts [2] : 0, 0%\n(mean count < 20)\n[1] see 'cooksCutoff' argument of ?results\n[2] see 'independentFiltering' argument of ?results\n\nNULL\nclosing plot device\nnull device \n 1 \nSession information:\n\nR version 4.3.3 (2024-02-29)\nPlatform: x86_64-conda-linux-gnu (64-bit)\nRunning under: Debian GNU/Linux 12 (bookworm)\n\nMatrix products: default\nBLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.33.so; LAPACK version 3.12.0\n\nlocale:\n [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 \n [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 \n [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C \n[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C \n\ntime zone: NA\ntzcode source: system (glibc)\n\nattached base packages:\n[1] stats4 tools stats graphics grDevices utils datasets \n[8] methods base \n\nother attached packages:\n [1] pheatmap_1.0.12 ggrepel_0.9.3 \n [3] ggplot2_3.5.2 tximport_1.28.0 \n [5] rjson_0.2.21 gplots_3.1.3.1 \n [7] RColorBrewer_1.1-3 DESeq2_1.40.2 \n [9] SummarizedExperiment_1.30.2 Biobase_2.60.0 \n[11] MatrixGenerics_1.12.2 matrixStats_1.5.0 \n[13] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1 \n[15] IRanges_2.34.1 S4Vectors_0.38.1 \n[17] BiocGenerics_0.46.0 getopt_1.20.3 \n\nloaded via a namespace (and not attached):\n [1] generics_0.1.4 bitops_1.0-9 KernSmooth_2.23-26 \n [4] gtools_3.9.5 lattice_0.22-7 magrittr_2.0.3 \n [7] caTools_1.18.3 grid_4.3.3 jsonlite_2.0.0 \n[10] Matrix_1.6-5 scales_1.4.0 codetools_0.2-20 \n[13] cli_3.6.5 rlang_1.1.6 crayon_1.5.3 \n[16] XVector_0.40.0 withr_3.0.2 base64enc_0.1-3 \n[19] DelayedArray_0.26.6 S4Arrays_1.0.4 parallel_4.3.3 \n[22] BiocParallel_1.34.2 dplyr_1.1.4 colorspace_2.1-1 \n[25] locfit_1.5-9.12 GenomeInfoDbData_1.2.11 vctrs_0.6.5 \n[28] R6_2.6.1 lifecycle_1.0.4 zlibbioc_1.46.0 \n[31] pkgconfig_2.0.3 pillar_1.11.0 gtable_0.3.6 \n[34] glue_1.8.0 Rcpp_1.1.0 tibble_3.3.0 \n[37] tidyselect_1.2.1 farver_2.1.2 labeling_0.4.3 \n[40] compiler_4.3.3 RCurl_1.98-1.17 \n", "update_time": "2026-09-17T22:37:24.290881", "user_email": "planemo@galaxyproject.org", "user_id": "ab426e56a688ed95" } ], "model_class": "WorkflowInvocationStep", "order_index": 5, "output_collections": {}, "outputs": { "counts_out": { "id": "cb5e47673389f186", "src": "hda", "uuid": "9c3d28d4-6168-4a18-8839-ba6d3e31ad83" }, "deseq_out": { "id": "1c570cff87abc172", "src": "hda", "uuid": "46ba9a21-7a67-4893-84ef-a6d45b9be978" }, "plots": { "id": "ade146db41b533bb", "src": "hda", "uuid": "d53e7a31-9620-47fa-9e6e-2b10101e67b0" } }, "state": "scheduled", "subworkflow": null, "subworkflow_invocation_id": null, "update_time": "2026-09-17T22:37:24.288705", "workflow_step_id": "d67aa88f27cf1ce3", "workflow_step_label": "deseq2", "workflow_step_uuid": "d1c5d57e-aa6e-4247-bcfd-d857e86e457e" } } }, "job": null, "output_problems": null, "problem_log": "Activated a virtualenv for Galaxy\n/Users/mvandenb/.planemo/gx_venv_3\nActivating virtualenv at /Users/mvandenb/.planemo/gx_venv_3\nUsing Python 3.14.6 environment at: /Users/mvandenb/.planemo/gx_venv_3\nChecked 313 packages in 16ms\nOption master_api_key has been deprecated in favor of bootstrap_admin_api_key\nTrying to resolve path for the 'email_ban_file' option but it's empty/None\nTrying to resolve path for the 'data_manager_config_file' option but it's empty/None\nUsing Python 3.14.6 environment at: /Users/mvandenb/.planemo/gx_venv_3\nUsing Python 3.14.6 environment at: /Users/mvandenb/.planemo/gx_venv_3\nChecked 2 packages in 4ms\nThe Galaxy client build is being skipped due to the SKIP_CLIENT_BUILD environment variable.\nActivating virtualenv at /Users/mvandenb/.planemo/gx_venv_3\nExecuting: galaxy \nWorking directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev\nExecuting: PYTHONPATH=lib GALAXY_CONFIG_FILE=/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy.yml OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES gunicorn 'galaxy.webapps.galaxy.fast_factory:factory()' --timeout 300 --pythonpath lib -k galaxy.webapps.galaxy.workers.Worker -b localhost:50627 --workers=1 --config python:galaxy.web_stack.gunicorn_config --no-control-socket\nWorking directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev\nExecuting: PYTHONPATH=lib GALAXY_CONFIG_FILE=/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy.yml celery --app galaxy.celery beat --loglevel DEBUG --schedule /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/gravity/celerybeat-schedule\nWorking directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev\nExecuting: npm_config_yes=true npx @galaxyproject/gx-it-proxy@>=0.0.6 --ip localhost --port 50631 --sessions /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/database/interactivetools_map.sqlite --verbose --proxyPathPrefix /interactivetool/ep\nWorking directory: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev\nExecuting: PYTHONPATH=lib GALAXY_CONFIG_FILE=/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy.yml celery --app galaxy.celery worker --concurrency 2 --loglevel DEBUG --pool threads --queues celery,galaxy.internal,galaxy.external \nWatching path /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/database/interactivetools_map.sqlite\nListening on localhost:50631\n[2026-09-18 00:34:38 +0200] [33505] [INFO] Starting gunicorn 26.0.0\n[2026-09-18 00:34:38 +0200] [33505] [INFO] Listening at: http://127.0.0.1:50627 (33505)\n[2026-09-18 00:34:38 +0200] [33505] [INFO] Using worker: galaxy.webapps.galaxy.workers.Worker\n[2026-09-18 00:34:38 +0200] [33541] [INFO] Booting worker with pid: 33541\nOption master_api_key has been deprecated in favor of bootstrap_admin_api_key\nTrying to resolve path for the 'email_ban_file' option but it's empty/None\nTrying to resolve path for the 'data_manager_config_file' option but it's empty/None\nOption master_api_key has been deprecated in favor of bootstrap_admin_api_key\nTrying to resolve path for the 'email_ban_file' option but it's empty/None\nTrying to resolve path for the 'data_manager_config_file' option but it's empty/None\nOption master_api_key has been deprecated in favor of bootstrap_admin_api_key\nTrying to resolve path for the 'email_ban_file' option but it's empty/None\nTrying to resolve path for the 'data_manager_config_file' option but it's empty/None\n[2026-09-18 00:34:41,334: DEBUG/MainProcess] | Worker: Preparing bootsteps.\n[2026-09-18 00:34:41,335: DEBUG/MainProcess] | Worker: Building graph...\n[2026-09-18 00:34:41,335: DEBUG/MainProcess] | Worker: New boot order: {Timer, Hub, Pool, Autoscaler, StateDB, Beat, Consumer}\n[2026-09-18 00:34:41,337: DEBUG/MainProcess] Setting default socket timeout to 30\n[2026-09-18 00:34:41,338: INFO/MainProcess] beat: Starting...\n[2026-09-18 00:34:41,338: DEBUG/MainProcess] | Consumer: Preparing bootsteps.\n[2026-09-18 00:34:41,339: DEBUG/MainProcess] | Consumer: Building graph...\n[2026-09-18 00:34:41,350: DEBUG/MainProcess] | Consumer: New boot order: {Connection, Events, Mingle, Tasks, DelayedDelivery, Heart, Agent, Control, Gossip, event loop}\n[2026-09-18 00:34:41,362: DEBUG/MainProcess] Current schedule:\n\n\n\n\n\n\n\n[2026-09-18 00:34:41,362: DEBUG/MainProcess] beat: Ticking with max interval->5.00 minutes\n[2026-09-18 00:34:41,363: DEBUG/MainProcess] beat: Waking up in 5.00 minutes.\n \n -------------- celery@Mac v5.6.3 (recovery)\n--- ***** ----- \n-- ******* ---- macOS-26.5.2-arm64-arm-64bit-Mach-O 2026-09-18 00:34:41\n- *** --- * --- \n- ** ---------- [config]\n- ** ---------- .> app: galaxy:0x111832a50\n- ** ---------- .> transport: sqlalchemy+sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/celery_broker.sqlite\n- ** ---------- .> results: sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/database/results.sqlite\n- *** --- * --- .> concurrency: 2 (thread)\n-- ******* ---- .> task events: OFF (enable -E to monitor tasks in this worker)\n--- ***** ----- \n -------------- [queues]\n .> celery exchange=celery(direct) key=celery\n .> galaxy.external exchange=galaxy.external(direct) key=galaxy.external\n .> galaxy.internal exchange=galaxy.internal(direct) key=galaxy.internal\n\n[tasks]\n . celery.accumulate\n . celery.backend_cleanup\n . celery.chain\n . celery.chord\n . celery.chord_unlock\n . celery.chunks\n . celery.group\n . celery.map\n . celery.starmap\n . galaxy.bulk_move_storage\n . galaxy.change_datatype\n . galaxy.clean_object_store_caches\n . galaxy.cleanup_expired_notifications\n . galaxy.cleanup_jwds\n . galaxy.cleanup_short_term_storage\n . galaxy.cleanup_stale_concurrency_slots\n . galaxy.compute_dataset_hash\n . galaxy.dispatch_pending_notifications\n . galaxy.emit_queue_metrics_task\n . galaxy.execute_workflow_completion_hook\n . galaxy.export_history\n . galaxy.fetch_data\n . galaxy.finish_job\n . galaxy.import_data_bundle\n . galaxy.import_model_store\n . galaxy.materialize\n . galaxy.prepare_dataset_collection_download\n . galaxy.prepare_history_content_download\n . galaxy.prepare_history_download\n . galaxy.prepare_invocation_download\n . galaxy.prepare_pdf_download\n . galaxy.prune_expired_bulk_storage_operations\n . galaxy.prune_history_audit_table\n . galaxy.prune_kombu_sqla_transport\n . galaxy.purge_datasets\n . galaxy.purge_hda\n . galaxy.purge_history_datasets\n . galaxy.queue_jobs\n . galaxy.recalculate_user_disk_usage\n . galaxy.recover_stale_bulk_storage_operation_runs\n . galaxy.refresh_gtn_database\n . galaxy.refresh_iwc_manifest\n . galaxy.renew_vault_token\n . galaxy.send_notification_to_recipients_async\n . galaxy.set_job_metadata\n . galaxy.set_metadata\n . galaxy.setup_fetch_data\n . galaxy.touch\n . galaxy.write_history_content_to\n . galaxy.write_history_to\n . galaxy.write_invocation_to\n\n[2026-09-18 00:34:41,607: DEBUG/MainProcess] | Worker: Starting Pool\n[2026-09-18 00:34:41,607: DEBUG/MainProcess] ^-- substep ok\n[2026-09-18 00:34:41,607: DEBUG/MainProcess] | Worker: Starting Consumer\n[2026-09-18 00:34:41,607: DEBUG/MainProcess] | Consumer: Starting Connection\n[2026-09-18 00:34:41,609: INFO/MainProcess] Connected to sqlalchemy+sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/celery_broker.sqlite\n[2026-09-18 00:34:41,609: DEBUG/MainProcess] ^-- substep ok\n[2026-09-18 00:34:41,609: DEBUG/MainProcess] | Consumer: Starting Events\n[2026-09-18 00:34:41,610: DEBUG/MainProcess] ^-- substep ok\n[2026-09-18 00:34:41,610: DEBUG/MainProcess] | Consumer: Starting Tasks\n[2026-09-18 00:34:41,626: DEBUG/MainProcess] ^-- substep ok\n[2026-09-18 00:34:41,626: DEBUG/MainProcess] | Consumer: Starting Heart\n[2026-09-18 00:34:41,626: DEBUG/MainProcess] ^-- substep ok\n[2026-09-18 00:34:41,626: DEBUG/MainProcess] | Consumer: Starting event loop\n[2026-09-18 00:34:41,626: INFO/MainProcess] celery@Mac ready.\nDEBUG:yacman.yacman:Using yacman version 1.0.0\n/Users/mvandenb/.planemo/gx_venv_3/lib/python3.14/site-packages/paste/urlparser.py:15: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n import pkg_resources\nDEBUG:galaxy.app:python path is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev, /Users/mvandenb/.planemo/gx_venv_3/bin, /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/lib, /opt/homebrew/Cellar/python@3.14/3.14.6/Frameworks/Python.framework/Versions/3.14/lib/python314.zip, /opt/homebrew/Cellar/python@3.14/3.14.6/Frameworks/Python.framework/Versions/3.14/lib/python3.14, /opt/homebrew/Cellar/python@3.14/3.14.6/Frameworks/Python.framework/Versions/3.14/lib/python3.14/lib-dynload, /Users/mvandenb/.planemo/gx_venv_3/lib/python3.14/site-packages, /Users/mvandenb/.planemo/gx_venv_3/lib/python3.14/site-packages/setuptools/_vendor\nDEBUG:galaxy.config:Configuration directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8\nDEBUG:galaxy.config:Data directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/database\nDEBUG:galaxy.config:Managed config directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8\nWARNING:galaxy.config:Option master_api_key has been deprecated in favor of bootstrap_admin_api_key\nWARNING:galaxy.config:Trying to resolve path for the 'email_ban_file' option but it's empty/None\nWARNING:galaxy.config:Trying to resolve path for the 'data_manager_config_file' option but it's empty/None\nDEBUG:galaxy.config:No extra version JSON file detected at /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/version.json\nINFO:galaxy.model.migrations:Creating database for URI [sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy.sqlite?isolation_level=IMMEDIATE]\nINFO:alembic.runtime.migration:Context impl SQLiteImpl.\nINFO:alembic.runtime.migration:Will assume non-transactional DDL.\nINFO:alembic.runtime.migration:Running stamp_revision -> fac9c76612f9\nDEBUG:alembic.runtime.migration:new branch insert fac9c76612f9\nINFO:alembic.runtime.migration:Context impl SQLiteImpl.\nINFO:alembic.runtime.migration:Will assume non-transactional DDL.\nINFO:alembic.runtime.migration:Running stamp_revision -> d4a650f47a3c\nDEBUG:alembic.runtime.migration:new branch insert d4a650f47a3c\nINFO:galaxy.app:Install database targeting Galaxy's database configuration.\nDEBUG:galaxy.web_stack:GunicornApplicationStack initialized\ngalaxy.web_stack.handlers INFO 2026-09-18 00:34:42,407 [pN:main,p:33541,tN:MainThread] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION', set the `assign_with` attribute on to override the default\ngalaxy.jobs INFO 2026-09-18 00:34:42,407 [pN:main,p:33541,tN:MainThread] Job handler assignment methods set to: db-transaction-isolation\ngalaxy.config.url_headers WARNING 2026-09-18 00:34:42,408 [pN:main,p:33541,tN:MainThread] URL headers configuration file not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/url_headers_conf.yml. Using null configuration.\ngalaxy.queue_worker INFO 2026-09-18 00:34:42,409 [pN:main,p:33541,tN:MainThread] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/celery_broker.sqlite\ngalaxy.datatypes.registry ERROR 2026-09-18 00:34:42,776 [pN:main,p:33541,tN:MainThread] Error importing datatype module galaxy.datatypes.html\nTraceback (most recent call last):\n File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/lib/galaxy/datatypes/registry.py\", line 235, in load_datatypes\n module = __import__(datatype_module)\nModuleNotFoundError: No module named 'galaxy.datatypes.html'\ngalaxy.visualization.genomes ERROR 2026-09-18 00:34:42,953 [pN:main.1,p:33541,tN:MainThread] Error reading twobit.loc\nTraceback (most recent call last):\n File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/lib/galaxy/visualization/genomes.py\", line 225, in reload_genomes\n with open(twobit_path) as f:\n ~~~~^^^^^^^^^^^^^\nFileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/tool-data/twobit.loc'\ngalaxy.util WARNING 2026-09-18 00:34:42,979 [pN:main.1,p:33541,tN:MainThread] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/config/plugins/activities\ngalaxy.tools WARNING 2026-09-18 00:34:42,980 [pN:main.1,p:33541,tN:MainThread] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file\ngalaxy.tool_util.toolbox.base INFO 2026-09-18 00:34:42,980 [pN:main.1,p:33541,tN:MainThread] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/tool_conf.xml\ngalaxy.tools WARNING 2026-09-18 00:34:42,992 [pN:main.1,p:33541,tN:MainThread] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file\ngalaxy.tool_util.toolbox.base INFO 2026-09-18 00:34:42,992 [pN:main.1,p:33541,tN:MainThread] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tools_conf.xml\ngalaxy.tools WARNING 2026-09-18 00:34:42,993 [pN:main.1,p:33541,tN:MainThread] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file\ngalaxy.tool_util.toolbox.base INFO 2026-09-18 00:34:42,993 [pN:main.1,p:33541,tN:MainThread] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/empty_tool_conf.xml\ngalaxy.tools.search WARNING 2026-09-18 00:34:43,001 [pN:main.1,p:33541,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/database/tool_search_index/default' uses outdated schema, creating a new index\ngalaxy.tools.search WARNING 2026-09-18 00:34:43,002 [pN:main.1,p:33541,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/database/tool_search_index/my_panel' uses outdated schema, creating a new index\ngalaxy.tools.search WARNING 2026-09-18 00:34:43,002 [pN:main.1,p:33541,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/database/tool_search_index/ontology:edam_operations' uses outdated schema, creating a new index\ngalaxy.tools.search WARNING 2026-09-18 00:34:43,003 [pN:main.1,p:33541,tN:MainThread] Index at '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/database/tool_search_index/ontology:edam_topics' uses outdated schema, creating a new index\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,006 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"igv_broad_genomes\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,006 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"bam_iobio\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,008 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"intermine_simple_display\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,009 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"igv_broad_genomes\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,010 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"igv_broad_genomes\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,012 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"igv_broad_genomes\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,012 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"q2view_display\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,013 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"q2view_display\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,014 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"igv_broad_genomes\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,014 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"vcf_iobio\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,015 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"igv_broad_genomes\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,015 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"igv_broad_genomes\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,016 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"biom_simple_display\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,016 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"icn3d_simple_display\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,016 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"icn3d_simple_display\".\ngalaxy.datatypes.display_applications.application ERROR 2026-09-18 00:34:43,017 [pN:main.1,p:33541,tN:MainThread] Error loading a set of Dynamic Display Application links: Unable to find data table named \"icn3d_simple_display\".\ngalaxy.visualization.plugins.registry INFO 2026-09-18 00:34:43,194 [pN:main.1,p:33541,tN:MainThread] VisualizationsRegistry, loaded plugin: example\ngalaxy.tours._impl INFO 2026-09-18 00:34:43,199 [pN:main.1,p:33541,tN:MainThread] Loaded tour 'core.galaxy_ui'\ngalaxy.tours._impl INFO 2026-09-18 00:34:43,202 [pN:main.1,p:33541,tN:MainThread] Loaded tour 'core.deferred'\ngalaxy.tours._impl INFO 2026-09-18 00:34:43,205 [pN:main.1,p:33541,tN:MainThread] Loaded tour 'core.windows'\ngalaxy.tours._impl INFO 2026-09-18 00:34:43,206 [pN:main.1,p:33541,tN:MainThread] Loaded tour 'core.visualizations'\ngalaxy.tours._impl INFO 2026-09-18 00:34:43,209 [pN:main.1,p:33541,tN:MainThread] Loaded tour 'core.history'\ngalaxy.workflow.scheduling_manager INFO 2026-09-18 00:34:43,223 [pN:main.1,p:33541,tN:MainThread] No workflow schedulers plugin config file defined, using default scheduler.\ngalaxy.web_stack.handlers INFO 2026-09-18 00:34:43,223 [pN:main.1,p:33541,tN:MainThread] WorkflowSchedulingManager: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION', set the `assign_with` attribute on to override the default\ngalaxy.jobs.handler INFO 2026-09-18 00:34:43,226 [pN:main.1,p:33541,tN:WorkflowRequestMonitor.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION' assignment method for handler 'main.1', tag(s): _default_, None\ngalaxy.workflow.completion_hooks INFO 2026-09-18 00:34:43,229 [pN:main.1,p:33541,tN:MainThread] Enabling workflow completion hook: send_notification\ngalaxy.workflow.completion_hooks INFO 2026-09-18 00:34:43,230 [pN:main.1,p:33541,tN:MainThread] Enabling workflow completion hook: export_to_file_source\ngalaxy.workflow.completion_monitor INFO 2026-09-18 00:34:43,230 [pN:main.1,p:33541,tN:MainThread] Starting workflow completion monitor\ngalaxy.jobs INFO 2026-09-18 00:34:43,231 [pN:main.1,p:33541,tN:MainThread] Handler 'main.1' will load all configured runner plugins\ngalaxy.jobs.handler INFO 2026-09-18 00:34:43,240 [pN:main.1,p:33541,tN:JobHandlerQueue.monitor_thread] Handler job grabber initialized with 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION' assignment method for handler 'main.1', tag(s): \ngalaxy.jobs.handler INFO 2026-09-18 00:34:43,240 [pN:main.1,p:33541,tN:MainThread] job handler queue started\ngalaxy.jobs.handler INFO 2026-09-18 00:34:43,241 [pN:main.1,p:33541,tN:MainThread] job handler stop queue started\ngalaxy.queue_worker INFO 2026-09-18 00:34:43,242 [pN:main.1,p:33541,tN:MainThread] Binding and starting galaxy control worker for main.1\ngalaxy.queue_worker INFO 2026-09-18 00:34:43,243 [pN:main.1,p:33541,tN:MainThread] Queuing async task rebuild_toolbox_search_index for main.1.\ngalaxy.app INFO 2026-09-18 00:34:43,262 [pN:main.1,p:33541,tN:MainThread] Galaxy app startup finished (1254.275 ms)\ngalaxy.queue_worker INFO 2026-09-18 00:34:43,265 [pN:main.1,p:33541,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.\ngalaxy.web_stack INFO 2026-09-18 00:34:48,013 [pN:main.1,p:33541,tN:MainThread] Galaxy server instance 'main.1' is running\n\u001b[92m\nServing on http://127.0.0.1:50627\n\u001b[0m\n[2026-09-18 00:34:52 +0200] [33541] [INFO] Started server process [33541]\n[2026-09-18 00:34:52 +0200] [33541] [INFO] Waiting for application startup.\n[2026-09-18 00:34:52 +0200] [33541] [INFO] Application startup complete.\nuvicorn.access INFO 2026-09-18 00:34:52,398 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50666 - \"GET /api/version HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:34:52,419 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50668 - \"GET /api/tools?in_panel=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:34:52,425 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50670 - \"GET /api/tools?in_panel=False HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:34:52,444 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50672 - \"GET /api/tool_shed_repositories HTTP/1.1\" 200\ngalaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-18 00:34:54,853 [pN:main.1,p:33541,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/bgruening/salmon' at 23:29e12b90949d\ngalaxy.queue_worker INFO 2026-09-18 00:35:01,079 [pN:main.1,p:33541,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.\ngalaxy.queue_worker INFO 2026-09-18 00:35:01,377 [pN:main.1,p:33541,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.\ngalaxy.util WARNING 2026-09-18 00:35:01,379 [pN:main.1,p:33541,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/config/plugins/activities\ngalaxy.tools WARNING 2026-09-18 00:35:01,380 [pN:main.1,p:33541,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file\ngalaxy.tool_util.toolbox.base INFO 2026-09-18 00:35:01,381 [pN:main.1,p:33541,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/tool_conf.xml\ngalaxy.tools WARNING 2026-09-18 00:35:01,382 [pN:main.1,p:33541,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file\ngalaxy.tool_util.toolbox.base INFO 2026-09-18 00:35:01,382 [pN:main.1,p:33541,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tools_conf.xml\ngalaxy.tools WARNING 2026-09-18 00:35:01,383 [pN:main.1,p:33541,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file\ngalaxy.tool_util.toolbox.base INFO 2026-09-18 00:35:01,384 [pN:main.1,p:33541,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/empty_tool_conf.xml\ngalaxy.queue_worker INFO 2026-09-18 00:35:01,395 [pN:main.1,p:33541,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.\ngalaxy.queue_worker INFO 2026-09-18 00:35:01,399 [pN:main.1,p:33541,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.\nuvicorn.access INFO 2026-09-18 00:35:01,499 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50674 - \"POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1\" 200\ngalaxy.queue_worker INFO 2026-09-18 00:35:02,094 [pN:main.1,p:33541,tN:Thread-4 (check)] Sending reload_toolbox control task.\ngalaxy.tool_shed.galaxy_install.install_manager INFO 2026-09-18 00:35:03,648 [pN:main.1,p:33541,tN:WSGI_0] Cloning repository 'https://toolshed.g2.bx.psu.edu/repos/iuc/deseq2' at 34:b060944b3989\ngalaxy.queue_worker INFO 2026-09-18 00:35:07,146 [pN:main.1,p:33541,tN:Thread-4 (check)] Queuing sync task reload_toolbox for main.1.\ngalaxy.queue_worker INFO 2026-09-18 00:35:07,543 [pN:main.1,p:33541,tN:Thread-2] Instance 'main.1' received 'reload_toolbox' task, executing now.\ngalaxy.util WARNING 2026-09-18 00:35:07,545 [pN:main.1,p:33541,tN:Thread-2] directory not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/config/plugins/activities\ngalaxy.tools WARNING 2026-09-18 00:35:07,546 [pN:main.1,p:33541,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file\ngalaxy.tool_util.toolbox.base INFO 2026-09-18 00:35:07,547 [pN:main.1,p:33541,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/tool_conf.xml\ngalaxy.tools WARNING 2026-09-18 00:35:07,547 [pN:main.1,p:33541,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file\ngalaxy.tool_util.toolbox.base INFO 2026-09-18 00:35:07,548 [pN:main.1,p:33541,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tools_conf.xml\ngalaxy.tools WARNING 2026-09-18 00:35:07,549 [pN:main.1,p:33541,tN:Thread-2] The default shed tool config file (/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_conf.xml) has been added to the tool_config_file option, if this is not the desired behavior, please set shed_tool_config_file to your primary shed-enabled tool config file\ngalaxy.tool_util.toolbox.base INFO 2026-09-18 00:35:07,549 [pN:main.1,p:33541,tN:Thread-2] Parsing the tool configuration /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/empty_tool_conf.xml\ngalaxy.queue_worker INFO 2026-09-18 00:35:07,561 [pN:main.1,p:33541,tN:Thread-2] Queuing async task rebuild_toolbox_search_index for main.1.\ngalaxy.queue_worker INFO 2026-09-18 00:35:07,566 [pN:main.1,p:33541,tN:Thread-2] Instance 'main.1' received 'rebuild_toolbox_search_index' task, executing now.\nuvicorn.access INFO 2026-09-18 00:35:07,637 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50686 - \"POST /api/tool_shed_repositories/new/install_repository_revision HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:07,649 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50694 - \"GET /api/users HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:07,664 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50696 - \"GET /api/configuration HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:07,710 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50698 - \"POST /api/users HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:07,719 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50700 - \"POST /api/users/ab426e56a688ed95/api_key HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:07,766 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50702 - \"POST /api/workflows/upload HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:07,790 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50704 - \"POST /api/histories HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:07,792 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50706 - \"GET /api/version HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:07,797 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50708 - \"GET /api/configuration HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:07,806 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.058 ms)\nuvicorn.access INFO 2026-09-18 00:35:07,866 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50710 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:07,886 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50712 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:07,901: INFO/MainProcess] Task galaxy.setup_fetch_data[c94d8bfa-5320-4d63-b73f-08a2fec1c7ae] received\n[2026-09-18 00:35:07,901: DEBUG/MainProcess] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'c94d8bfa-5320-4d63-b73f-08a2fec1c7ae', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'c94d8bfa-5320-4d63-b73f-08a2fec1c7ae', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c94d8bfa-5320-4d63-b73f-08a2fec1c7ae', 'parent_id': None, 'argsrepr': '(1,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:08,130: INFO/MainProcess] setup plugin alembic.autogenerate.schemas\n[2026-09-18 00:35:08,131: INFO/MainProcess] setup plugin alembic.autogenerate.tables\n[2026-09-18 00:35:08,131: INFO/MainProcess] setup plugin alembic.autogenerate.types\n[2026-09-18 00:35:08,131: INFO/MainProcess] setup plugin alembic.autogenerate.constraints\n[2026-09-18 00:35:08,131: INFO/MainProcess] setup plugin alembic.autogenerate.defaults\n[2026-09-18 00:35:08,131: INFO/MainProcess] setup plugin alembic.autogenerate.comments\nuvicorn.access INFO 2026-09-18 00:35:08,156 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50714 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\ngalaxy.queue_worker INFO 2026-09-18 00:35:08,164 [pN:main.1,p:33541,tN:Thread-4 (check)] Sending reload_toolbox control task.\n[2026-09-18 00:35:08,239: DEBUG/MainProcess] python path is: /Users/mvandenb/.planemo/gx_venv_3/bin, /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/lib, /opt/homebrew/Cellar/python@3.14/3.14.6/Frameworks/Python.framework/Versions/3.14/lib/python314.zip, /opt/homebrew/Cellar/python@3.14/3.14.6/Frameworks/Python.framework/Versions/3.14/lib/python3.14, /opt/homebrew/Cellar/python@3.14/3.14.6/Frameworks/Python.framework/Versions/3.14/lib/python3.14/lib-dynload, /Users/mvandenb/.planemo/gx_venv_3/lib/python3.14/site-packages\n[2026-09-18 00:35:08,240: DEBUG/MainProcess] Configuration directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8\n[2026-09-18 00:35:08,240: DEBUG/MainProcess] Data directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/database\n[2026-09-18 00:35:08,240: DEBUG/MainProcess] Managed config directory is /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8\n[2026-09-18 00:35:08,250: WARNING/MainProcess] Option master_api_key has been deprecated in favor of bootstrap_admin_api_key\n[2026-09-18 00:35:08,250: WARNING/MainProcess] Trying to resolve path for the 'email_ban_file' option but it's empty/None\n[2026-09-18 00:35:08,250: WARNING/MainProcess] Trying to resolve path for the 'data_manager_config_file' option but it's empty/None\n[2026-09-18 00:35:08,251: DEBUG/MainProcess] No extra version JSON file detected at /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/version.json\n[2026-09-18 00:35:08,252: INFO/MainProcess] Install database targeting Galaxy's database configuration.\n[2026-09-18 00:35:08,257: DEBUG/main] WeblessApplicationStack initialized\n[2026-09-18 00:35:08,260: DEBUG/main] Read job configuration from file: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_conf.yml\n[2026-09-18 00:35:08,262: DEBUG/main] Database does not support WITH FOR UPDATE statement, cannot use DB-SKIP-LOCKED handler assignment\n[2026-09-18 00:35:08,262: INFO/main] JobConfiguration: No job handler assignment method is set, defaulting to 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION', set the `assign_with` attribute on to override the default\n[2026-09-18 00:35:08,263: INFO/main] Job handler assignment methods set to: db-transaction-isolation\n[2026-09-18 00:35:08,263: DEBUG/main] default set to child with id or tag 'local'\n[2026-09-18 00:35:08,263: DEBUG/main] Done loading job configuration\n[2026-09-18 00:35:08,263: WARNING/main] URL headers configuration file not found: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/url_headers_conf.yml. Using null configuration.\n[2026-09-18 00:35:08,264: INFO/main] Initializing main Galaxy Queue Worker on sqlalchemy+sqlite:////private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/celery_broker.sqlite\n[2026-09-18 00:35:08,289: WARNING/main] /Users/mvandenb/.planemo/gx_venv_3/lib/python3.14/site-packages/fs/__init__.py:4: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n __import__(\"pkg_resources\").declare_namespace(__name__) # type: ignore\n\nuvicorn.access INFO 2026-09-18 00:35:08,417 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50716 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:08,550: DEBUG/main] Loading datatypes from /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/lib/galaxy/config/sample/datatypes_conf.xml.sample\n[2026-09-18 00:35:08,550: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.h.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.c.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cpp.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.py.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.go.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.rs.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension source.cs.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markdown.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension rmd.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hep.root.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:JP2 from the datatype registry for extension jp2.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Ab1 from the datatype registry for extension ab1.\n[2026-09-18 00:35:08,551: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a2m.\n[2026-09-18 00:35:08,552: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Amos from the datatype registry for extension afg.\n[2026-09-18 00:35:08,552: DEBUG/main] Retrieved datatype module galaxy.datatypes.goldenpath:GoldenPath from the datatype registry for extension agp.\n[2026-09-18 00:35:08,552: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension alto.\n[2026-09-18 00:35:08,552: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension page.xml.\n[2026-09-18 00:35:08,552: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension abbyy.xml.\n[2026-09-18 00:35:08,552: ERROR/main] Error importing datatype module galaxy.datatypes.html\nTraceback (most recent call last):\n File \"/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/lib/galaxy/datatypes/registry.py\", line 235, in load_datatypes\n module = __import__(datatype_module)\nModuleNotFoundError: No module named 'galaxy.datatypes.html'\n[2026-09-18 00:35:08,553: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_cog_profile.\n[2026-09-18 00:35:08,553: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_composite.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension anvio_classifier.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioContigsDB from the datatype registry for extension anvio_contigs_db.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioDB from the datatype registry for extension anvio_db.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioGenomesDB from the datatype registry for extension anvio_genomes_db.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioPanDB from the datatype registry for extension anvio_pan_db.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioComposite from the datatype registry for extension anvio_pfam_profile.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioProfileDB from the datatype registry for extension anvio_profile_db.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioSamplesDB from the datatype registry for extension anvio_samples_db.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension anvio_state.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.anvio:AnvioStructureDB from the datatype registry for extension anvio_structure_db.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension anvio_variability.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Arff from the datatype registry for extension arff.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Paf from the datatype registry for extension paf.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Taf from the datatype registry for extension taf.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Gfa1 from the datatype registry for extension gfa1.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Gfa2 from the datatype registry for extension gfa2.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension asn1.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension asn1-binary.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Axt from the datatype registry for extension axt.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:FeatureLocationIndex from the datatype registry for extension fli.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bam from the datatype registry for extension bam.\n[2026-09-18 00:35:08,554: DEBUG/main] Loaded preferred visualization definition: bam -> igv\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bai.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BamInputSorted from the datatype registry for extension qname_input_sorted.bam.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BamQuerynameSorted from the datatype registry for extension qname_sorted.bam.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BamNative from the datatype registry for extension unsorted.bam.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ProBam from the datatype registry for extension probam.\n[2026-09-18 00:35:08,554: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CRAM from the datatype registry for extension cram.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Bed from the datatype registry for extension bed.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:BedGraph from the datatype registry for extension bedgraph.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:BedStrict from the datatype registry for extension bedstrict.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Bed6 from the datatype registry for extension bed6.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Bed12 from the datatype registry for extension bed12.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ProBed from the datatype registry for extension probed.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.chrominfo:ChromInfo from the datatype registry for extension len.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:DAA from the datatype registry for extension daa.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RMA6 from the datatype registry for extension rma6.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:DMND from the datatype registry for extension dmnd.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Parquet from the datatype registry for extension parquet.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension arrow.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Idat from the datatype registry for extension idat.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BigBed from the datatype registry for extension bigbed.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BigWig from the datatype registry for extension bigwig.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cxb.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ChromatinInteractions from the datatype registry for extension chrint.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension csv.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:GeoCSV from the datatype registry for extension geocsv.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension tsv.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:TSV from the datatype registry for extension intermine_tabular.\n[2026-09-18 00:35:08,555: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:CustomTrack from the datatype registry for extension customtrack.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieColorIndex from the datatype registry for extension bowtie_color_index.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.ngsindex:BowtieBaseIndex from the datatype registry for extension bowtie_base_index.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:csFasta from the datatype registry for extension csfasta.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension data.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gz.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension binary.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension las.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension laz.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension pnts.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension d3_hierarchy.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:CytoscapeJson from the datatype registry for extension cytoscapejson.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension freq.json.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:ImgtJson from the datatype registry for extension imgt.json.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:GeoJson from the datatype registry for extension geojson.\n[2026-09-18 00:35:08,556: DEBUG/main] Loaded preferred visualization definition: geojson -> openlayers\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:VitessceJson from the datatype registry for extension vitessce.json.\n[2026-09-18 00:35:08,556: DEBUG/main] Loaded preferred visualization definition: vitessce.json -> vitessce\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:AuspiceJson from the datatype registry for extension auspice.json.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:DataManagerJson from the datatype registry for extension data_manager_json.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:DotBracket from the datatype registry for extension dbn.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension fai.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension fasta.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fastg from the datatype registry for extension fastg.\n[2026-09-18 00:35:08,556: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fastq from the datatype registry for extension fastq.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqSanger from the datatype registry for extension fastqsanger.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqSolexa from the datatype registry for extension fastqsolexa.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqCSSanger from the datatype registry for extension fastqcssanger.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:FastqIllumina from the datatype registry for extension fastqillumina.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:SequenceSplitLocations from the datatype registry for extension fqtoc.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Eland from the datatype registry for extension eland.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:ElandMulti from the datatype registry for extension elandmulti.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.tracks:GeneTrack from the datatype registry for extension genetrack.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension a3m.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Gff from the datatype registry for extension gff.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Gff3 from the datatype registry for extension gff3.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Gif from the datatype registry for extension gif.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Gmaj from the datatype registry for extension gmaj.zip.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension graph_dot.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Gtf from the datatype registry for extension gtf.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension toolshed.gz.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hdf4.\n[2026-09-18 00:35:08,557: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5.\n[2026-09-18 00:35:08,558: DEBUG/main] Loaded preferred visualization definition: h5 -> h5web\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension scool.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Grib from the datatype registry for extension grib.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Loom from the datatype registry for extension loom.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Anndata from the datatype registry for extension h5ad.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension h5mu.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Visium from the datatype registry for extension visium.tar.gz.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mz5.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mzmlb.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5 from the datatype registry for extension mbi.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hyphy_results.json.\n[2026-09-18 00:35:08,558: DEBUG/main] Loaded preferred visualization definition: hyphy_results.json -> hyphyvision\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension hivtrace.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Hic from the datatype registry for extension hic.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Cool from the datatype registry for extension cool.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MCool from the datatype registry for extension mcool.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:H5MLM from the datatype registry for extension h5mlm.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:LudwigModel from the datatype registry for extension ludwig_model.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension html.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension ludwig_report.html.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Interval from the datatype registry for extension interval.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension jellyfish.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_ktab.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_hist.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension fastk_prof.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension fastk_ktab_tar.\n[2026-09-18 00:35:08,558: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Numpy from the datatype registry for extension npy.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.isa:IsaTab from the datatype registry for extension isa-tab.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.isa:IsaJson from the datatype registry for extension isa-json.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension picard_interval_list.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_interval.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gatk_report.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_dbsnp.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_tranche.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension gatk_recal.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnn.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cns.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension cnr.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hhr.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Jpg from the datatype registry for extension jpg.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tiff.\n[2026-09-18 00:35:08,640: DEBUG/main] Loaded preferred visualization definition: tiff -> tiffviewer\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf2.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tf8.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension btf.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension tif.\n[2026-09-18 00:35:08,640: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension svs.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension scn.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension bif.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:OMETiff from the datatype registry for extension ome.tiff.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Dicom from the datatype registry for extension dcm.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vms.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension vmu.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Hamamatsu from the datatype registry for extension ndpi.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Mirax from the datatype registry for extension mrxs.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Sakura from the datatype registry for extension svslide.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Bmp from the datatype registry for extension bmp.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Im from the datatype registry for extension im.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pcd from the datatype registry for extension pcd.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pcx from the datatype registry for extension pcx.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Ppm from the datatype registry for extension ppm.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Psd from the datatype registry for extension psd.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Xbm from the datatype registry for extension xbm.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Xpm from the datatype registry for extension xpm.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Rgb from the datatype registry for extension rgb.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pbm from the datatype registry for extension pbm.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pgm from the datatype registry for extension pgm.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nrrd.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nrrd from the datatype registry for extension nhdr.\n[2026-09-18 00:35:08,641: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:RNADotPlotMatrix from the datatype registry for extension rna_eps.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Artifact from the datatype registry for extension qza.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Visualization from the datatype registry for extension qzv.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.qiime2:QIIME2Metadata from the datatype registry for extension qiime2.tabular.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension zip.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedZipArchive from the datatype registry for extension ncbi_genome_dataset.zip.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedZarrZipArchive from the datatype registry for extension zarr.zip.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedOMEZarrZipArchive from the datatype registry for extension ome_zarr.zip.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SpatialData from the datatype registry for extension spatialdata.zip.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension tar.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension directory.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension bwa_index.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension bwa_mem2_index.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension egapx_local_cache.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension lexicmap_index.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Directory from the datatype registry for extension kmindex.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:ZarrDirectory from the datatype registry for extension zarr.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:OMEZarr from the datatype registry for extension ome_zarr.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension yaml.\n[2026-09-18 00:35:08,642: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mrm.\n[2026-09-18 00:35:08,643: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Dta from the datatype registry for extension dta.\n[2026-09-18 00:35:08,643: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Dta2d from the datatype registry for extension dta2d.\n[2026-09-18 00:35:08,643: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Edta from the datatype registry for extension edta.\n[2026-09-18 00:35:08,643: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension pepxml.\n[2026-09-18 00:35:08,643: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension raw_pepxml.\n[2026-09-18 00:35:08,643: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension peptideprophet_pepxml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXml from the datatype registry for extension interprophet_pepxml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ProtXML from the datatype registry for extension protxml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ParamXml from the datatype registry for extension paramxml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Kroenik from the datatype registry for extension kroenik.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepList from the datatype registry for extension peplist.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PSMS from the datatype registry for extension psms.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PepXmlReport from the datatype registry for extension pepxml.tsv.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ProtXmlReport from the datatype registry for extension protxml.tsv.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MascotDat from the datatype registry for extension mascotdat.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzIdentML from the datatype registry for extension mzid.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:IdXML from the datatype registry for extension idxml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:TandemXML from the datatype registry for extension tandem.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sirius.ms.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ThermoRAW from the datatype registry for extension thermo.raw.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BafTar from the datatype registry for extension brukerbaf.d.tar.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:YepTar from the datatype registry for extension agilentbrukeryep.d.tar.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:TdfTar from the datatype registry for extension brukertdf.d.tar.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MassHunterTar from the datatype registry for extension agilentmasshunter.d.tar.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MassLynxTar from the datatype registry for extension watersmasslynx.raw.tar.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:WiffTar from the datatype registry for extension wiff.tar.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Wiff2Tar from the datatype registry for extension wiff2.tar.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MascotXML from the datatype registry for extension mascotxml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzTab from the datatype registry for extension mztab.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzTab2 from the datatype registry for extension mztab2.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzML from the datatype registry for extension mzml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:NmrML from the datatype registry for extension nmrml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Meryldb from the datatype registry for extension meryldb.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bref3 from the datatype registry for extension bref3.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Mgf from the datatype registry for extension mgf.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Wiff from the datatype registry for extension wiff.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Wiff2 from the datatype registry for extension wiff2.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzXML from the datatype registry for extension mzxml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzData from the datatype registry for extension mzdata.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Ms2 from the datatype registry for extension ms2.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:MzQuantML from the datatype registry for extension mzq.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SQlite from the datatype registry for extension sqlite.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MzSQlite from the datatype registry for extension mz.sqlite.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OSW from the datatype registry for extension osw.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:PQP from the datatype registry for extension pqp.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:TraML from the datatype registry for extension traml.\n[2026-09-18 00:35:08,644: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:TrafoXML from the datatype registry for extension trafoxml.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:FeatureXML from the datatype registry for extension featurexml.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ConsensusXML from the datatype registry for extension consensusxml.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:UniProtXML from the datatype registry for extension uniprotxml.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:XquestXML from the datatype registry for extension xquest.xml.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:XquestSpecXML from the datatype registry for extension spec.xml.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:QCML from the datatype registry for extension qcml.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension mzqc.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Msp from the datatype registry for extension msp.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:SPLibNoIndex from the datatype registry for extension splib_noindex.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:SPLib from the datatype registry for extension splib.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BlibSQlite from the datatype registry for extension blib.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:DlibSQlite from the datatype registry for extension dlib.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ElibSQlite from the datatype registry for extension elib.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:XHunterAslFormat from the datatype registry for extension hlf.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:IdpDB from the datatype registry for extension idpdb.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:Sf3 from the datatype registry for extension sf3.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension cps.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:ConnectivityTable from the datatype registry for extension ct.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:PostgresqlArchive from the datatype registry for extension postgresql.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MongoDBArchive from the datatype registry for extension mongodb.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GeneNoteBook from the datatype registry for extension genenotebook.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SearchGuiArchive from the datatype registry for extension searchgui_archive.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5Archive from the datatype registry for extension fast5.tar.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveGz from the datatype registry for extension fast5.tar.gz.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveBz2 from the datatype registry for extension fast5.tar.bz2.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Fast5ArchiveXz from the datatype registry for extension fast5.tar.xz.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Pod5 from the datatype registry for extension pod5.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension peptideshaker_archive.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension percin.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension percout.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hardklor.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension kronik.\n[2026-09-18 00:35:08,645: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:ImzML from the datatype registry for extension imzml.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Analyze75 from the datatype registry for extension analyze75.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nifti1 from the datatype registry for extension nii1.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Nifti2 from the datatype registry for extension nii2.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Gifti from the datatype registry for extension gii.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tck from the datatype registry for extension tck.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Trk from the datatype registry for extension trk.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Mrc2014 from the datatype registry for extension mrc.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Star from the datatype registry for extension star.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.proteomics:PEFF from the datatype registry for extension peff.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension toml.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension colab.tar.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.flow:FCS from the datatype registry for extension fcs.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowtext.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowclr.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowmfi.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat1.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat2.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowstat3.\n[2026-09-18 00:35:08,646: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension flowscore.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowframe.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension fsom.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension flowset.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Tiff from the datatype registry for extension amnisflow.cif.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension metacyto_clr.txt.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.metacyto:mSummary from the datatype registry for extension metacyto_summary.txt.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.metacyto:mStats from the datatype registry for extension metacyto_stats.txt.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_compute_matrix_archive.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension deeptools_coverage_matrix.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:NetCDF from the datatype registry for extension netcdf.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Eps from the datatype registry for extension eps.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Rast from the datatype registry for extension rast.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Laj from the datatype registry for extension laj.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Lav from the datatype registry for extension lav.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Maf from the datatype registry for extension maf.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:MafCustomTrack from the datatype registry for extension mafcustomtrack.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:MatrixMarket from the datatype registry for extension mtx.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CMAP from the datatype registry for extension cmap.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ENCODEPeak from the datatype registry for extension encodepeak.\n[2026-09-18 00:35:08,647: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:FourDNPairs from the datatype registry for extension 4dn_pairs.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:FourDNPairsam from the datatype registry for extension 4dn_pairsam.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Pdf from the datatype registry for extension pdf.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Pileup from the datatype registry for extension pileup.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Psl from the datatype registry for extension psl.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Obo from the datatype registry for extension obo.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Owl from the datatype registry for extension owl.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.images:Png from the datatype registry for extension png.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore from the datatype registry for extension qual.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSolexa from the datatype registry for extension qualsolexa.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreIllumina from the datatype registry for extension qualillumina.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScoreSOLiD from the datatype registry for extension qualsolid.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.qualityscore:QualityScore454 from the datatype registry for extension qual454.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Roadmaps from the datatype registry for extension roadmaps.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Sam from the datatype registry for extension sam.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Scf from the datatype registry for extension scf.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Sequences from the datatype registry for extension sequences.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:SnpEffDb from the datatype registry for extension snpeffdb.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:SnpSiftDbNSFP from the datatype registry for extension snpsiftdbnsfp.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dbnsfp.tabular.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Sff from the datatype registry for extension sff.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Sra from the datatype registry for extension sra.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:SraManifest from the datatype registry for extension sra_manifest.tabular.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension svg.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Taxonomy from the datatype registry for extension taxonomy.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension tabular.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:TwoBit from the datatype registry for extension twobit.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:SQmass from the datatype registry for extension sqmass.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GeminiSQLite from the datatype registry for extension gemini.sqlite.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ChiraSQLite from the datatype registry for extension chira.sqlite.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CuffDiffSQlite from the datatype registry for extension cuffdiff.sqlite.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GAFASQLite from the datatype registry for extension gafa.sqlite.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:NcbiTaxonomySQlite from the datatype registry for extension ncbitaxonomy.sqlite.\n[2026-09-18 00:35:08,648: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension txt.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:LineCount from the datatype registry for extension linecount.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:MemePsp from the datatype registry for extension memepsp.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:MEMEXml from the datatype registry for extension memexml.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:CisML from the datatype registry for extension cisml.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Tei from the datatype registry for extension tei.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xml.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:GenericXml from the datatype registry for extension xsd.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Dzi from the datatype registry for extension dzi.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Vcf from the datatype registry for extension vcf.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Bcf from the datatype registry for extension bcf_bgzip.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:BcfUncompressed from the datatype registry for extension bcf_uncompressed.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.assembly:Velvet from the datatype registry for extension velvet.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:Wiggle from the datatype registry for extension wig.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension interval_index.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension odgi.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension vg.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.loci.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.dist.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.snarls.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.gamp.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.min.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.zipcodes.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension vg.gg.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gbz.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gbwt.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hal.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hal.pg.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension hal.hg.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension xg.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension gam.\n[2026-09-18 00:35:08,649: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf2.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension protobuf3.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension onnx.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tabix.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:IntervalTabix from the datatype registry for extension interval_tabix.gz.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:JuicerMediumTabix from the datatype registry for extension juicer_medium_tabix.gz.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:BedTabix from the datatype registry for extension bed_tabix.gz.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:GffTabix from the datatype registry for extension gff_tabix.gz.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension bgzip.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension gwas_bgzip.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:CompressedArchive from the datatype registry for extension gwas_tabix.gz.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:VcfGz from the datatype registry for extension vcf_bgzip.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bus.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension kallisto.idx.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Phyloxml from the datatype registry for extension phyloxml.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension newick.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Newick from the datatype registry for extension nhx.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Nexus from the datatype registry for extension nex.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:IQTree from the datatype registry for extension iqtree.\n[2026-09-18 00:35:08,650: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension beast.trees.\n[2026-09-18 00:35:08,651: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mldist.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Affybatch from the datatype registry for extension affybatch.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratgeno from the datatype registry for extension eigenstratgeno.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Eigenstratpca from the datatype registry for extension eigenstratpca.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Eset from the datatype registry for extension eset.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Fped from the datatype registry for extension fped.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Fphe from the datatype registry for extension fphe.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:GenomeGraphs from the datatype registry for extension gg.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:ldIndep from the datatype registry for extension ldindep.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:MAlist from the datatype registry for extension malist.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Lped from the datatype registry for extension lped.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Pbed from the datatype registry for extension pbed.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Pheno from the datatype registry for extension pheno.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Pphe from the datatype registry for extension pphe.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:RexpBase from the datatype registry for extension rexpbase.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Rgenetics from the datatype registry for extension rgenetics.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:Snptest from the datatype registry for extension snptest.\n[2026-09-18 00:35:08,652: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:SNPMatrix from the datatype registry for extension snpmatrix.\n[2026-09-18 00:35:08,653: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension xls.\n[2026-09-18 00:35:08,653: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Ipynb from the datatype registry for extension ipynb.\n[2026-09-18 00:35:08,653: DEBUG/main] Loaded preferred visualization definition: ipynb -> jupyterlite\n[2026-09-18 00:35:08,653: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension json.\n[2026-09-18 00:35:08,653: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension tool_markdown.\n[2026-09-18 00:35:08,653: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:ExpressionJson from the datatype registry for extension expression.json.\n[2026-09-18 00:35:08,653: DEBUG/main] Retrieved datatype module galaxy.datatypes.graph:Xgmml from the datatype registry for extension xgmml.\n[2026-09-18 00:35:08,653: DEBUG/main] Retrieved datatype module galaxy.datatypes.graph:Sif from the datatype registry for extension sif.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Triples from the datatype registry for extension triples.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:HDT from the datatype registry for extension hdt.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:NTriples from the datatype registry for extension nt.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:N3 from the datatype registry for extension n3.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Turtle from the datatype registry for extension ttl.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Rdf from the datatype registry for extension rdf.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Jsonld from the datatype registry for extension jsonld.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.triples:Sbol from the datatype registry for extension sbol.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ExcelXls from the datatype registry for extension excel.xls.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Xlsx from the datatype registry for extension xlsx.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Docx from the datatype registry for extension docx.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Pptx from the datatype registry for extension pptx.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension btwisted.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cai.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cat_db.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension charge.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension checktrans.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension chips.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codcmp.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension coderet.\n[2026-09-18 00:35:08,654: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension compseq.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgplot.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cpgreport.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cusp.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension cut.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dan.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension digest.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dreg.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension einverted.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension epestfind.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension equicktandem.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension est2genome.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension etandem.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension freak.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzznuc.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzzpro.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fuzztran.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gaf.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension garnier.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension geecee.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension helixturnhelix.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hmoment.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension isochore.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension match.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nametable.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension needle.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgreport.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension newcpgseek.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension noreturn.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension palindrome.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepcoil.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepinfo.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pepstats.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension polydot.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension preg.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prettyseq.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension primersearch.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showfeat.\n[2026-09-18 00:35:08,655: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension showorf.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension sixpack.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension strider.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension supermatcher.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension syco.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension textsearch.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension vectorstrip.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wobble.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension wordcount.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension dbmotif.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension diffseq.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension excel.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feattable.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension motif.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension regions.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension seqtable.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension simple.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension table.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension tagseq.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension acedb.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension clustal.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension codata.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension embl.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension fitch.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension gcg.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Genbank from the datatype registry for extension genbank.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hennig86.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ig.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifer.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension jackknifernon.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mega.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension meganon.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ncbi.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexus.\n[2026-09-18 00:35:08,656: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension nexusnon.\n[2026-09-18 00:35:08,657: DEBUG/main] Retrieved datatype module galaxy.datatypes.phylip:Phylip from the datatype registry for extension phylip.\n[2026-09-18 00:35:08,657: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension phylipnon.\n[2026-09-18 00:35:08,657: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pir.\n[2026-09-18 00:35:08,657: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension staden.\n[2026-09-18 00:35:08,657: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension swiss.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Msf from the datatype registry for extension msf.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx0.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx1.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx10.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx2.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension markx3.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension pair.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension score.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srs.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension srspair.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.annotation:SnapHmm from the datatype registry for extension snaphmm.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.annotation:Augustus from the datatype registry for extension augustus.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:ICM from the datatype registry for extension icm.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:InfernalCM from the datatype registry for extension cm.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Hmmer2 from the datatype registry for extension hmm2.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Hmmer3 from the datatype registry for extension hmm3.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:Stockholm_1_0 from the datatype registry for extension stockholm.\n[2026-09-18 00:35:08,658: DEBUG/main] Retrieved datatype module galaxy.datatypes.msa:MauveXmfa from the datatype registry for extension xmfa.\n[2026-09-18 00:35:08,659: DEBUG/main] Retrieved datatype module galaxy.datatypes.microarrays:Cel from the datatype registry for extension cel.\n[2026-09-18 00:35:08,659: DEBUG/main] Retrieved datatype module galaxy.datatypes.microarrays:Gpr from the datatype registry for extension gpr.\n[2026-09-18 00:35:08,659: DEBUG/main] Retrieved datatype module galaxy.datatypes.microarrays:Gal from the datatype registry for extension gal.\n[2026-09-18 00:35:08,659: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension rds.\n[2026-09-18 00:35:08,659: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension phyloseq.\n[2026-09-18 00:35:08,659: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.\n[2026-09-18 00:35:08,659: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.sce.\n[2026-09-18 00:35:08,659: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.raw.\n[2026-09-18 00:35:08,659: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.msnbase.raw.\n[2026-09-18 00:35:08,661: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.findchrompeaks.\n[2026-09-18 00:35:08,661: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.group.\n[2026-09-18 00:35:08,661: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.retcor.\n[2026-09-18 00:35:08,661: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.xcms.fillpeaks.\n[2026-09-18 00:35:08,661: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.positive.\n[2026-09-18 00:35:08,661: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.negative.\n[2026-09-18 00:35:08,661: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RData from the datatype registry for extension rdata.camera.quick.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.hdf5:HDF5SummarizedExperiment from the datatype registry for extension rdata.se.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rdock_as.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rrd.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Prm from the datatype registry for extension prm.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliCountGraph from the datatype registry for extension oxlicg.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliNodeGraph from the datatype registry for extension oxling.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliTagSet from the datatype registry for extension oxlits.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliStopTags from the datatype registry for extension oxlist.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliSubset from the datatype registry for extension oxliss.\n[2026-09-18 00:35:08,662: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:OxliGraphLabels from the datatype registry for extension oxligl.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:STL from the datatype registry for extension stl.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyAscii from the datatype registry for extension plyascii.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:PlyBinary from the datatype registry for extension plybinary.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkAscii from the datatype registry for extension vtkascii.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkBinary from the datatype registry for extension vtkbinary.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtpAscii from the datatype registry for extension vtpascii.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtpBinary from the datatype registry for extension vtpbinary.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Biom1 from the datatype registry for extension biom1.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Biom2 from the datatype registry for extension biom2.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:MashSketch from the datatype registry for extension msh.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:SourmashSignature from the datatype registry for extension sourmash.sig.\n[2026-09-18 00:35:08,663: DEBUG/main] Retrieved datatype module galaxy.datatypes.interval:ScIdx from the datatype registry for extension scidx.\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:SMILES from the datatype registry for extension smi.\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:SDF from the datatype registry for extension sdf.\n[2026-09-18 00:35:08,664: DEBUG/main] Loaded preferred visualization definition: sdf -> molstar\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:InChI from the datatype registry for extension inchi.\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:MOL from the datatype registry for extension mol.\n[2026-09-18 00:35:08,664: DEBUG/main] Loaded preferred visualization definition: mol -> molstar\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:MOL2 from the datatype registry for extension mol2.\n[2026-09-18 00:35:08,664: DEBUG/main] Loaded preferred visualization definition: mol2 -> molstar\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:CML from the datatype registry for extension cml.\n[2026-09-18 00:35:08,664: DEBUG/main] Loaded preferred visualization definition: cml -> molstar\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:FPS from the datatype registry for extension fps.\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:OBFS from the datatype registry for extension obfs.\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:DRF from the datatype registry for extension drf.\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PHAR from the datatype registry for extension phar.\n[2026-09-18 00:35:08,664: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PDB from the datatype registry for extension pdb.\n[2026-09-18 00:35:08,665: DEBUG/main] Loaded preferred visualization definition: pdb -> molstar\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PDBQT from the datatype registry for extension pdbqt.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:PQR from the datatype registry for extension pqr.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:Cell from the datatype registry for extension cell.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:CIF from the datatype registry for extension cif.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:XYZ from the datatype registry for extension xyz.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:ExtendedXYZ from the datatype registry for extension extxyz.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:Magres from the datatype registry for extension magres.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Trr from the datatype registry for extension trr.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Dcd from the datatype registry for extension dcd.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension top.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension prmtop.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension itp.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mdp.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension ndx.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension xvg.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Xtc from the datatype registry for extension xtc.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Cpt from the datatype registry for extension cpt.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Edr from the datatype registry for extension edr.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tpr.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:GRO from the datatype registry for extension gro.\n[2026-09-18 00:35:08,665: DEBUG/main] Loaded preferred visualization definition: gro -> molstar\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension inpcrd.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Vel from the datatype registry for extension vel.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:grd from the datatype registry for extension grd.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.molecules:grdtgz from the datatype registry for extension grd.tgz.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.otu.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Otu from the datatype registry for extension mothur.list.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.sabund.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Sabund from the datatype registry for extension mothur.rabund.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.shared.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:GroupAbund from the datatype registry for extension mothur.relabund.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Names from the datatype registry for extension mothur.names.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.design.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Summary from the datatype registry for extension mothur.summary.\n[2026-09-18 00:35:08,665: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Group from the datatype registry for extension mothur.groups.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Oligos from the datatype registry for extension mothur.oligos.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.sequence:Fasta from the datatype registry for extension mothur.align.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.accnos.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AccNos from the datatype registry for extension mothur.otulabels.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension mothur.otu.corr.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SecondaryStructureMap from the datatype registry for extension mothur.map.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AlignCheck from the datatype registry for extension mothur.align.check.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:AlignReport from the datatype registry for extension mothur.align.report.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:LaneMask from the datatype registry for extension mothur.filter.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:DistanceMatrix from the datatype registry for extension mothur.dist.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension mothur.tre.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:PairwiseDistanceMatrix from the datatype registry for extension mothur.pair.dist.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SquareDistanceMatrix from the datatype registry for extension mothur.square.dist.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:LowerTriangleDistanceMatrix from the datatype registry for extension mothur.lower.dist.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.ref.taxonomy.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.seq.taxonomy.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:RefTaxonomy from the datatype registry for extension mothur.rdp.taxonomy.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:ConsensusTaxonomy from the datatype registry for extension mothur.cons.taxonomy.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:TaxonomySummary from the datatype registry for extension mothur.tax.summary.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Frequency from the datatype registry for extension mothur.freq.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.quan.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.quan.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.masked.quan.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Quantile from the datatype registry for extension mothur.filtered.masked.quan.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:Axes from the datatype registry for extension mothur.axes.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:SffFlow from the datatype registry for extension mothur.sff.flow.\n[2026-09-18 00:35:08,666: DEBUG/main] Retrieved datatype module galaxy.datatypes.mothur:CountTable from the datatype registry for extension mothur.count_table.\n[2026-09-18 00:35:08,667: DEBUG/main] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDB from the datatype registry for extension neostore.\n[2026-09-18 00:35:08,667: DEBUG/main] Retrieved datatype module galaxy.datatypes.neo4j:Neo4jDBzip from the datatype registry for extension neostore.zip.\n[2026-09-18 00:35:08,667: DEBUG/main] Retrieved datatype module galaxy.datatypes.tracks:UCSCTrackHub from the datatype registry for extension trackhub.\n[2026-09-18 00:35:08,667: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastXml from the datatype registry for extension blastxml.\n[2026-09-18 00:35:08,667: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb from the datatype registry for extension blastdbn.\n[2026-09-18 00:35:08,667: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb from the datatype registry for extension blastdbp.\n[2026-09-18 00:35:08,667: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb from the datatype registry for extension blastdbd.\n[2026-09-18 00:35:08,667: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:LastDb from the datatype registry for extension lastdb.\n[2026-09-18 00:35:08,667: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastNucDb5 from the datatype registry for extension blastdbn5.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastProtDb5 from the datatype registry for extension blastdbp5.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.blast:BlastDomainDb5 from the datatype registry for extension blastdbd5.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension maskinfo-asn1.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:GenericAsn1Binary from the datatype registry for extension maskinfo-asn1-binary.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:GenericAsn1 from the datatype registry for extension pssm-asn1.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.plant_tribes:PlantTribesKsComponents from the datatype registry for extension ptkscmp.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.plant_tribes:Smat from the datatype registry for extension smat.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:GenotypeMatrix from the datatype registry for extension alohomora_gts.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_map.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_maf.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension alohomora_ped.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension linkage_pedin.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:DataIn from the datatype registry for extension linkage_datain.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:MarkerMap from the datatype registry for extension linkage_map.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_ihaplo.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension allegro_descent.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:AllegroLOD from the datatype registry for extension allegro_fparam.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.genetics:IdeasPre from the datatype registry for extension ideaspre.\n[2026-09-18 00:35:08,668: DEBUG/main] Retrieved datatype module galaxy.datatypes.xml:Sbml from the datatype registry for extension sbml.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.spaln:SpalnNuclDb from the datatype registry for extension spalndbnp.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.spaln:SpalnProtDb from the datatype registry for extension spalndba.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_dada.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_errorrates.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension dada2_mergepairs.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_sequencetable.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension dada2_uniques.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:RDS from the datatype registry for extension ampvis2.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension ckpt.\n[2026-09-18 00:35:08,669: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension tgz.\n[2026-09-18 00:35:08,670: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Wav from the datatype registry for extension wav.\n[2026-09-18 00:35:08,670: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mp3 from the datatype registry for extension mp3.\n[2026-09-18 00:35:08,670: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Ogg from the datatype registry for extension ogg.\n[2026-09-18 00:35:08,670: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Wma from the datatype registry for extension wma.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mkv from the datatype registry for extension mkv.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mp4 from the datatype registry for extension mp4.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:M4a from the datatype registry for extension m4a.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Flv from the datatype registry for extension flv.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Flac from the datatype registry for extension flac.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Webm from the datatype registry for extension webm.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mpg from the datatype registry for extension mpg.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Mov from the datatype registry for extension mov.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Avi from the datatype registry for extension avi.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.media:Wmv from the datatype registry for extension wmv.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.speech:TextGrid from the datatype registry for extension textgrid.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.speech:BPF from the datatype registry for extension par.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension ffindex.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Data from the datatype registry for extension ffdata.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Pretext from the datatype registry for extension pretext.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Html from the datatype registry for extension immuneml_receptors.html.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:HexrdMaterials from the datatype registry for extension hexrd.materials.h5.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension npz.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:HexrdImagesNpz from the datatype registry for extension hexrd.images.npz.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:HexrdEtaOmeNpz from the datatype registry for extension hexrd.eta_ome.npz.\n[2026-09-18 00:35:08,671: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Npz from the datatype registry for extension hexrd.scored_orientations.npz.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:Tabular from the datatype registry for extension hexrd.accepted_orientations.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Yaml from the datatype registry for extension hexrd.yml.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTess from the datatype registry for extension neper.tess.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperTesr from the datatype registry for extension neper.tesr.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPoints from the datatype registry for extension neper.points.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperPointsTabular from the datatype registry for extension neper.points.tsv.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:NeperMultiScaleCell from the datatype registry for extension neper.mscell.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshMsh from the datatype registry for extension gmsh.msh.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GmshGeo from the datatype registry for extension gmsh.geo.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:ZsetGeof from the datatype registry for extension zset.geof.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:VtkXml from the datatype registry for extension vtkxml.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:GocadSGrid from the datatype registry for extension gocad.sg.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:FeflowFem from the datatype registry for extension feflow.fem.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.constructive_solid_geometry:AsciiRaster from the datatype registry for extension raster.asc.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension stl.\n[2026-09-18 00:35:08,672: DEBUG/main] Overriding conflicting datatype with extension 'stl', using datatype from /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/lib/galaxy/config/sample/datatypes_conf.xml.sample.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Text from the datatype registry for extension pov.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:PithyaResult from the datatype registry for extension pithya.result.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:PithyaProperty from the datatype registry for extension pithya.property.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:PithyaModel from the datatype registry for extension pithya.model.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:BCSLts from the datatype registry for extension bcsl.ts.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:BCSLmodel from the datatype registry for extension bcsl.model.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:StormSample from the datatype registry for extension storm.sample.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:StormCheck from the datatype registry for extension storm.check.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:CTLresult from the datatype registry for extension ctl.result.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Castep from the datatype registry for extension castep.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Param from the datatype registry for extension param.\n[2026-09-18 00:35:08,672: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:FormattedDensity from the datatype registry for extension den_fmt.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.larch:AthenaProject from the datatype registry for extension prj.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.larch:FEFFInput from the datatype registry for extension inp.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension sp.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension gds.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.tabular:CSV from the datatype registry for extension feff.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension feffit.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bil.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.data:Text from the datatype registry for extension hdr.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.gis:Shapefile from the datatype registry for extension shp.\n[2026-09-18 00:35:08,673: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:FITS from the datatype registry for extension fits.\n[2026-09-18 00:35:08,673: DEBUG/main] Loaded preferred visualization definition: fits -> aladin\n[2026-09-18 00:35:08,674: DEBUG/main] Retrieved datatype module galaxy.datatypes.chain:Chain from the datatype registry for extension chain.\n[2026-09-18 00:35:08,674: DEBUG/main] Retrieved datatype module galaxy.datatypes.chain:Net from the datatype registry for extension ucsc.net.\n[2026-09-18 00:35:08,674: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension bcsp.\n[2026-09-18 00:35:08,674: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension rd.\n[2026-09-18 00:35:08,674: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Safetensors from the datatype registry for extension safetensors.\n[2026-09-18 00:35:08,674: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension mlmodel.\n[2026-09-18 00:35:08,674: DEBUG/main] Retrieved datatype module galaxy.datatypes.binary:Binary from the datatype registry for extension deacon.idx.\n[2026-09-18 00:35:08,674: DEBUG/main] Retrieved datatype module galaxy.datatypes.text:Json from the datatype registry for extension rmsx.json.\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded preferred visualization definition: rmsx.json -> rmsxflipbook\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:PlantTribesKsComponents'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.plant_tribes:Smat'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Sabund'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Otu'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:GroupAbund'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SecondaryStructureMap'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LowerTriangleDistanceMatrix'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:SquareDistanceMatrix'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:PairwiseDistanceMatrix'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Oligos'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Quantile'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Frequency'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:LaneMask'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:RefTaxonomy'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.mothur:Axes'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyAscii'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:PlyBinary'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtpAscii'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtpBinary'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkXml'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkAscii'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:VtkBinary'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTess'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:NeperTesr'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GmshMsh'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:GocadSGrid'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:FeflowFem'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.constructive_solid_geometry:AsciiRaster'\n[2026-09-18 00:35:08,674: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.goldenpath:GoldenPath'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:ScIdx'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Vcf'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:JP2'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:TwoBit'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:GeminiSQLite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQmass'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MzSQlite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OSW'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:PQP'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:IdpDB'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:ElibSQlite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:DlibSQlite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BlibSQlite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:ChiraSQLite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CuffDiffSQlite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:GAFASQLite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:NcbiTaxonomySQlite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:SQlite'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5MLM'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Hic'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cool'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MCool'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Loom'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Anndata'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Biom2'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdMaterials'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:H5'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Grib'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdImagesNpz'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:HexrdEtaOmeNpz'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Npz'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bam'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamQuerynameSorted'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BamNative'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CRAM'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sff'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Sra'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:NetCDF'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:DAA'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:RMA6'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:DMND'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Parquet'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:BafTar'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:TdfTar'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassHunterTar'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:MassLynxTar'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:YepTar'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:WiffTar'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveGz'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveXz'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5ArchiveBz2'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Fast5Archive'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pod5'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Meryldb'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Bref3'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:PostgresqlArchive'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:ICM'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Idat'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Trr'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Dcd'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xtc'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Cpt'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Edr'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Vel'\n[2026-09-18 00:35:08,675: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Xlsx'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Docx'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pptx'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Numpy'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Metadata'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Artifact'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qiime2:QIIME2Visualization'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:SpatialData'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedOMEZarrZipArchive'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZarrZipArchive'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:CompressedZipArchive'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:Pretext'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.annotation:Augustus'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Owl'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.chain:Chain'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.chain:Net'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Rdf'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.blast:BlastXml'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Gifti'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Phyloxml'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Dzi'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:Sbml'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Dta2d'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Edta'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ConsensusXML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:IdXML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:FeatureXML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MascotXML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Mgf'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Ms2'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Msp'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzData'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzIdentML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzQuantML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzTab2'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ParamXml'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:MzXML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:NmrML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Kroenik'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepList'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PSMS'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PepXml'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ProtXML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:SPLib'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TandemXML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:ThermoRAW'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TraML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:TrafoXML'\n[2026-09-18 00:35:08,676: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:UniProtXML'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestXML'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:XquestSpecXML'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:QCML'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:Wiff'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.proteomics:PEFF'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CML'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Sbol'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.xml:GenericXml'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:HDT'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Turtle'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:NTriples'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.triples:Jsonld'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Maf'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Lav'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:MemePsp'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastg'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:csFasta'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScoreSOLiD'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.qualityscore:QualityScore454'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:SDF'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PDB'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Cell'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:CIF'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:ExtendedXYZ'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:XYZ'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:Magres'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:MOL2'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:InChI'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:FPS'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:PQR'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.molecules:GRO'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.phylip:Phylip'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fasta'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqCSSanger'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:FastqSanger'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Fastq'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Wiggle'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Html'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pdf'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Axt'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:Genbank'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Bed'\n[2026-09-18 00:35:08,677: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:CustomTrack'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gtf'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Gff3'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Pileup'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Psl'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Paf'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Taf'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.interval:Interval'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:FourDNPairs'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:FourDNPairsam'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:Sam'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.data:Newick'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.data:Nexus'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:IQTree'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Obo'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Arff'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Ipynb'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Biom1'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:ImgtJson'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:CytoscapeJson'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:GeoJson'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:VitessceJson'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaResult'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLts'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Json'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:GenotypeMatrix'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:DataIn'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:MarkerMap'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.genetics:AllegroLOD'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:RNADotPlotMatrix'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.sequence:DotBracket'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CMAP'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:ConnectivityTable'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:GeoCSV'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:CSV'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mSummary'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.metacyto:mStats'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:TSV'\n[2026-09-18 00:35:08,678: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.tabular:MatrixMarket'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer2'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:Hmmer3'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:Stockholm_1_0'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:MauveXmfa'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.msa:InfernalCM'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.annotation:SnapHmm'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Cel'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gpr'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.microarrays:Gal'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:RData'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:RDS'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Mrc2014'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Jpg'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Png'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:OMETiff'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Tiff'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Dicom'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Bmp'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Gif'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Im'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcd'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pcx'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Ppm'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Psd'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Xbm'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Rgb'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pbm'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Pgm'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Xpm'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Eps'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Rast'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Tck'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Trk'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti1'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Nifti2'\n[2026-09-18 00:35:08,679: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.images:Star'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Wav'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp3'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mp4'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:M4a'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Flv'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Ogg'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mpg'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mov'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Avi'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Wmv'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Wma'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Webm'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.media:Mkv'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.speech:TextGrid'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.speech:BPF'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.larch:FEFFInput'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.larch:AthenaProject'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Castep'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:CTLresult'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:FormattedDensity'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Param'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:Yaml'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliCountGraph'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliNodeGraph'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliTagSet'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliStopTags'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliSubset'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:OxliGraphLabels'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.binary:FITS'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.neo4j:Neo4jDBzip'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaProperty'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:PithyaModel'\n[2026-09-18 00:35:08,680: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:BCSLmodel'\n[2026-09-18 00:35:08,681: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:StormSample'\n[2026-09-18 00:35:08,681: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:StormCheck'\n[2026-09-18 00:35:08,681: DEBUG/main] Loaded sniffer for datatype 'galaxy.datatypes.text:SourmashSignature'\n[2026-09-18 00:35:08,682: DEBUG/main] Build site file [tool-data/shared/ucsc/ucsc_build_sites.txt] not found using sample [tool-data/shared/ucsc/ucsc_build_sites.txt.sample].\n[2026-09-18 00:35:08,682: DEBUG/main] Loaded build site 'ucsc': tool-data/shared/ucsc/ucsc_build_sites.txt.sample with display sites: ['main', 'test', 'archaea', 'ucla']\n[2026-09-18 00:35:08,682: DEBUG/main] Loaded build site 'gbrowse': tool-data/shared/gbrowse/gbrowse_build_sites.txt with display sites: ['modencode', 'sgd_yeast', 'tair', 'wormbase', 'wormbase_ws120', 'wormbase_ws140', 'wormbase_ws170', 'wormbase_ws180', 'wormbase_ws190', 'wormbase_ws200', 'wormbase_ws204', 'wormbase_ws210', 'wormbase_ws220', 'wormbase_ws225']\n[2026-09-18 00:35:08,682: DEBUG/main] Loaded build site 'ensembl': tool-data/shared/ensembl/ensembl_sites.txt\n[2026-09-18 00:35:08,682: DEBUG/main] Loaded build site 'ensembl_data_url': tool-data/shared/ensembl/ensembl_sites_data_URL.txt\n[2026-09-18 00:35:08,682: DEBUG/main] Build site file [tool-data/shared/igv/igv_build_sites.txt] not found using sample [tool-data/shared/igv/igv_build_sites.txt.sample].\n[2026-09-18 00:35:08,682: DEBUG/main] Loaded build site 'igv': tool-data/shared/igv/igv_build_sites.txt.sample\n[2026-09-18 00:35:08,682: DEBUG/main] Build site file [tool-data/shared/rviewer/rviewer_build_sites.txt] not found using sample [tool-data/shared/rviewer/rviewer_build_sites.txt.sample].\n[2026-09-18 00:35:08,682: DEBUG/main] Loaded build site 'rviewer': tool-data/shared/rviewer/rviewer_build_sites.txt.sample\n[2026-09-18 00:35:08,686: DEBUG/main] Loaded 0 lines from '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/galaxy-dev/tool-data/shed/salmon_indexes_versioned.loc' for 'salmon_indexes_versioned'\n[2026-09-18 00:35:08,686: DEBUG/main] Loaded tool data table 'salmon_indexes_versioned' from file '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/shed_tool_data_table_conf.xml'\n[2026-09-18 00:35:08,686: DEBUG/main] Loading references to tool sheds from /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/tool_sheds_conf.xml\n[2026-09-18 00:35:08,686: DEBUG/main] Loaded reference to tool shed: toolshed.g2.bx.psu.edu\nuvicorn.access INFO 2026-09-18 00:35:08,687 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50718 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:08,783: DEBUG/main] No parameter model for tool '__DATA_FETCH__': Cannot generate a tool parameter model for upload_dataset inputs\n[2026-09-18 00:35:08,806: DEBUG/main] (1) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1\n[2026-09-18 00:35:08,855: DEBUG/main] Job wrapper for Job [1] prepared (16.674 ms)\n[2026-09-18 00:35:08,856: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (72.376 ms)\n[2026-09-18 00:35:08,868: INFO/main] Task galaxy.setup_fetch_data[c94d8bfa-5320-4d63-b73f-08a2fec1c7ae] succeeded in 0.9668463747948408s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\n[2026-09-18 00:35:08,915: INFO/main] Task galaxy.fetch_data[df70d2f0-9e16-437a-80ea-b43bde03742f] received\n[2026-09-18 00:35:08,915: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'df70d2f0-9e16-437a-80ea-b43bde03742f', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'df70d2f0-9e16-437a-80ea-b43bde03742f', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c94d8bfa-5320-4d63-b73f-08a2fec1c7ae', 'parent_id': 'c94d8bfa-5320-4d63-b73f-08a2fec1c7ae', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 1}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'df70d2f0-9e16-437a-80ea-b43bde03742f', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:08,948 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50720 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:09,211 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50722 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:09,475 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50726 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:09,745 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50728 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:10,016 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50730 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:10,298 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50732 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:10,567 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50734 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:10,836 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50736 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nOption master_api_key has been deprecated in favor of bootstrap_admin_api_key\nOption master_api_key has been deprecated in favor of bootstrap_admin_api_key\nTrying to resolve path for the 'email_ban_file' option but it's empty/None\nTrying to resolve path for the 'data_manager_config_file' option but it's empty/None\nTrying to resolve path for the 'email_ban_file' option but it's empty/None\nTrying to resolve path for the 'data_manager_config_file' option but it's empty/None\nuvicorn.access INFO 2026-09-18 00:35:11,101 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50738 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:11,362 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50740 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:11,631 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50742 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:11,893 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50744 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:12,162 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50746 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:12,433 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50748 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:12,702 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50750 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:12,971 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50752 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:13,243 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50754 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:13,519 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50756 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:13,559: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (4643.139 ms)\n[2026-09-18 00:35:13,565: INFO/main] Task galaxy.fetch_data[df70d2f0-9e16-437a-80ea-b43bde03742f] succeeded in 4.649844124913216s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1'\nuvicorn.access INFO 2026-09-18 00:35:13,791 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50758 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:13,972: INFO/main] Task galaxy.set_job_metadata[f2b99e19-9f3c-464b-b7ca-15fd444ec4b5] received\n[2026-09-18 00:35:13,973: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'f2b99e19-9f3c-464b-b7ca-15fd444ec4b5', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'f2b99e19-9f3c-464b-b7ca-15fd444ec4b5', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c94d8bfa-5320-4d63-b73f-08a2fec1c7ae', 'parent_id': 'df70d2f0-9e16-437a-80ea-b43bde03742f', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 1}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'f2b99e19-9f3c-464b-b7ca-15fd444ec4b5', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '61685b8f-6fad-4ade-b187-c10b3c685e45'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:14,029: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (55.053 ms)\n[2026-09-18 00:35:14,033: INFO/main] Task galaxy.set_job_metadata[f2b99e19-9f3c-464b-b7ca-15fd444ec4b5] succeeded in 0.05999808292835951s: None\nuvicorn.access INFO 2026-09-18 00:35:14,061 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50760 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:14,338 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50762 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:14,615 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50764 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:14,888 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50766 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:14,991: INFO/main] Task galaxy.finish_job[d52ec8ff-80e7-4561-badb-7d40574e9827] received\n[2026-09-18 00:35:14,991: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', 'd52ec8ff-80e7-4561-badb-7d40574e9827', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': 'd52ec8ff-80e7-4561-badb-7d40574e9827', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c94d8bfa-5320-4d63-b73f-08a2fec1c7ae', 'parent_id': 'f2b99e19-9f3c-464b-b7ca-15fd444ec4b5', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 1, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request... kwargs:{})\n[2026-09-18 00:35:15,006: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1/outputs/dataset_10154cd9-fadd-4b3c-8eda-c980273d7660.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/1/0/1/dataset_10154cd9-fadd-4b3c-8eda-c980273d7660.dat\n[2026-09-18 00:35:15,009: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'SRR5085167_forward.fastqsanger.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1/working/gxupload_0', 'object_id': 1}]}]}]\n[2026-09-18 00:35:15,037: INFO/main] Collecting metrics for Job 1 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/1\n[2026-09-18 00:35:15,041: DEBUG/main] job_wrapper.finish for job 1 executed (43.478 ms)\n[2026-09-18 00:35:15,041: INFO/main] Successfully executed Celery task finish_job finish_job (49.113 ms)\n[2026-09-18 00:35:15,043: INFO/main] Task galaxy.finish_job[d52ec8ff-80e7-4561-badb-7d40574e9827] succeeded in 0.051557499915361404s: None\nuvicorn.access INFO 2026-09-18 00:35:15,158 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50768 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:15,167 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.084 ms)\nuvicorn.access INFO 2026-09-18 00:35:15,196 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50770 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:15,205 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50772 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:15,476 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50774 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:15,756 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50776 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:16,012: INFO/main] Task galaxy.compute_dataset_hash[8ee2f9b1-fbbe-44f5-9b58-0f434e41a4b4] received\n[2026-09-18 00:35:16,012: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', '8ee2f9b1-fbbe-44f5-9b58-0f434e41a4b4', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': '8ee2f9b1-fbbe-44f5-9b58-0f434e41a4b4', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c94d8bfa-5320-4d63-b73f-08a2fec1c7ae', 'parent_id': 'd52ec8ff-80e7-4561-badb-7d40574e9827', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=1, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '8ee2f9b1-fbbe-44f5-9b58-0f434e41a4b4', 'reply_to': 'a0fc44b4-38dd-35c5-9a57-80ac039ff6fa', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '6b994743-9eb7-4865-8246-d308a81d76f7'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:16,019: INFO/main] Task galaxy.setup_fetch_data[c637b3eb-8bc4-4008-ada6-7e6e34d6218b] received\n[2026-09-18 00:35:16,020: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'c637b3eb-8bc4-4008-ada6-7e6e34d6218b', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'c637b3eb-8bc4-4008-ada6-7e6e34d6218b', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c637b3eb-8bc4-4008-ada6-7e6e34d6218b', 'parent_id': None, 'argsrepr': '(2,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:16,029: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (15.971 ms)\n[2026-09-18 00:35:16,036: INFO/main] Task galaxy.compute_dataset_hash[8ee2f9b1-fbbe-44f5-9b58-0f434e41a4b4] succeeded in 0.022951625287532806s: None\nuvicorn.access INFO 2026-09-18 00:35:16,037 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50778 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:16,039: DEBUG/main] (2) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2\n[2026-09-18 00:35:16,075: DEBUG/main] Job wrapper for Job [2] prepared (9.479 ms)\n[2026-09-18 00:35:16,075: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (54.472 ms)\n[2026-09-18 00:35:16,089: INFO/main] Task galaxy.setup_fetch_data[c637b3eb-8bc4-4008-ada6-7e6e34d6218b] succeeded in 0.06867495831102133s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:16,308 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50780 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:16,582 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50783 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:16,858 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50785 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:17,042: INFO/main] Task galaxy.fetch_data[80761a11-9bdd-4771-9ad8-9c8012b7ce38] received\n[2026-09-18 00:35:17,042: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '80761a11-9bdd-4771-9ad8-9c8012b7ce38', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '80761a11-9bdd-4771-9ad8-9c8012b7ce38', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c637b3eb-8bc4-4008-ada6-7e6e34d6218b', 'parent_id': 'c637b3eb-8bc4-4008-ada6-7e6e34d6218b', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 2}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '80761a11-9bdd-4771-9ad8-9c8012b7ce38', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\n[2026-09-18 00:35:17,120: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (77.133 ms)\nuvicorn.access INFO 2026-09-18 00:35:17,122 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50787 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:17,125: INFO/main] Task galaxy.fetch_data[80761a11-9bdd-4771-9ad8-9c8012b7ce38] succeeded in 0.08178920857608318s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2'\nuvicorn.access INFO 2026-09-18 00:35:17,397 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50789 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:17,676 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50791 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:17,948 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50793 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:18,060: INFO/main] Task galaxy.set_job_metadata[929e5763-03c2-42b1-8893-9a1bf40dfe66] received\n[2026-09-18 00:35:18,060: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '929e5763-03c2-42b1-8893-9a1bf40dfe66', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '929e5763-03c2-42b1-8893-9a1bf40dfe66', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c637b3eb-8bc4-4008-ada6-7e6e34d6218b', 'parent_id': '80761a11-9bdd-4771-9ad8-9c8012b7ce38', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 2}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '929e5763-03c2-42b1-8893-9a1bf40dfe66', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '3446ffbd-c600-4c36-9d45-133d64deaa0d'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:18,183: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (122.172 ms)\n[2026-09-18 00:35:18,187: INFO/main] Task galaxy.set_job_metadata[929e5763-03c2-42b1-8893-9a1bf40dfe66] succeeded in 0.12626900058239698s: None\nuvicorn.access INFO 2026-09-18 00:35:18,218 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50795 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:18,496 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50797 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:18,775 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50799 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:19,054 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50801 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:19,078: INFO/main] Task galaxy.finish_job[c49b3405-16e2-4faa-945a-ba3af2d32497] received\n[2026-09-18 00:35:19,078: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', 'c49b3405-16e2-4faa-945a-ba3af2d32497', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': 'c49b3405-16e2-4faa-945a-ba3af2d32497', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c637b3eb-8bc4-4008-ada6-7e6e34d6218b', 'parent_id': '929e5763-03c2-42b1-8893-9a1bf40dfe66', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 2, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:19,328 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50803 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:19,371: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2/outputs/dataset_e0200b37-84c3-4836-a919-72b9416f9613.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/e/0/2/dataset_e0200b37-84c3-4836-a919-72b9416f9613.dat\n[2026-09-18 00:35:19,372: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'SRR5085167_reverse.fastqsanger.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2/working/gxupload_0', 'object_id': 2}]}]}]\n[2026-09-18 00:35:19,384: INFO/main] Collecting metrics for Job 2 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/2\n[2026-09-18 00:35:19,386: DEBUG/main] job_wrapper.finish for job 2 executed (18.437 ms)\n[2026-09-18 00:35:19,386: INFO/main] Successfully executed Celery task finish_job finish_job (307.505 ms)\n[2026-09-18 00:35:19,388: INFO/main] Task galaxy.finish_job[c49b3405-16e2-4faa-945a-ba3af2d32497] succeeded in 0.3095661662518978s: None\nuvicorn.access INFO 2026-09-18 00:35:19,604 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50805 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:19,614 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.061 ms)\nuvicorn.access INFO 2026-09-18 00:35:19,641 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50807 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:19,650 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50809 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:19,922 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50811 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:20,200 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50813 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:20,377: INFO/main] Task galaxy.compute_dataset_hash[e0373f67-4131-4fc4-8515-0a5307dbe4d1] received\n[2026-09-18 00:35:20,378: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', 'e0373f67-4131-4fc4-8515-0a5307dbe4d1', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': 'e0373f67-4131-4fc4-8515-0a5307dbe4d1', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'c637b3eb-8bc4-4008-ada6-7e6e34d6218b', 'parent_id': 'c49b3405-16e2-4faa-945a-ba3af2d32497', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=2, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'e0373f67-4131-4fc4-8515-0a5307dbe4d1', 'reply_to': 'a0fc44b4-38dd-35c5-9a57-80ac039ff6fa', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'ede19784-bcc9-40fb-883a-48f59ecad390'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:20,382: INFO/main] Task galaxy.setup_fetch_data[b1ba9027-f25d-4eb8-896a-927981bbae70] received\n[2026-09-18 00:35:20,383: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'b1ba9027-f25d-4eb8-896a-927981bbae70', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'b1ba9027-f25d-4eb8-896a-927981bbae70', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'b1ba9027-f25d-4eb8-896a-927981bbae70', 'parent_id': None, 'argsrepr': '(3,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:20,389: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (10.181 ms)\n[2026-09-18 00:35:20,394: INFO/main] Task galaxy.compute_dataset_hash[e0373f67-4131-4fc4-8515-0a5307dbe4d1] succeeded in 0.015831167809665203s: None\n[2026-09-18 00:35:20,399: DEBUG/main] (3) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3\n[2026-09-18 00:35:20,424: DEBUG/main] Job wrapper for Job [3] prepared (10.284 ms)\n[2026-09-18 00:35:20,424: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (40.559 ms)\n[2026-09-18 00:35:20,427: INFO/main] Task galaxy.setup_fetch_data[b1ba9027-f25d-4eb8-896a-927981bbae70] succeeded in 0.04450270812958479s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:20,465 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50815 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:20,744 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50817 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:21,019 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50819 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:21,292 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50821 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:21,391: INFO/main] Task galaxy.fetch_data[fcd663ff-6225-4900-84af-e6e822a5df0b] received\n[2026-09-18 00:35:21,391: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'fcd663ff-6225-4900-84af-e6e822a5df0b', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'fcd663ff-6225-4900-84af-e6e822a5df0b', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'b1ba9027-f25d-4eb8-896a-927981bbae70', 'parent_id': 'b1ba9027-f25d-4eb8-896a-927981bbae70', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 3}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'fcd663ff-6225-4900-84af-e6e822a5df0b', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:21,554 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50823 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:21,822 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50825 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:22,095 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50827 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:22,357 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50829 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:22,627 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50831 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:22,898 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50833 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:23,070: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (1677.863 ms)\n[2026-09-18 00:35:23,074: INFO/main] Task galaxy.fetch_data[fcd663ff-6225-4900-84af-e6e822a5df0b] succeeded in 1.6829091245308518s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3'\nuvicorn.access INFO 2026-09-18 00:35:23,167 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50835 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:23,404: INFO/main] Task galaxy.set_job_metadata[a4c8bb88-fb46-410f-b6e9-9710b07f1c1b] received\n[2026-09-18 00:35:23,405: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'a4c8bb88-fb46-410f-b6e9-9710b07f1c1b', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'a4c8bb88-fb46-410f-b6e9-9710b07f1c1b', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'b1ba9027-f25d-4eb8-896a-927981bbae70', 'parent_id': 'fcd663ff-6225-4900-84af-e6e822a5df0b', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 3}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'a4c8bb88-fb46-410f-b6e9-9710b07f1c1b', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '6a13cc8e-5f4d-4032-89f6-d86cfa05496c'}, 'reply_to':... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:23,438 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50837 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:23,453: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (47.292 ms)\n[2026-09-18 00:35:23,457: INFO/main] Task galaxy.set_job_metadata[a4c8bb88-fb46-410f-b6e9-9710b07f1c1b] succeeded in 0.0518288342282176s: None\nuvicorn.access INFO 2026-09-18 00:35:23,715 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50839 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:23,984 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50841 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:24,263 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50843 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:24,416: INFO/main] Task galaxy.finish_job[d4dfafd4-9b39-41d0-8289-2ae4db22b966] received\n[2026-09-18 00:35:24,416: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', 'd4dfafd4-9b39-41d0-8289-2ae4db22b966', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': 'd4dfafd4-9b39-41d0-8289-2ae4db22b966', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'b1ba9027-f25d-4eb8-896a-927981bbae70', 'parent_id': 'a4c8bb88-fb46-410f-b6e9-9710b07f1c1b', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 3, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request... kwargs:{})\n[2026-09-18 00:35:24,427: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3/outputs/dataset_c2e8c51a-e868-4846-bbfa-0ea50c3b46e7.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/c/2/e/dataset_c2e8c51a-e868-4846-bbfa-0ea50c3b46e7.dat\n[2026-09-18 00:35:24,430: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'SRR5085168_forward.fastqsanger.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3/working/gxupload_0', 'object_id': 3}]}]}]\n[2026-09-18 00:35:24,449: INFO/main] Collecting metrics for Job 3 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/3\n[2026-09-18 00:35:24,453: DEBUG/main] job_wrapper.finish for job 3 executed (31.427 ms)\n[2026-09-18 00:35:24,453: INFO/main] Successfully executed Celery task finish_job finish_job (36.424 ms)\n[2026-09-18 00:35:24,455: INFO/main] Task galaxy.finish_job[d4dfafd4-9b39-41d0-8289-2ae4db22b966] succeeded in 0.038882458582520485s: None\nuvicorn.access INFO 2026-09-18 00:35:24,536 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50845 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:24,545 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.064 ms)\nuvicorn.access INFO 2026-09-18 00:35:24,567 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50847 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:24,575 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50849 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:24,852 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50851 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:25,123 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50853 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:25,397 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50855 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:25,426: INFO/main] Task galaxy.compute_dataset_hash[f547624b-a34c-4e3d-978a-e48db6c3d557] received\n[2026-09-18 00:35:25,426: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', 'f547624b-a34c-4e3d-978a-e48db6c3d557', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': 'f547624b-a34c-4e3d-978a-e48db6c3d557', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'b1ba9027-f25d-4eb8-896a-927981bbae70', 'parent_id': 'd4dfafd4-9b39-41d0-8289-2ae4db22b966', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=3, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'f547624b-a34c-4e3d-978a-e48db6c3d557', 'reply_to': '2108afad-e84a-3586-ab31-61faf434b7d6', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '9858d1b4-15b1-431a-a232-3e2b7c2fc69e'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:25,430: INFO/main] Task galaxy.setup_fetch_data[08514007-4ee6-4a69-b5e5-d26e7dc6349a] received\n[2026-09-18 00:35:25,430: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '08514007-4ee6-4a69-b5e5-d26e7dc6349a', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '08514007-4ee6-4a69-b5e5-d26e7dc6349a', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '08514007-4ee6-4a69-b5e5-d26e7dc6349a', 'parent_id': None, 'argsrepr': '(4,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:25,437: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (10.811 ms)\n[2026-09-18 00:35:25,441: INFO/main] Task galaxy.compute_dataset_hash[f547624b-a34c-4e3d-978a-e48db6c3d557] succeeded in 0.01489270944148302s: None\n[2026-09-18 00:35:25,449: DEBUG/main] (4) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4\n[2026-09-18 00:35:25,475: DEBUG/main] Job wrapper for Job [4] prepared (9.635 ms)\n[2026-09-18 00:35:25,475: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (43.784 ms)\n[2026-09-18 00:35:25,479: INFO/main] Task galaxy.setup_fetch_data[08514007-4ee6-4a69-b5e5-d26e7dc6349a] succeeded in 0.047934249974787235s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:25,667 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50857 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:25,943 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50859 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:26,216 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50861 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:26,449: INFO/main] Task galaxy.fetch_data[7482eb82-5ea2-409b-a297-5023b1fc0fed] received\n[2026-09-18 00:35:26,449: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '7482eb82-5ea2-409b-a297-5023b1fc0fed', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '7482eb82-5ea2-409b-a297-5023b1fc0fed', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '08514007-4ee6-4a69-b5e5-d26e7dc6349a', 'parent_id': '08514007-4ee6-4a69-b5e5-d26e7dc6349a', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 4}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '7482eb82-5ea2-409b-a297-5023b1fc0fed', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:26,483 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50863 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:26,517: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (67.228 ms)\n[2026-09-18 00:35:26,521: INFO/main] Task galaxy.fetch_data[7482eb82-5ea2-409b-a297-5023b1fc0fed] succeeded in 0.07128162495791912s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4'\nuvicorn.access INFO 2026-09-18 00:35:26,754 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50865 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:27,029 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50867 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:27,307 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50869 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:27,460: INFO/main] Task galaxy.set_job_metadata[3a59c469-b060-481e-9e05-2cf9b38244ea] received\n[2026-09-18 00:35:27,460: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '3a59c469-b060-481e-9e05-2cf9b38244ea', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '3a59c469-b060-481e-9e05-2cf9b38244ea', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '08514007-4ee6-4a69-b5e5-d26e7dc6349a', 'parent_id': '7482eb82-5ea2-409b-a297-5023b1fc0fed', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 4}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '3a59c469-b060-481e-9e05-2cf9b38244ea', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '85b55c4d-6a07-4158-a41c-7fc4083cc399'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:27,511: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (50.063 ms)\n[2026-09-18 00:35:27,515: INFO/main] Task galaxy.set_job_metadata[3a59c469-b060-481e-9e05-2cf9b38244ea] succeeded in 0.054411666467785835s: None\nuvicorn.access INFO 2026-09-18 00:35:27,574 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50871 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:27,851 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50873 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:28,126 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50875 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:28,414 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50877 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:28,478: INFO/main] Task galaxy.finish_job[44d624f6-6956-4d70-bac2-4837129ffa36] received\n[2026-09-18 00:35:28,478: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '44d624f6-6956-4d70-bac2-4837129ffa36', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '44d624f6-6956-4d70-bac2-4837129ffa36', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '08514007-4ee6-4a69-b5e5-d26e7dc6349a', 'parent_id': '3a59c469-b060-481e-9e05-2cf9b38244ea', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 4, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request... kwargs:{})\n[2026-09-18 00:35:28,486: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4/outputs/dataset_6d8e9a44-4c63-4a3c-8f12-444a74147d8e.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/6/d/8/dataset_6d8e9a44-4c63-4a3c-8f12-444a74147d8e.dat\n[2026-09-18 00:35:28,488: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'SRR5085168_reverse.fastqsanger.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4/working/gxupload_0', 'object_id': 4}]}]}]\n[2026-09-18 00:35:28,503: INFO/main] Collecting metrics for Job 4 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/4\n[2026-09-18 00:35:28,506: DEBUG/main] job_wrapper.finish for job 4 executed (23.554 ms)\n[2026-09-18 00:35:28,506: INFO/main] Successfully executed Celery task finish_job finish_job (27.410 ms)\n[2026-09-18 00:35:28,509: INFO/main] Task galaxy.finish_job[44d624f6-6956-4d70-bac2-4837129ffa36] succeeded in 0.030612832866609097s: None\nuvicorn.access INFO 2026-09-18 00:35:28,689 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50879 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:28,699 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.052 ms)\nuvicorn.access INFO 2026-09-18 00:35:28,725 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50881 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:28,734 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50883 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:29,009 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50885 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:29,296 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50887 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:29,492: INFO/main] Task galaxy.compute_dataset_hash[cb643344-07dd-4f79-ab2a-0e71169e12ad] received\n[2026-09-18 00:35:29,492: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', 'cb643344-07dd-4f79-ab2a-0e71169e12ad', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': 'cb643344-07dd-4f79-ab2a-0e71169e12ad', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '08514007-4ee6-4a69-b5e5-d26e7dc6349a', 'parent_id': '44d624f6-6956-4d70-bac2-4837129ffa36', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=4, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'cb643344-07dd-4f79-ab2a-0e71169e12ad', 'reply_to': 'a0fc44b4-38dd-35c5-9a57-80ac039ff6fa', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '17bce92d-b755-4d1f-8a9b-c4c146067c59'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:29,497: INFO/main] Task galaxy.setup_fetch_data[3c40d107-6b4d-4356-ac5b-799bd5907845] received\n[2026-09-18 00:35:29,497: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '3c40d107-6b4d-4356-ac5b-799bd5907845', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '3c40d107-6b4d-4356-ac5b-799bd5907845', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3c40d107-6b4d-4356-ac5b-799bd5907845', 'parent_id': None, 'argsrepr': '(5,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:29,502: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (9.290 ms)\n[2026-09-18 00:35:29,509: INFO/main] Task galaxy.compute_dataset_hash[cb643344-07dd-4f79-ab2a-0e71169e12ad] succeeded in 0.01642591692507267s: None\n[2026-09-18 00:35:29,512: DEBUG/main] (5) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5\n[2026-09-18 00:35:29,537: DEBUG/main] Job wrapper for Job [5] prepared (9.911 ms)\n[2026-09-18 00:35:29,537: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (39.285 ms)\n[2026-09-18 00:35:29,541: INFO/main] Task galaxy.setup_fetch_data[3c40d107-6b4d-4356-ac5b-799bd5907845] succeeded in 0.043375750072300434s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:29,567 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50889 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:29,836 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50891 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:30,106 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50893 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:30,378 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50895 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:30,515: INFO/main] Task galaxy.fetch_data[7213f4c9-ae8c-4748-9e12-7984a6f1caa9] received\n[2026-09-18 00:35:30,515: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '7213f4c9-ae8c-4748-9e12-7984a6f1caa9', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '7213f4c9-ae8c-4748-9e12-7984a6f1caa9', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3c40d107-6b4d-4356-ac5b-799bd5907845', 'parent_id': '3c40d107-6b4d-4356-ac5b-799bd5907845', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 5}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '7213f4c9-ae8c-4748-9e12-7984a6f1caa9', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\n[2026-09-18 00:35:30,586: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (69.601 ms)\n[2026-09-18 00:35:30,590: INFO/main] Task galaxy.fetch_data[7213f4c9-ae8c-4748-9e12-7984a6f1caa9] succeeded in 0.07431195769459009s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5'\nuvicorn.access INFO 2026-09-18 00:35:30,649 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50897 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:30,924 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50899 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:31,194 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50901 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:31,473 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50903 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:31,527: INFO/main] Task galaxy.set_job_metadata[0b0542a1-6a73-4351-a045-1b27d1e3b265] received\n[2026-09-18 00:35:31,527: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '0b0542a1-6a73-4351-a045-1b27d1e3b265', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '0b0542a1-6a73-4351-a045-1b27d1e3b265', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3c40d107-6b4d-4356-ac5b-799bd5907845', 'parent_id': '7213f4c9-ae8c-4748-9e12-7984a6f1caa9', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 5}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '0b0542a1-6a73-4351-a045-1b27d1e3b265', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '509f993f-0106-4ba8-a419-de0a4f6dcce6'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:31,572: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (44.002 ms)\n[2026-09-18 00:35:31,577: INFO/main] Task galaxy.set_job_metadata[0b0542a1-6a73-4351-a045-1b27d1e3b265] succeeded in 0.04888541717082262s: None\nuvicorn.access INFO 2026-09-18 00:35:31,740 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50905 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:32,022 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50907 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:32,297 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50909 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:32,545: INFO/main] Task galaxy.finish_job[16d77caa-098d-49ae-9186-db0ceb9b345a] received\n[2026-09-18 00:35:32,545: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '16d77caa-098d-49ae-9186-db0ceb9b345a', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '16d77caa-098d-49ae-9186-db0ceb9b345a', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3c40d107-6b4d-4356-ac5b-799bd5907845', 'parent_id': '0b0542a1-6a73-4351-a045-1b27d1e3b265', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 5, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request... kwargs:{})\n[2026-09-18 00:35:32,553: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5/outputs/dataset_be6e434a-5cfd-4572-976e-540558021743.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/b/e/6/dataset_be6e434a-5cfd-4572-976e-540558021743.dat\n[2026-09-18 00:35:32,555: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'SRR5085169_forward.fastqsanger.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5/working/gxupload_0', 'object_id': 5}]}]}]\nuvicorn.access INFO 2026-09-18 00:35:32,565 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50911 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:32,576: INFO/main] Collecting metrics for Job 5 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/5\n[2026-09-18 00:35:32,580: DEBUG/main] job_wrapper.finish for job 5 executed (30.931 ms)\n[2026-09-18 00:35:32,581: INFO/main] Successfully executed Celery task finish_job finish_job (34.755 ms)\n[2026-09-18 00:35:32,583: INFO/main] Task galaxy.finish_job[16d77caa-098d-49ae-9186-db0ceb9b345a] succeeded in 0.037720249965786934s: None\nuvicorn.access INFO 2026-09-18 00:35:32,838 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50913 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:32,850 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.079 ms)\nuvicorn.access INFO 2026-09-18 00:35:32,877 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50915 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:32,886 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50917 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:33,165 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50919 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:33,447 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50921 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:33,563: INFO/main] Task galaxy.compute_dataset_hash[b4affed7-4e04-4e7f-a049-895277be6716] received\n[2026-09-18 00:35:33,564: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', 'b4affed7-4e04-4e7f-a049-895277be6716', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': 'b4affed7-4e04-4e7f-a049-895277be6716', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3c40d107-6b4d-4356-ac5b-799bd5907845', 'parent_id': '16d77caa-098d-49ae-9186-db0ceb9b345a', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=5, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'b4affed7-4e04-4e7f-a049-895277be6716', 'reply_to': '2108afad-e84a-3586-ab31-61faf434b7d6', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '09ecf8ae-9420-4318-a9d9-972dcb800f30'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:33,569: INFO/main] Task galaxy.setup_fetch_data[3f6d221b-cd53-4403-b31c-001fa3cf7372] received\n[2026-09-18 00:35:33,569: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', '3f6d221b-cd53-4403-b31c-001fa3cf7372', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': '3f6d221b-cd53-4403-b31c-001fa3cf7372', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3f6d221b-cd53-4403-b31c-001fa3cf7372', 'parent_id': None, 'argsrepr': '(6,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:33,575: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (10.005 ms)\n[2026-09-18 00:35:33,579: INFO/main] Task galaxy.compute_dataset_hash[b4affed7-4e04-4e7f-a049-895277be6716] succeeded in 0.015017124824225903s: None\n[2026-09-18 00:35:33,585: DEBUG/main] (6) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6\n[2026-09-18 00:35:33,609: DEBUG/main] Job wrapper for Job [6] prepared (9.049 ms)\n[2026-09-18 00:35:33,609: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (39.383 ms)\n[2026-09-18 00:35:33,613: INFO/main] Task galaxy.setup_fetch_data[3f6d221b-cd53-4403-b31c-001fa3cf7372] succeeded in 0.04315799940377474s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:33,716 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50923 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:33,987 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50925 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:34,262 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50927 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:34,546 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50929 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:34,584: INFO/main] Task galaxy.fetch_data[d660bfac-73e9-4fee-b396-118ddf6fcaff] received\n[2026-09-18 00:35:34,584: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'd660bfac-73e9-4fee-b396-118ddf6fcaff', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'd660bfac-73e9-4fee-b396-118ddf6fcaff', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3f6d221b-cd53-4403-b31c-001fa3cf7372', 'parent_id': '3f6d221b-cd53-4403-b31c-001fa3cf7372', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 6}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'd660bfac-73e9-4fee-b396-118ddf6fcaff', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\n[2026-09-18 00:35:34,654: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (68.668 ms)\n[2026-09-18 00:35:34,657: INFO/main] Task galaxy.fetch_data[d660bfac-73e9-4fee-b396-118ddf6fcaff] succeeded in 0.07275354117155075s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6'\nuvicorn.access INFO 2026-09-18 00:35:34,831 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50931 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:35,113 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50933 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:35,388 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50935 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:35,605: INFO/main] Task galaxy.set_job_metadata[101bf41f-b6b1-4287-acbf-04d88507f56d] received\n[2026-09-18 00:35:35,605: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '101bf41f-b6b1-4287-acbf-04d88507f56d', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '101bf41f-b6b1-4287-acbf-04d88507f56d', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3f6d221b-cd53-4403-b31c-001fa3cf7372', 'parent_id': 'd660bfac-73e9-4fee-b396-118ddf6fcaff', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 6}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '101bf41f-b6b1-4287-acbf-04d88507f56d', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '92bdb627-e7d1-492e-82fd-007919adc654'}, 'reply_to':... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:35,654 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50937 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:35,657: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (51.390 ms)\n[2026-09-18 00:35:35,661: INFO/main] Task galaxy.set_job_metadata[101bf41f-b6b1-4287-acbf-04d88507f56d] succeeded in 0.05586337484419346s: None\nuvicorn.access INFO 2026-09-18 00:35:35,932 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50939 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:36,211 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50941 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:36,490 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50944 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:36,620: INFO/main] Task galaxy.finish_job[3aa2b791-936d-4b27-9202-2d53ffb529da] received\n[2026-09-18 00:35:36,620: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '3aa2b791-936d-4b27-9202-2d53ffb529da', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '3aa2b791-936d-4b27-9202-2d53ffb529da', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3f6d221b-cd53-4403-b31c-001fa3cf7372', 'parent_id': '101bf41f-b6b1-4287-acbf-04d88507f56d', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 6, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request... kwargs:{})\n[2026-09-18 00:35:36,628: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6/outputs/dataset_04956493-9ef8-4169-a6f7-26235a410e1e.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/0/4/9/dataset_04956493-9ef8-4169-a6f7-26235a410e1e.dat\n[2026-09-18 00:35:36,630: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'SRR5085169_reverse.fastqsanger.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6/working/gxupload_0', 'object_id': 6}]}]}]\n[2026-09-18 00:35:36,646: INFO/main] Collecting metrics for Job 6 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/6\n[2026-09-18 00:35:36,649: DEBUG/main] job_wrapper.finish for job 6 executed (24.919 ms)\n[2026-09-18 00:35:36,649: INFO/main] Successfully executed Celery task finish_job finish_job (28.906 ms)\n[2026-09-18 00:35:36,652: INFO/main] Task galaxy.finish_job[3aa2b791-936d-4b27-9202-2d53ffb529da] succeeded in 0.03134404215961695s: None\nuvicorn.access INFO 2026-09-18 00:35:36,764 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50946 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:36,772 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.045 ms)\nuvicorn.access INFO 2026-09-18 00:35:36,798 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50948 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:36,807 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50950 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:37,080 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50952 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:37,349 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50954 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:37,633: INFO/main] Task galaxy.compute_dataset_hash[c113ad73-7c77-429d-8ad6-1fe89e740831] received\n[2026-09-18 00:35:37,633: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', 'c113ad73-7c77-429d-8ad6-1fe89e740831', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': 'c113ad73-7c77-429d-8ad6-1fe89e740831', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': '3f6d221b-cd53-4403-b31c-001fa3cf7372', 'parent_id': '3aa2b791-936d-4b27-9202-2d53ffb529da', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=6, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'c113ad73-7c77-429d-8ad6-1fe89e740831', 'reply_to': 'a0fc44b4-38dd-35c5-9a57-80ac039ff6fa', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '979b99db-b586-4094-8041-991ea301ac5a'}, 'reply_to':... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:37,633 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50956 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:37,637: INFO/main] Task galaxy.setup_fetch_data[dab2ff32-d5f5-44e0-89c8-b6d09ea94185] received\n[2026-09-18 00:35:37,637: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'dab2ff32-d5f5-44e0-89c8-b6d09ea94185', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'dab2ff32-d5f5-44e0-89c8-b6d09ea94185', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'dab2ff32-d5f5-44e0-89c8-b6d09ea94185', 'parent_id': None, 'argsrepr': '(7,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:37,643: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (9.496 ms)\n[2026-09-18 00:35:37,649: INFO/main] Task galaxy.compute_dataset_hash[c113ad73-7c77-429d-8ad6-1fe89e740831] succeeded in 0.015352582558989525s: None\n[2026-09-18 00:35:37,651: DEBUG/main] (7) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7\n[2026-09-18 00:35:37,674: DEBUG/main] Job wrapper for Job [7] prepared (8.376 ms)\n[2026-09-18 00:35:37,674: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (36.748 ms)\n[2026-09-18 00:35:37,678: INFO/main] Task galaxy.setup_fetch_data[dab2ff32-d5f5-44e0-89c8-b6d09ea94185] succeeded in 0.040519374422729015s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:37,903 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50958 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:38,189 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50960 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:38,468 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50962 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:38,651: INFO/main] Task galaxy.fetch_data[7fcdec94-d215-467c-b20f-bb221b6d646b] received\n[2026-09-18 00:35:38,651: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '7fcdec94-d215-467c-b20f-bb221b6d646b', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '7fcdec94-d215-467c-b20f-bb221b6d646b', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'dab2ff32-d5f5-44e0-89c8-b6d09ea94185', 'parent_id': 'dab2ff32-d5f5-44e0-89c8-b6d09ea94185', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 7}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '7fcdec94-d215-467c-b20f-bb221b6d646b', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\n[2026-09-18 00:35:38,729: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (76.624 ms)\n[2026-09-18 00:35:38,733: INFO/main] Task galaxy.fetch_data[7fcdec94-d215-467c-b20f-bb221b6d646b] succeeded in 0.08081837464123964s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7'\nuvicorn.access INFO 2026-09-18 00:35:38,738 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50964 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:39,019 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50966 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:39,289 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50968 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:39,568 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50970 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:39,673: INFO/main] Task galaxy.set_job_metadata[fe0b6aa8-8bf5-499a-a153-08418e5486f5] received\n[2026-09-18 00:35:39,673: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'fe0b6aa8-8bf5-499a-a153-08418e5486f5', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'fe0b6aa8-8bf5-499a-a153-08418e5486f5', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'dab2ff32-d5f5-44e0-89c8-b6d09ea94185', 'parent_id': '7fcdec94-d215-467c-b20f-bb221b6d646b', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 7}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'fe0b6aa8-8bf5-499a-a153-08418e5486f5', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '9de02548-884b-47a5-b5f8-560a52da4e1a'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:39,726: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (52.032 ms)\n[2026-09-18 00:35:39,730: INFO/main] Task galaxy.set_job_metadata[fe0b6aa8-8bf5-499a-a153-08418e5486f5] succeeded in 0.0566944582387805s: None\nuvicorn.access INFO 2026-09-18 00:35:39,839 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50972 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:40,123 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50974 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:40,399 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50976 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:40,683: INFO/main] Task galaxy.finish_job[161da3c4-28e9-4ab9-9de3-1d019c1ffa86] received\n[2026-09-18 00:35:40,683: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '161da3c4-28e9-4ab9-9de3-1d019c1ffa86', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '161da3c4-28e9-4ab9-9de3-1d019c1ffa86', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'dab2ff32-d5f5-44e0-89c8-b6d09ea94185', 'parent_id': 'fe0b6aa8-8bf5-499a-a153-08418e5486f5', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 7, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:40,685 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50978 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:40,694: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7/outputs/dataset_6e39692e-9cf2-4bb9-a40e-c4fee4b16d4c.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/6/e/3/dataset_6e39692e-9cf2-4bb9-a40e-c4fee4b16d4c.dat\n[2026-09-18 00:35:40,697: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'SRR5085170_forward.fastqsanger.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7/working/gxupload_0', 'object_id': 7}]}]}]\n[2026-09-18 00:35:40,718: INFO/main] Collecting metrics for Job 7 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/7\n[2026-09-18 00:35:40,722: DEBUG/main] job_wrapper.finish for job 7 executed (31.878 ms)\n[2026-09-18 00:35:40,722: INFO/main] Successfully executed Celery task finish_job finish_job (37.903 ms)\n[2026-09-18 00:35:40,725: INFO/main] Task galaxy.finish_job[161da3c4-28e9-4ab9-9de3-1d019c1ffa86] succeeded in 0.040651666931807995s: None\nuvicorn.access INFO 2026-09-18 00:35:40,957 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50980 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:40,967 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.077 ms)\nuvicorn.access INFO 2026-09-18 00:35:40,997 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50982 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:41,006 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50984 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:41,282 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50986 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:41,561 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50988 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:41,697: INFO/main] Task galaxy.compute_dataset_hash[0517098a-57bc-438c-b090-34cd2e189160] received\n[2026-09-18 00:35:41,697: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', '0517098a-57bc-438c-b090-34cd2e189160', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': '0517098a-57bc-438c-b090-34cd2e189160', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'dab2ff32-d5f5-44e0-89c8-b6d09ea94185', 'parent_id': '161da3c4-28e9-4ab9-9de3-1d019c1ffa86', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=7, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '0517098a-57bc-438c-b090-34cd2e189160', 'reply_to': '2108afad-e84a-3586-ab31-61faf434b7d6', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'e48227be-c54c-4907-ac5f-56d19bb91296'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:41,703: INFO/main] Task galaxy.setup_fetch_data[d7b38a8a-782a-48f5-a351-05d0c8864368] received\n[2026-09-18 00:35:41,703: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'd7b38a8a-782a-48f5-a351-05d0c8864368', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'd7b38a8a-782a-48f5-a351-05d0c8864368', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'd7b38a8a-782a-48f5-a351-05d0c8864368', 'parent_id': None, 'argsrepr': '(8,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:41,711: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (12.596 ms)\n[2026-09-18 00:35:41,719: INFO/main] Task galaxy.compute_dataset_hash[0517098a-57bc-438c-b090-34cd2e189160] succeeded in 0.020627707242965698s: None\n[2026-09-18 00:35:41,721: DEBUG/main] (8) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8\n[2026-09-18 00:35:41,747: DEBUG/main] Job wrapper for Job [8] prepared (8.911 ms)\n[2026-09-18 00:35:41,747: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (42.903 ms)\n[2026-09-18 00:35:41,750: INFO/main] Task galaxy.setup_fetch_data[d7b38a8a-782a-48f5-a351-05d0c8864368] succeeded in 0.04696475062519312s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:41,828 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50990 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:42,108 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50992 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:42,381 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50994 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:42,660 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50996 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:42,717: INFO/main] Task galaxy.fetch_data[98dbbe24-b405-4939-847b-1bc73690205b] received\n[2026-09-18 00:35:42,718: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '98dbbe24-b405-4939-847b-1bc73690205b', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '98dbbe24-b405-4939-847b-1bc73690205b', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'd7b38a8a-782a-48f5-a351-05d0c8864368', 'parent_id': 'd7b38a8a-782a-48f5-a351-05d0c8864368', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 8}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '98dbbe24-b405-4939-847b-1bc73690205b', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\n[2026-09-18 00:35:42,786: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (67.933 ms)\n[2026-09-18 00:35:42,791: INFO/main] Task galaxy.fetch_data[98dbbe24-b405-4939-847b-1bc73690205b] succeeded in 0.07245962508022785s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8'\nuvicorn.access INFO 2026-09-18 00:35:42,930 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:50998 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:43,209 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51000 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:43,477 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51002 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:43,731: INFO/main] Task galaxy.set_job_metadata[9d4dd69d-3182-4f41-b9d1-4786d1e722c6] received\n[2026-09-18 00:35:43,731: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '9d4dd69d-3182-4f41-b9d1-4786d1e722c6', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '9d4dd69d-3182-4f41-b9d1-4786d1e722c6', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'd7b38a8a-782a-48f5-a351-05d0c8864368', 'parent_id': '98dbbe24-b405-4939-847b-1bc73690205b', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 8}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '9d4dd69d-3182-4f41-b9d1-4786d1e722c6', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'd55feb84-8998-4205-8889-287c9016bf30'}, 'reply_to':... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:43,749 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51004 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:43,788: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (56.077 ms)\n[2026-09-18 00:35:43,793: INFO/main] Task galaxy.set_job_metadata[9d4dd69d-3182-4f41-b9d1-4786d1e722c6] succeeded in 0.060938834212720394s: None\nuvicorn.access INFO 2026-09-18 00:35:44,025 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51006 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:44,304 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51008 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:44,583 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51010 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:44,752: INFO/main] Task galaxy.finish_job[98a6d70d-5bff-4a59-95f0-3b787b3def13] received\n[2026-09-18 00:35:44,752: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '98a6d70d-5bff-4a59-95f0-3b787b3def13', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '98a6d70d-5bff-4a59-95f0-3b787b3def13', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'd7b38a8a-782a-48f5-a351-05d0c8864368', 'parent_id': '9d4dd69d-3182-4f41-b9d1-4786d1e722c6', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 8, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request... kwargs:{})\n[2026-09-18 00:35:44,764: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8/outputs/dataset_6efd6e94-b2e8-4ebf-aae6-0919e9a1c674.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/6/e/f/dataset_6efd6e94-b2e8-4ebf-aae6-0919e9a1c674.dat\n[2026-09-18 00:35:44,766: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'SRR5085170_reverse.fastqsanger.gz', 'dbkey': '?', 'ext': 'fastqsanger.gz', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded fastqsanger.gz file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8/working/gxupload_0', 'object_id': 8}]}]}]\n[2026-09-18 00:35:44,789: INFO/main] Collecting metrics for Job 8 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/8\n[2026-09-18 00:35:44,793: DEBUG/main] job_wrapper.finish for job 8 executed (34.875 ms)\n[2026-09-18 00:35:44,793: INFO/main] Successfully executed Celery task finish_job finish_job (40.469 ms)\n[2026-09-18 00:35:44,796: INFO/main] Task galaxy.finish_job[98a6d70d-5bff-4a59-95f0-3b787b3def13] succeeded in 0.04338087514042854s: None\nuvicorn.access INFO 2026-09-18 00:35:44,855 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51012 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:44,901 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51014 - \"POST /api/dataset_collections HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:44,907 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.037 ms)\nuvicorn.access INFO 2026-09-18 00:35:44,928 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51016 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:44,937 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51018 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:45,210 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51021 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:45,483 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51024 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:45,752 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51026 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:45,771: INFO/main] Task galaxy.compute_dataset_hash[59407ffc-e2bf-45e3-b62e-8c904db58a1b] received\n[2026-09-18 00:35:45,771: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', '59407ffc-e2bf-45e3-b62e-8c904db58a1b', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': '59407ffc-e2bf-45e3-b62e-8c904db58a1b', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'd7b38a8a-782a-48f5-a351-05d0c8864368', 'parent_id': '98a6d70d-5bff-4a59-95f0-3b787b3def13', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=8, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '59407ffc-e2bf-45e3-b62e-8c904db58a1b', 'reply_to': 'a0fc44b4-38dd-35c5-9a57-80ac039ff6fa', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'fca7c2b3-5670-4fad-aebf-bc0bb8cab4fb'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:45,774: INFO/main] Task galaxy.setup_fetch_data[f4054819-fe10-4c33-b53c-90de17b9a7c0] received\n[2026-09-18 00:35:45,774: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'f4054819-fe10-4c33-b53c-90de17b9a7c0', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'f4054819-fe10-4c33-b53c-90de17b9a7c0', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'f4054819-fe10-4c33-b53c-90de17b9a7c0', 'parent_id': None, 'argsrepr': '(9,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:45,779: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (7.549 ms)\n[2026-09-18 00:35:45,782: INFO/main] Task galaxy.compute_dataset_hash[59407ffc-e2bf-45e3-b62e-8c904db58a1b] succeeded in 0.010783292353153229s: None\n[2026-09-18 00:35:45,786: DEBUG/main] (9) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9\n[2026-09-18 00:35:45,808: DEBUG/main] Job wrapper for Job [9] prepared (8.525 ms)\n[2026-09-18 00:35:45,808: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (33.303 ms)\n[2026-09-18 00:35:45,812: INFO/main] Task galaxy.setup_fetch_data[f4054819-fe10-4c33-b53c-90de17b9a7c0] succeeded in 0.03757645841687918s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:46,019 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51029 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:46,284 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51031 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:46,554 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51033 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:46,789: INFO/main] Task galaxy.fetch_data[42eb39f7-1feb-4947-80bc-a595bca0674d] received\n[2026-09-18 00:35:46,789: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '42eb39f7-1feb-4947-80bc-a595bca0674d', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '42eb39f7-1feb-4947-80bc-a595bca0674d', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'f4054819-fe10-4c33-b53c-90de17b9a7c0', 'parent_id': 'f4054819-fe10-4c33-b53c-90de17b9a7c0', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 9}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '42eb39f7-1feb-4947-80bc-a595bca0674d', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:46,820 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51035 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:46,855: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (65.449 ms)\n[2026-09-18 00:35:46,859: INFO/main] Task galaxy.fetch_data[42eb39f7-1feb-4947-80bc-a595bca0674d] succeeded in 0.069733208976686s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9'\nuvicorn.access INFO 2026-09-18 00:35:47,099 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51037 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:47,372 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51039 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:47,641 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51041 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:47,804: INFO/main] Task galaxy.set_job_metadata[82eb4f46-df8e-4106-8910-f16fe9b280bf] received\n[2026-09-18 00:35:47,804: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', '82eb4f46-df8e-4106-8910-f16fe9b280bf', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': '82eb4f46-df8e-4106-8910-f16fe9b280bf', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'f4054819-fe10-4c33-b53c-90de17b9a7c0', 'parent_id': '42eb39f7-1feb-4947-80bc-a595bca0674d', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 9}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '82eb4f46-df8e-4106-8910-f16fe9b280bf', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'bd85474e-d329-4768-9d8e-faffeab7d390'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:47,861: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (55.996 ms)\n[2026-09-18 00:35:47,865: INFO/main] Task galaxy.set_job_metadata[82eb4f46-df8e-4106-8910-f16fe9b280bf] succeeded in 0.060398333705961704s: None\nuvicorn.access INFO 2026-09-18 00:35:47,909 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51043 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:48,184 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51045 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:48,463 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51047 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:48,734 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51049 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:48,825: INFO/main] Task galaxy.finish_job[d58ec5ae-00d1-447e-9a27-4de27fe2a7f7] received\n[2026-09-18 00:35:48,825: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', 'd58ec5ae-00d1-447e-9a27-4de27fe2a7f7', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': 'd58ec5ae-00d1-447e-9a27-4de27fe2a7f7', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'f4054819-fe10-4c33-b53c-90de17b9a7c0', 'parent_id': '82eb4f46-df8e-4106-8910-f16fe9b280bf', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 9, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request... kwargs:{})\n[2026-09-18 00:35:48,838: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9/outputs/dataset_92fd78af-c743-4925-9063-bddbc393e415.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/9/2/f/dataset_92fd78af-c743-4925-9063-bddbc393e415.dat\n[2026-09-18 00:35:48,840: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'transcriptome.fasta', 'dbkey': '?', 'ext': 'fasta', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded fasta file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9/working/data_fetch_upload_b73s3lw7', 'object_id': 9}]}]}]\n[2026-09-18 00:35:48,867: INFO/main] Collecting metrics for Job 9 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/9\n[2026-09-18 00:35:48,871: DEBUG/main] job_wrapper.finish for job 9 executed (38.997 ms)\n[2026-09-18 00:35:48,871: INFO/main] Successfully executed Celery task finish_job finish_job (45.081 ms)\n[2026-09-18 00:35:48,874: INFO/main] Task galaxy.finish_job[d58ec5ae-00d1-447e-9a27-4de27fe2a7f7] succeeded in 0.0482843741774559s: None\nuvicorn.access INFO 2026-09-18 00:35:49,011 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51051 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:49,022 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.064 ms)\nuvicorn.access INFO 2026-09-18 00:35:49,050 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51053 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:49,059 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51055 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:49,323 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51058 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:49,601 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51060 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:49,836: INFO/main] Task galaxy.compute_dataset_hash[2820fc83-55c3-4df9-8465-aa19099fa56a] received\n[2026-09-18 00:35:49,837: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', '2820fc83-55c3-4df9-8465-aa19099fa56a', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': '2820fc83-55c3-4df9-8465-aa19099fa56a', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'f4054819-fe10-4c33-b53c-90de17b9a7c0', 'parent_id': 'd58ec5ae-00d1-447e-9a27-4de27fe2a7f7', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=9, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '2820fc83-55c3-4df9-8465-aa19099fa56a', 'reply_to': '2108afad-e84a-3586-ab31-61faf434b7d6', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'fda77bcf-d878-431c-87a2-3711685ca2a3'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:49,843: INFO/main] Task galaxy.setup_fetch_data[e8838e27-ebb3-443a-ad82-65cc7a5d5c04] received\n[2026-09-18 00:35:49,844: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'e8838e27-ebb3-443a-ad82-65cc7a5d5c04', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'e8838e27-ebb3-443a-ad82-65cc7a5d5c04', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8838e27-ebb3-443a-ad82-65cc7a5d5c04', 'parent_id': None, 'argsrepr': '(10,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:49,850: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (11.744 ms)\n[2026-09-18 00:35:49,858: INFO/main] Task galaxy.compute_dataset_hash[2820fc83-55c3-4df9-8465-aa19099fa56a] succeeded in 0.02018070872873068s: None\n[2026-09-18 00:35:49,860: DEBUG/main] (10) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10\nuvicorn.access INFO 2026-09-18 00:35:49,875 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51062 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:49,885: DEBUG/main] Job wrapper for Job [10] prepared (9.170 ms)\n[2026-09-18 00:35:49,885: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (40.827 ms)\n[2026-09-18 00:35:49,889: INFO/main] Task galaxy.setup_fetch_data[e8838e27-ebb3-443a-ad82-65cc7a5d5c04] succeeded in 0.04479416739195585s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:50,160 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51064 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:50,435 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51066 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:50,702 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51069 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:50,858: INFO/main] Task galaxy.fetch_data[1eded48d-3c09-4cb0-a3e3-85bc664d5cde] received\n[2026-09-18 00:35:50,858: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', '1eded48d-3c09-4cb0-a3e3-85bc664d5cde', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': '1eded48d-3c09-4cb0-a3e3-85bc664d5cde', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8838e27-ebb3-443a-ad82-65cc7a5d5c04', 'parent_id': 'e8838e27-ebb3-443a-ad82-65cc7a5d5c04', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 10}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '1eded48d-3c09-4cb0-a3e3-85bc664d5cde', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\n[2026-09-18 00:35:50,926: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (67.100 ms)\n[2026-09-18 00:35:50,930: INFO/main] Task galaxy.fetch_data[1eded48d-3c09-4cb0-a3e3-85bc664d5cde] succeeded in 0.07109462469816208s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10'\nuvicorn.access INFO 2026-09-18 00:35:50,965 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51071 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:51,242 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51075 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:51,520 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51077 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:51,794 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51080 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:51,869: INFO/main] Task galaxy.set_job_metadata[e5467177-88e9-45d8-bf58-2fe68df2970f] received\n[2026-09-18 00:35:51,869: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'e5467177-88e9-45d8-bf58-2fe68df2970f', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'e5467177-88e9-45d8-bf58-2fe68df2970f', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8838e27-ebb3-443a-ad82-65cc7a5d5c04', 'parent_id': '1eded48d-3c09-4cb0-a3e3-85bc664d5cde', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 10}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'e5467177-88e9-45d8-bf58-2fe68df2970f', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': 'ab0521c0-ca1c-48bd-9141-a8dd59988f2d'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:51,921: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (51.291 ms)\n[2026-09-18 00:35:51,925: INFO/main] Task galaxy.set_job_metadata[e5467177-88e9-45d8-bf58-2fe68df2970f] succeeded in 0.05541004240512848s: None\nuvicorn.access INFO 2026-09-18 00:35:52,068 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51082 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:52,341 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51084 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:52,613 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51086 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:52,884: INFO/main] Task galaxy.finish_job[ace9dc3b-1002-4d1e-a0a0-2088b90c22bc] received\n[2026-09-18 00:35:52,884: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', 'ace9dc3b-1002-4d1e-a0a0-2088b90c22bc', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': 'ace9dc3b-1002-4d1e-a0a0-2088b90c22bc', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8838e27-ebb3-443a-ad82-65cc7a5d5c04', 'parent_id': 'e5467177-88e9-45d8-bf58-2fe68df2970f', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 10, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n ... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:52,892 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51089 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:52,896: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10/outputs/dataset_780cf916-4908-4afe-b6d2-33585818cad7.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/7/8/0/dataset_780cf916-4908-4afe-b6d2-33585818cad7.dat\n[2026-09-18 00:35:52,898: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'sample_metadata.tabular', 'dbkey': '?', 'ext': 'tabular', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded tabular file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10/working/data_fetch_upload_nhq1hied', 'object_id': 10}]}]}]\n[2026-09-18 00:35:52,916: INFO/main] Collecting metrics for Job 10 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/10\n[2026-09-18 00:35:52,920: DEBUG/main] job_wrapper.finish for job 10 executed (29.139 ms)\n[2026-09-18 00:35:52,920: INFO/main] Successfully executed Celery task finish_job finish_job (34.897 ms)\n[2026-09-18 00:35:52,922: INFO/main] Task galaxy.finish_job[ace9dc3b-1002-4d1e-a0a0-2088b90c22bc] succeeded in 0.03774762433022261s: None\nuvicorn.access INFO 2026-09-18 00:35:53,161 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51091 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\ngalaxy.tools INFO 2026-09-18 00:35:53,170 [pN:main.1,p:33541,tN:AnyIO worker thread] Validated and populated state for tool request (0.059 ms)\nuvicorn.access INFO 2026-09-18 00:35:53,204 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51093 - \"POST /api/tools/fetch HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:53,213 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51095 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:53,486 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51097 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:53,756 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51100 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:53,905: INFO/main] Task galaxy.compute_dataset_hash[5635dddb-9edb-47a1-aeb8-a788f79c904c] received\n[2026-09-18 00:35:53,905: DEBUG/main] TaskPool: Apply (args:('galaxy.compute_dataset_hash', '5635dddb-9edb-47a1-aeb8-a788f79c904c', {'lang': 'py', 'task': 'galaxy.compute_dataset_hash', 'id': '5635dddb-9edb-47a1-aeb8-a788f79c904c', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'e8838e27-ebb3-443a-ad82-65cc7a5d5c04', 'parent_id': 'ace9dc3b-1002-4d1e-a0a0-2088b90c22bc', 'argsrepr': '()', 'kwargsrepr': \"{'request': ComputeDatasetHashTaskRequest(dataset_id=10, extra_files_path=None, hash_function='SHA-256', user=None)}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': '5635dddb-9edb-47a1-aeb8-a788f79c904c', 'reply_to': 'a0fc44b4-38dd-35c5-9a57-80ac039ff6fa', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.internal'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '583201d3-8347-4a95-8563-85aac1cec650'}, 'reply_to':... kwargs:{})\n[2026-09-18 00:35:53,913: INFO/main] Task galaxy.setup_fetch_data[fcd38944-5d5d-47ba-86ff-ea46a17f4a88] received\n[2026-09-18 00:35:53,913: DEBUG/main] TaskPool: Apply (args:('galaxy.setup_fetch_data', 'fcd38944-5d5d-47ba-86ff-ea46a17f4a88', {'lang': 'py', 'task': 'galaxy.setup_fetch_data', 'id': 'fcd38944-5d5d-47ba-86ff-ea46a17f4a88', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'fcd38944-5d5d-47ba-86ff-ea46a17f4a88', 'parent_id': None, 'argsrepr': '(11,)', 'kwargsrepr': '{\\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n --request \\\\\\'$request_path\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:53,920: INFO/main] Successfully executed Celery task compute_dataset_hash to compute dataset hash and store in database compute_dataset_hash to compute dataset hash and store in database (13.893 ms)\n[2026-09-18 00:35:53,925: INFO/main] Task galaxy.compute_dataset_hash[5635dddb-9edb-47a1-aeb8-a788f79c904c] succeeded in 0.018410000018775463s: None\n[2026-09-18 00:35:53,930: DEBUG/main] (11) Working directory for job is: /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11\n[2026-09-18 00:35:53,956: DEBUG/main] Job wrapper for Job [11] prepared (10.339 ms)\n[2026-09-18 00:35:53,956: INFO/main] Successfully executed Celery task setup_fetch_data setup_fetch_data (42.414 ms)\n[2026-09-18 00:35:53,960: INFO/main] Task galaxy.setup_fetch_data[fcd38944-5d5d-47ba-86ff-ea46a17f4a88] succeeded in 0.04661970864981413s: ('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11/request.json', {'file_sources': [{...}, {...}, {...}, {...}, {...}, {...}], 'config': {'symlink_allowlist': [...], 'fetch_url_allowlist': [...], 'library_import_dir': None, 'user_library_import_dir': None, 'ftp_upload_dir': '/Users/mvandenb/src/worktrees/foundry/brc-c-auris/ebola-test/test-data', 'ftp_upload_purge': False, 'tmp_dir': None, 'listings_expiry_time': 60}})\nuvicorn.access INFO 2026-09-18 00:35:54,029 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51102 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:54,298 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51104 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:54,573 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51106 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:54,854 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51108 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:54,922: INFO/main] Task galaxy.fetch_data[e54e0463-8214-4b98-98cc-ecb389d9ff00] received\n[2026-09-18 00:35:54,922: DEBUG/main] TaskPool: Apply (args:('galaxy.fetch_data', 'e54e0463-8214-4b98-98cc-ecb389d9ff00', {'lang': 'py', 'task': 'galaxy.fetch_data', 'id': 'e54e0463-8214-4b98-98cc-ecb389d9ff00', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'fcd38944-5d5d-47ba-86ff-ea46a17f4a88', 'parent_id': 'fcd38944-5d5d-47ba-86ff-ea46a17f4a88', 'argsrepr': \"(('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11', '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11/request.json', {'file_sources': [...], 'config': {...}}),)\", 'kwargsrepr': \"{'job_id': 11}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'e54e0463-8214-4b98-98cc-ecb389d9ff00', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'},... kwargs:{})\n[2026-09-18 00:35:54,992: INFO/main] Successfully executed Celery task fetch_data to Run fetch_data fetch_data to Run fetch_data (68.842 ms)\n[2026-09-18 00:35:54,996: INFO/main] Task galaxy.fetch_data[e54e0463-8214-4b98-98cc-ecb389d9ff00] succeeded in 0.07331574987620115s: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11'\nuvicorn.access INFO 2026-09-18 00:35:55,127 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51110 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:55,401 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51112 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:55,677 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51114 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:55,940: INFO/main] Task galaxy.set_job_metadata[d6816c97-afc5-4d09-b346-948fabeae7fb] received\n[2026-09-18 00:35:55,941: DEBUG/main] TaskPool: Apply (args:('galaxy.set_job_metadata', 'd6816c97-afc5-4d09-b346-948fabeae7fb', {'lang': 'py', 'task': 'galaxy.set_job_metadata', 'id': 'd6816c97-afc5-4d09-b346-948fabeae7fb', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'fcd38944-5d5d-47ba-86ff-ea46a17f4a88', 'parent_id': 'e54e0463-8214-4b98-98cc-ecb389d9ff00', 'argsrepr': \"('/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11',)\", 'kwargsrepr': \"{'extended_metadata_collection': False, 'job_id': 11}\", 'origin': 'gen33506@Mac', 'ignore_result': False, 'replaced_task_nesting': 0, 'stamped_headers': None, 'stamps': {}, 'properties': {'correlation_id': 'd6816c97-afc5-4d09-b346-948fabeae7fb', 'reply_to': 'd51dfb2c-37ff-3b8c-989d-ce4fde795da1', 'delivery_mode': 2, 'delivery_info': {'exchange': '', 'routing_key': 'galaxy.external'}, 'priority': 0, 'body_encoding': 'base64', 'delivery_tag': '937e370b-605e-47fc-b7cf-4a08cf1519d6'}, 'reply_to':... kwargs:{})\nuvicorn.access INFO 2026-09-18 00:35:55,948 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51116 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:55,993: INFO/main] Successfully executed Celery task set_job_metadata to set metadata for job set_job_metadata to set metadata for job (51.108 ms)\n[2026-09-18 00:35:55,996: INFO/main] Task galaxy.set_job_metadata[d6816c97-afc5-4d09-b346-948fabeae7fb] succeeded in 0.05529491696506739s: None\nuvicorn.access INFO 2026-09-18 00:35:56,226 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51118 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:56,499 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51120 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:56,775 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51122 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\n[2026-09-18 00:35:56,961: INFO/main] Task galaxy.finish_job[24d1cf9d-656b-4f8f-8058-33ab37074655] received\n[2026-09-18 00:35:56,961: DEBUG/main] TaskPool: Apply (args:('galaxy.finish_job', '24d1cf9d-656b-4f8f-8058-33ab37074655', {'lang': 'py', 'task': 'galaxy.finish_job', 'id': '24d1cf9d-656b-4f8f-8058-33ab37074655', 'shadow': None, 'eta': None, 'expires': None, 'group': None, 'group_index': None, 'retries': 0, 'timelimit': [None, None], 'root_id': 'fcd38944-5d5d-47ba-86ff-ea46a17f4a88', 'parent_id': 'd6816c97-afc5-4d09-b346-948fabeae7fb', 'argsrepr': '()', 'kwargsrepr': '{\\'job_id\\': 11, \\'raw_tool_source\\': \\'\\n \\n \\n operation_0224\\n \\n \\n python \\\\\\'$__tool_directory__/data_fetch.py\\\\\\'\\n --galaxy-root \\\\\\'$GALAXY_ROOT_DIR\\\\\\'\\n --datatypes-registry \\\\\\'$GALAXY_DATATYPES_CONF_FILE\\\\\\'\\n --request-version \\\\\\'$request_version\\\\\\'\\n ... kwargs:{})\n[2026-09-18 00:35:56,976: DEBUG/main] finish(): Moved /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11/outputs/dataset_1c5a4296-cbb5-4821-bdb7-ba0e4a0034ef.dat to /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/files/1/c/5/dataset_1c5a4296-cbb5-4821-bdb7-ba0e4a0034ef.dat\n[2026-09-18 00:35:56,978: DEBUG/main] unnamed outputs [{'__unnamed_outputs': [{'destination': {'type': 'hdas'}, 'elements': [{'name': 'tx2gene.tabular', 'dbkey': '?', 'ext': 'tabular', 'link_data_only': False, 'sources': [], 'hashes': [], 'info': 'uploaded tabular file', 'state': 'ok', 'filename': '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11/working/data_fetch_upload_ynv5kl7n', 'object_id': 11}]}]}]\n[2026-09-18 00:35:56,996: INFO/main] Collecting metrics for Job 11 in /private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp867gdeb8/job_working_directory/000/11\n[2026-09-18 00:35:57,002: DEBUG/main] job_wrapper.finish for job 11 executed (33.284 ms)\n[2026-09-18 00:35:57,002: INFO/main] Successfully executed Celery task finish_job finish_job (39.817 ms)\n[2026-09-18 00:35:57,005: INFO/main] Task galaxy.finish_job[24d1cf9d-656b-4f8f-8058-33ab37074655] succeeded in 0.043228792026638985s: None\nuvicorn.access INFO 2026-09-18 00:35:57,050 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51124 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,060 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51126 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,070 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51128 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,078 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51130 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,085 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51132 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,093 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51134 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,100 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51136 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,106 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51138 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,113 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51140 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,120 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51142 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,127 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51144 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,134 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51146 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,142 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51148 - \"GET /api/jobs/ab426e56a688ed95?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,157 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51150 - \"GET /api/datasets/ab426e56a688ed95?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,165 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51152 - \"GET /api/jobs/d67aa88f27cf1ce3?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,173 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51154 - \"GET /api/datasets/d67aa88f27cf1ce3?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,181 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51156 - \"GET /api/jobs/2cb54babe410fc94?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,189 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51158 - \"GET /api/datasets/2cb54babe410fc94?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,196 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51160 - \"GET /api/jobs/4e0ba31121077773?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,205 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51162 - \"GET /api/datasets/4e0ba31121077773?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,212 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51164 - \"GET /api/jobs/1c80d65d322b105c?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,219 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51166 - \"GET /api/datasets/1c80d65d322b105c?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,227 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51168 - \"GET /api/jobs/99bd1f66aad6c7b5?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,237 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51170 - \"GET /api/datasets/99bd1f66aad6c7b5?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,244 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51172 - \"GET /api/jobs/3e4592b97329669a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,252 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51174 - \"GET /api/datasets/3e4592b97329669a?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,259 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51176 - \"GET /api/jobs/fceaa9d00d78e49d?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,267 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51178 - \"GET /api/datasets/fceaa9d00d78e49d?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,274 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51180 - \"GET /api/jobs/9dfa17f44c905ecf?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,287 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51182 - \"GET /api/datasets/9dfa17f44c905ecf?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,294 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51184 - \"GET /api/jobs/4e5a7135364a358a?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,303 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51186 - \"GET /api/datasets/4e5a7135364a358a?hda_ldda=hda HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,311 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51188 - \"GET /api/jobs/ee96573fcbe71150?full=True HTTP/1.1\" 200\nuvicorn.access INFO 2026-09-18 00:35:57,318 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51190 - \"GET /api/datasets/ee96573fcbe71150?hda_ldda=hda HTTP/1.1\" 200\ngalaxy.workflow.run_request INFO 2026-09-18 00:35:57,349 [pN:main.1,p:33541,tN:AnyIO worker thread] Creating a step_state for step.id 3\ngalaxy.workflow.run_request INFO 2026-09-18 00:35:57,350 [pN:main.1,p:33541,tN:AnyIO worker thread] Creating a step_state for step.id 4\ngalaxy.workflow.run_request INFO 2026-09-18 00:35:57,350 [pN:main.1,p:33541,tN:AnyIO worker thread] Creating a step_state for step.id 5\ngalaxy.workflow.run_request INFO 2026-09-18 00:35:57,350 [pN:main.1,p:33541,tN:AnyIO worker thread] Creating a step_state for step.id 6\ngalaxy.workflow.run_request INFO 2026-09-18 00:35:57,351 [pN:main.1,p:33541,tN:AnyIO worker thread] Creating a step_state for step.id 1\ngalaxy.workflow.run_request INFO 2026-09-18 00:35:57,351 [pN:main.1,p:33541,tN:AnyIO worker thread] Creating a step_state for step.id 2\ngalaxy.web_stack.handlers INFO 2026-09-18 00:35:57,351 [pN:main.1,p:33541,tN:AnyIO worker thread] (WorkflowInvocation[unflushed]) Handler '_default_' assigned using 'HANDLER_ASSIGNMENT_METHODS.DB_TRANSACTION_ISOLATION' assignment method\nuvicorn.access INFO 2026-09-18 00:35:57,362 [pN:main.1,p:33541,tN:MainThread] 127.0.0.1:51192 - \"POST /api/workflows/ab426e56a688ed95/invocations HTTP/1.1\" 200\n", "start_datetime": "2026-09-18T00:35:07.767366", "status": "success" }, "doc": "Test outline for Ebola Virus Infection RNA-seq Analysis (A549 WT vs PTPN13-KO)", "has_data": true, "id": "galaxy-workflow.gxwf.yml_0", "test_type": "galaxy_workflow" } ], "version": "0.1" }