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Updating anvil-production README for prod-24-12-31-12-34-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "3": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/results.html", | ||
| "date1": "Tue Dec 31 12:50:39 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| -t split_file_to_collection --tool-version 6cbe2f30c2d7 | ||
| -t reshape2_melt --tool-version 317ed0ee8bf2 | ||
| -t fasta_compute_length --tool-version 7d37cfda8e00 | ||
| -t bamtools --tool-version 4d343c1f606b | ||
| -t samtools_idxstats --tool-version 7a6034296ae9 | ||
| -t bcftools_gtcheck --tool-version 672b6c02fbc7 | ||
| -t bcftools_reheader --tool-version 9ef52d95114b | ||
| -t bcftools_plugin_tag2tag --tool-version bdfdf5f6e950 | ||
| -t vcfgenotypes --tool-version a60ae8af21a1 | ||
| -t flye --tool-version 3ee0ef312022 | ||
| -t poretools_tabular --tool-version 2cb2feb94f0e | ||
| -t deeptools_multi_bigwig_summary --tool-version 3c9f0c486cca | ||
| -t unicycler --tool-version 9e3e80cc4ad4 | ||
| -t ivar_removereads --tool-version ee2beb764a7b | ||
| -t hisat2 --tool-version 26371a1df031 |
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reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/errors/0a1a961a801ca0a4.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "0a1a961a801ca0a4", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-12-31T13:07:25.930251", | ||
| "create_time": "2024-12-31T13:07:07.929525", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "95dd2429516525a4", | ||
| "external_id": "gxy-jfx6d", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/74/registry.xml' '/galaxy/server/database/jobs_directory/000/74/upload_params.json' '116:/galaxy/server/database/objects/9/e/0/dataset_9e0797b2-a08b-43f2-b8b7-500e3ddedafb_files:/galaxy/server/database/objects/9/e/0/dataset_9e0797b2-a08b-43f2-b8b7-500e3ddedafb.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_tz1xxcll\"", | ||
| "files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"ecoli_05.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_7uqim3b5\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"fastq.gz\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "a04a7b0bd34a37e5", | ||
| "src": "hda", | ||
| "uuid": "9e0797b2-a08b-43f2-b8b7-500e3ddedafb" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
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47
reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/errors/2349a9c060cdec3b.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "2349a9c060cdec3b", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-12-31T13:00:21.380150", | ||
| "create_time": "2024-12-31T13:00:10.004290", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/fasta_compute_length/1.0.4", | ||
| "history_id": "95dd2429516525a4", | ||
| "external_id": "gxy-dcs56", | ||
| "command_line": "python '/cvmfs/cloud.galaxyproject.org/tools/toolshed.g2.bx.psu.edu/repos/devteam/fasta_compute_length/5cbde03c1103/fasta_compute_length/fasta_compute_length.py' '/galaxy/server/database/objects/d/7/6/dataset_d76ace8d-9133-498b-aa43-fa4c0e862fe0.dat' '/galaxy/server/database/objects/b/7/1/dataset_b7100fc5-e808-4833-b97b-8e30a9e26dee.dat' 0 id_and_desc", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "ref": "{\"__current_case__\": 0, \"input\": {\"values\": [{\"id\": 79, \"src\": \"hda\"}]}, \"keep_first\": \"0\", \"keep_first_word\": false, \"ref_source\": \"history\"}" | ||
| }, | ||
| "inputs": { | ||
| "ref|input": { | ||
| "id": "211d208b0d360e57", | ||
| "src": "hda", | ||
| "uuid": "d76ace8d-9133-498b-aa43-fa4c0e862fe0" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output": { | ||
| "id": "3089e669ca433774", | ||
| "src": "hda", | ||
| "uuid": "b7100fc5-e808-4833-b97b-8e30a9e26dee" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
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reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/errors/251a6a71cd75b040.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "251a6a71cd75b040", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-12-31T13:13:07.614998", | ||
| "create_time": "2024-12-31T13:12:56.738414", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "95dd2429516525a4", | ||
| "external_id": "gxy-tc6mv", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/108/registry.xml' '/galaxy/server/database/jobs_directory/000/108/upload_params.json' '159:/galaxy/server/database/objects/2/2/a/dataset_22a6a45e-10b0-4f16-905a-537d6fbf2b6a_files:/galaxy/server/database/objects/2/2/a/dataset_22a6a45e-10b0-4f16-905a-537d6fbf2b6a.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_q9c6j07p\"", | ||
| "files_metadata": "{\"__current_case__\": 79, \"file_type\": \"fastq.gz\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"ecoli_hifi_03.fastq.gz\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_qun_y7ee\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"fastq.gz\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "f7267778d42d9305", | ||
| "src": "hda", | ||
| "uuid": "22a6a45e-10b0-4f16-905a-537d6fbf2b6a" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
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reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/errors/34c72ddbc8041772.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "34c72ddbc8041772", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-12-31T13:51:11.052670", | ||
| "create_time": "2024-12-31T13:51:03.907036", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1", | ||
| "history_id": "95dd2429516525a4", | ||
| "external_id": "gxy-brfb2", | ||
| "command_line": "set -o pipefail; ln -s '/galaxy/server/database/objects/4/8/8/dataset_488c234e-c22b-4cff-bd8c-203d005e7484.dat' genome.fa && hisat2-build -p ${GALAXY_SLOTS:-1} genome.fa genome && seqtk seq -1 '/galaxy/server/database/objects/c/7/9/dataset_c7917917-e2af-4216-b945-e13145b07444.dat' > input_f.fastq && seqtk seq -2 '/galaxy/server/database/objects/c/7/9/dataset_c7917917-e2af-4216-b945-e13145b07444.dat' > input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1 input_f.fastq -2 input_r.fastq | samtools sort --no-PG -l 0 -T \"${TMPDIR:-.}\" -O bam | samtools view --no-PG -O bam -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/1/2/d/dataset_12d88b2b-6069-4052-9cf8-d8fa37501716.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "adv": "{\"alignment_options\": {\"__current_case__\": 0, \"alignment_options_selector\": \"defaults\"}, \"input_options\": {\"__current_case__\": 0, \"input_options_selector\": \"defaults\"}, \"other_options\": {\"__current_case__\": 0, \"other_options_selector\": \"defaults\"}, \"output_options\": {\"__current_case__\": 0, \"output_options_selector\": \"defaults\"}, \"reporting_options\": {\"__current_case__\": 0, \"reporting_options_selector\": \"defaults\"}, \"sam_options\": {\"__current_case__\": 0, \"sam_options_selector\": \"defaults\"}, \"scoring_options\": {\"__current_case__\": 0, \"scoring_options_selector\": \"defaults\"}, \"spliced_options\": {\"__current_case__\": 0, \"spliced_options_selector\": \"defaults\"}}", | ||
| "sum": "{\"new_summary\": false, \"summary_file\": false}", | ||
| "library": "{\"__current_case__\": 3, \"input_1\": {\"values\": [{\"id\": 317, \"src\": \"hda\"}]}, \"paired_options\": {\"__current_case__\": 0, \"paired_options_selector\": \"defaults\"}, \"rna_strandness\": \"\", \"type\": \"paired_interleaved\"}", | ||
| "reference_genome": "{\"__current_case__\": 1, \"history_item\": {\"values\": [{\"id\": 316, \"src\": \"hda\"}]}, \"source\": \"history\"}" | ||
| }, | ||
| "inputs": { | ||
| "reference_genome|history_item": { | ||
| "id": "390450121c94ef76", | ||
| "src": "hda", | ||
| "uuid": "488c234e-c22b-4cff-bd8c-203d005e7484" | ||
| }, | ||
| "library|input_1": { | ||
| "id": "4b180e9cfc6d438d", | ||
| "src": "hda", | ||
| "uuid": "c7917917-e2af-4216-b945-e13145b07444" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_alignments": { | ||
| "id": "35e6c3c6865d2c86", | ||
| "src": "hda", | ||
| "uuid": "12d88b2b-6069-4052-9cf8-d8fa37501716" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
44 changes: 44 additions & 0 deletions
44
reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/errors/4c4dfe02f57d6a77.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "4c4dfe02f57d6a77", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-12-31T12:54:49.312863", | ||
| "create_time": "2024-12-31T12:54:39.568177", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "upload1", | ||
| "history_id": "95dd2429516525a4", | ||
| "external_id": "gxy-tstrg", | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/13/registry.xml' '/galaxy/server/database/jobs_directory/000/13/upload_params.json' '42:/galaxy/server/database/objects/7/b/2/dataset_7b2a2a21-f086-4507-9d26-59a2d2bfaa2e_files:/galaxy/server/database/objects/7/b/2/dataset_7b2a2a21-f086-4507-9d26-59a2d2bfaa2e.dat'", | ||
| "traceback": null, | ||
| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_mjon3utm\"", | ||
| "files_metadata": "{\"__current_case__\": 205, \"file_type\": \"mgf\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"demo758Dacentroid.mgf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_2lg15zp4\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"mgf\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "9847d4d86c82517d", | ||
| "src": "hda", | ||
| "uuid": "7b2a2a21-f086-4507-9d26-59a2d2bfaa2e" | ||
| } | ||
| }, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
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reports/anvil-production/tool-tests/prod-24-12-31-12-34-1/errors/5a21c288eacf40f7.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,82 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "5a21c288eacf40f7", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "update_time": "2024-12-31T13:36:31.882457", | ||
| "create_time": "2024-12-31T13:33:41.598669", | ||
| "galaxy_version": "23.1", | ||
| "command_version": null, | ||
| "copied_from_job_id": null, | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.5.1+galaxy0", | ||
| "history_id": "95dd2429516525a4", | ||
| "external_id": "gxy-b98kx", | ||
| "command_line": "ln -s '/galaxy/server/database/objects/5/7/d/dataset_57de3c51-f1e2-4519-b452-6d28c9657528.dat' fq1.fastq && ln -s '/galaxy/server/database/objects/b/5/f/dataset_b5ff3a53-49fa-493d-aebd-13b5385da7c0.dat' fq2.fastq && ln -s '/galaxy/server/database/objects/6/8/e/dataset_68ec68fa-59ef-4c5e-97e7-f61630eafe85.dat' 'lr.fasta' && unicycler -t \"${GALAXY_SLOTS:-4}\" -o ./ --verbosity 3 -1 'fq1.fastq' -2 'fq2.fastq' -l lr.fasta --mode 'normal' --min_fasta_length '100' --linear_seqs '0' --min_kmer_frac '0.2' --max_kmer_frac '0.95' --kmer_count '10' --depth_filter '0.25' --start_gene_id '90.0' --start_gene_cov '95.0' --min_component_size '1000' --min_dead_end_size '1000' --scores '3,-6,-5,-2' --keep 2 && mkdir 'spades_graphs' && mv 00*gfa './spades_graphs/' && samtools view -@ \"${GALAXY_SLOTS:-4}\" -u 'read_alignment/long_read_alignments.sam' | samtools sort -@ \"${GALAXY_SLOTS:-4}\" -o 'read_alignment/long_read_alignments.bam'", | ||
| "traceback": null, | ||
| "params": { | ||
| "__input_ext": "\"input\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "reuse": "[]", | ||
| "keep": "\"2\"", | ||
| "lr_align": "{\"contamination\": null, \"low_score\": \"\", \"no_simple_bridges\": false, \"scores\": \"3,-6,-5,-2\"}", | ||
| "graph_clean": "{\"min_component_size\": \"1000\", \"min_dead_end_size\": \"1000\"}", | ||
| "rotation": "{\"no_rotate\": false, \"start_gene_cov\": \"95.0\", \"start_gene_id\": \"90.0\", \"start_genes\": null}", | ||
| "spades": "{\"depth_filter\": \"0.25\", \"kmer_count\": \"10\", \"kmers\": \"\", \"largest_component\": false, \"max_kmer_frac\": \"0.95\", \"min_kmer_frac\": \"0.2\"}", | ||
| "min_anchor_seg_len": "\"\"", | ||
| "linear_seqs": "\"0\"", | ||
| "min_fasta_length": "\"100\"", | ||
| "mode": "\"normal\"", | ||
| "paired_unpaired": "{\"__current_case__\": 0, \"fastq_input1\": {\"values\": [{\"id\": 244, \"src\": \"hda\"}]}, \"fastq_input2\": {\"values\": [{\"id\": 245, \"src\": \"hda\"}]}, \"fastq_input_selector\": \"paired\"}" | ||
| }, | ||
| "inputs": { | ||
| "paired_unpaired|fastq_input1": { | ||
| "id": "d3a4ba506822f4dc", | ||
| "src": "hda", | ||
| "uuid": "57de3c51-f1e2-4519-b452-6d28c9657528" | ||
| }, | ||
| "paired_unpaired|fastq_input2": { | ||
| "id": "3eac1656bc31345a", | ||
| "src": "hda", | ||
| "uuid": "b5ff3a53-49fa-493d-aebd-13b5385da7c0" | ||
| }, | ||
| "long": { | ||
| "id": "a95d6ae61b1d3e23", | ||
| "src": "hda", | ||
| "uuid": "68ec68fa-59ef-4c5e-97e7-f61630eafe85" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "assembly_graph": { | ||
| "id": "1295adfd292a4453", | ||
| "src": "hda", | ||
| "uuid": "a0068cb7-0aa4-4c0d-ae8a-13f3e0b02271" | ||
| }, | ||
| "assembly": { | ||
| "id": "3f039bef8436fd70", | ||
| "src": "hda", | ||
| "uuid": "32133e34-12d0-452e-994a-962950bc0a14" | ||
| }, | ||
| "bam_file": { | ||
| "id": "d6499f9dfb496684", | ||
| "src": "hda", | ||
| "uuid": "2835e0d0-cad1-4431-971f-10dcf9761841" | ||
| } | ||
| }, | ||
| "output_collections": { | ||
| "spades_collection": { | ||
| "id": "5cacb9183a040f53", | ||
| "src": "hdca" | ||
| } | ||
| }, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stderr": "", | ||
| "stdout": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "user_email": "tests@fake.org", | ||
| "job_metrics": [] | ||
| } |
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