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Updating anvil-edge README for edge-24-08-31-18-14-1
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7 changes: 7 additions & 0 deletions
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reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/chunk.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| { | ||
| "11": { | ||
| "run1": "https://htmlpreview.github.io/?https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/results.html", | ||
| "date1": "Sat Aug 31 18:29:37 2024", | ||
| "tools": "https://github.com/anvilproject/galaxy-tests/blob/main/reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/tools.yml" | ||
| } | ||
| } |
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reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/chunk.txt
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| -t datamash_ops --tool-version 746e8e4bf929 | ||
| -t deeptools_plot_pca --tool-version 69264da0ce77 | ||
| -t seq_filter_by_id --tool-version 141612f8c3e3 | ||
| -t bwameth --tool-version 29bdbc353f20 | ||
| -t medaka_consensus --tool-version db25ec99c3ea | ||
| -t poretools_nucdist --tool-version a57b6350fd5d | ||
| -t rseqc --tool-version 1a052c827e88 | ||
| -t rseqc --tool-version dbedfc5f5a3c | ||
| -t samtools_fastx --tool-version a8d69aee190e | ||
| -t samtools_slice_bam --tool-version a4a10c7924d1 | ||
| -t anndata_inspect --tool-version 688357ad5e61 | ||
| -t anndata_inspect --tool-version 286a24ac079c | ||
| -t anndata_inspect --tool-version ee98d611afc6 | ||
| -t scater_create_qcmetric_ready_sce --tool-version 8f333f90d8d6 | ||
| -t scater_create_qcmetric_ready_sce --tool-version fd808de478b1 | ||
| -t gtf2gene_list --tool-version 1a642de6db01 | ||
| -t scanpy_run_umap --tool-version 0f98603d0116 | ||
| -t scanpy_run_umap --tool-version abae3d11d920 | ||
| -t text_processing --tool-version ddf54b12c295 | ||
| -t text_processing --tool-version 9ff72e942410 | ||
| -t lofreq_alnqual --tool-version 09d6e4693887 | ||
| -t bcftools_plugin_missing2ref --tool-version dfef7a353ed0 | ||
| -t bcftools_merge --tool-version e03f2f3ac3a9 | ||
| -t vcfannotategenotypes --tool-version 84959112d9a6 | ||
| -t vcfsort --tool-version f0580efedada | ||
| -t ivar_variants --tool-version f95f403841ad |
68 changes: 68 additions & 0 deletions
68
reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/errors/05f70b9d3d210140.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "05f70b9d3d210140", | ||
| "history_id": "42754f3568e7f6b9", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-08-31T19:05:35.476801", | ||
| "update_time": "2024-08-31T19:05:42.293515", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-k6x9g", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "cat '/galaxy/server/database/jobs_directory/000/137/configs/tmpnvdhffmc' && python '/galaxy/server/database/jobs_directory/000/137/configs/tmpnvdhffmc'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"h5ad\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "inspect": "{\"__current_case__\": 5, \"info\": \"uns\", \"uns_info\": \"rank_genes_groups\"}" | ||
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| "src": "hda", | ||
| "uuid": "aee0fc11-eb45-4347-998f-3a4c44b87f18" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "uns_rank_genes_groups_names": { | ||
| "id": "a9a2e33c8a994588", | ||
| "src": "hda", | ||
| "uuid": "deef86e1-9053-4ae2-a2fa-636afe74d314" | ||
| }, | ||
| "uns_rank_genes_groups_scores": { | ||
| "id": "5f9fad671a92ddab", | ||
| "src": "hda", | ||
| "uuid": "4fe47765-d092-4096-a7d0-71640f60d89b" | ||
| }, | ||
| "uns_rank_genes_groups_logfoldchanges": { | ||
| "id": "7adcf7c440bbb359", | ||
| "src": "hda", | ||
| "uuid": "b8a161bc-4378-4809-b876-91da9045bb4b" | ||
| }, | ||
| "uns_rank_genes_groups_pvals": { | ||
| "id": "6d5d503bc4fa0801", | ||
| "src": "hda", | ||
| "uuid": "14f71f6d-a8f7-4f0c-a23d-7cc2eb565914" | ||
| }, | ||
| "uns_rank_genes_groups_pvals_adj": { | ||
| "id": "dbcc7bff40ef4bcf", | ||
| "src": "hda", | ||
| "uuid": "4e4da96a-eed1-4029-b3de-e9b091ba87e0" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "\n\nimport anndata as ad\n \n \nimport pandas as pd\nfrom scipy import io\n\npd.options.display.precision = 15\n\nadata = ad.read('/galaxy/server/database/objects/a/e/e/dataset_aee0fc11-eb45-4347-998f-3a4c44b87f18.dat')\n\npd.DataFrame(adata.uns['rank_genes_groups']['logfoldchanges']).to_csv(\"/galaxy/server/database/objects/b/8/a/dataset_b8a161bc-4378-4809-b876-91da9045bb4b.dat\", sep=\"\\t\", index = False)\npd.DataFrame(adata.uns['rank_genes_groups']['names']).to_csv(\"/galaxy/server/database/objects/d/e/e/dataset_deef86e1-9053-4ae2-a2fa-636afe74d314.dat\", sep=\"\\t\", index = False)\npd.DataFrame(adata.uns['rank_genes_groups']['pvals']).to_csv(\"/galaxy/server/database/objects/1/4/f/dataset_14f71f6d-a8f7-4f0c-a23d-7cc2eb565914.dat\", sep=\"\\t\", index = False)\npd.DataFrame(adata.uns['rank_genes_groups']['pvals_adj']).to_csv(\"/galaxy/server/database/objects/4/e/4/dataset_4e4da96a-eed1-4029-b3de-e9b091ba87e0.dat\", sep=\"\\t\", index = False)\npd.DataFrame(adata.uns['rank_genes_groups']['scores']).to_csv(\"/galaxy/server/database/objects/4/f/e/dataset_4fe47765-d092-4096-a7d0-71640f60d89b.dat\", sep=\"\\t\", index = False)\n\n", | ||
| "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "\n\nimport anndata as ad\n \n \nimport pandas as pd\nfrom scipy import io\n\npd.options.display.precision = 15\n\nadata = ad.read('/galaxy/server/database/objects/a/e/e/dataset_aee0fc11-eb45-4347-998f-3a4c44b87f18.dat')\n\npd.DataFrame(adata.uns['rank_genes_groups']['logfoldchanges']).to_csv(\"/galaxy/server/database/objects/b/8/a/dataset_b8a161bc-4378-4809-b876-91da9045bb4b.dat\", sep=\"\\t\", index = False)\npd.DataFrame(adata.uns['rank_genes_groups']['names']).to_csv(\"/galaxy/server/database/objects/d/e/e/dataset_deef86e1-9053-4ae2-a2fa-636afe74d314.dat\", sep=\"\\t\", index = False)\npd.DataFrame(adata.uns['rank_genes_groups']['pvals']).to_csv(\"/galaxy/server/database/objects/1/4/f/dataset_14f71f6d-a8f7-4f0c-a23d-7cc2eb565914.dat\", sep=\"\\t\", index = False)\npd.DataFrame(adata.uns['rank_genes_groups']['pvals_adj']).to_csv(\"/galaxy/server/database/objects/4/e/4/dataset_4e4da96a-eed1-4029-b3de-e9b091ba87e0.dat\", sep=\"\\t\", index = False)\npd.DataFrame(adata.uns['rank_genes_groups']['scores']).to_csv(\"/galaxy/server/database/objects/4/f/e/dataset_4fe47765-d092-4096-a7d0-71640f60d89b.dat\", sep=\"\\t\", index = False)\n\n", | ||
| "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/errors/3fccce1e5ef7dc54.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "3fccce1e5ef7dc54", | ||
| "history_id": "42754f3568e7f6b9", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-08-31T19:24:48.476536", | ||
| "update_time": "2024-08-31T19:24:58.002547", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-7qczv", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/221/registry.xml' '/galaxy/server/database/jobs_directory/000/221/upload_params.json' '299:/galaxy/server/database/objects/9/7/1/dataset_971d97b9-ee7e-4481-a6a4-21a6461a810d_files:/galaxy/server/database/objects/9/7/1/dataset_971d97b9-ee7e-4481-a6a4-21a6461a810d.dat'", | ||
| "user_email": "tests@fake.org", | ||
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| "params": { | ||
| "paramfile": "\"/galaxy/server/database/tmp/upload_params_ff0m315i\"", | ||
| "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"merge.4.a.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_o7uamdpr\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"vcf\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "4941c51fb0d278e8", | ||
| "src": "hda", | ||
| "uuid": "971d97b9-ee7e-4481-a6a4-21a6461a810d" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
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| "job_stderr": null, | ||
| "stdout": "", | ||
| "stderr": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/errors/4792aab3e3e68708.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "4792aab3e3e68708", | ||
| "history_id": "42754f3568e7f6b9", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-08-31T19:17:27.460665", | ||
| "update_time": "2024-08-31T19:17:38.815385", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-7rrqd", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/182/registry.xml' '/galaxy/server/database/jobs_directory/000/182/upload_params.json' '260:/galaxy/server/database/objects/d/7/0/dataset_d70a6fad-cf42-403e-8cbc-7ff3897bc9fa_files:/galaxy/server/database/objects/d/7/0/dataset_d70a6fad-cf42-403e-8cbc-7ff3897bc9fa.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
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| "files_metadata": "{\"__current_case__\": 708, \"file_type\": \"auto\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
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| "file_count": "\"auto\"", | ||
| "file_type": "\"auto\"" | ||
| }, | ||
| "inputs": {}, | ||
| "outputs": { | ||
| "output0": { | ||
| "id": "668e51a8ddbcc2e6", | ||
| "src": "hda", | ||
| "uuid": "d70a6fad-cf42-403e-8cbc-7ff3897bc9fa" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "", | ||
| "tool_stderr": "", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "", | ||
| "stderr": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
45 changes: 45 additions & 0 deletions
45
reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/errors/47bda04bd1ba0aca.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,45 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "47bda04bd1ba0aca", | ||
| "history_id": "42754f3568e7f6b9", | ||
| "tool_id": "upload1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-08-31T19:24:04.176940", | ||
| "update_time": "2024-08-31T19:24:14.981952", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-dscls", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "python '/galaxy/server/database/tools/data_source/upload.py' '/galaxy/server' '/galaxy/server/database/jobs_directory/000/216/registry.xml' '/galaxy/server/database/jobs_directory/000/216/upload_params.json' '294:/galaxy/server/database/objects/2/2/e/dataset_22e10a34-0d21-431c-85b6-c57a5f085d4c_files:/galaxy/server/database/objects/2/2/e/dataset_22e10a34-0d21-431c-85b6-c57a5f085d4c.dat'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
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| "files_metadata": "{\"__current_case__\": 342, \"file_type\": \"vcf\"}", | ||
| "dbkey": "\"?\"", | ||
| "force_composite": "\"false\"", | ||
| "files": "[{\"NAME\": \"merge.2.a.vcf\", \"__index__\": 0, \"auto_decompress\": \"Yes\", \"dbkey\": \"\", \"file_data\": \"/galaxy/server/database/tmp/upload_file_data_m2ojatwg\", \"file_type\": \"\", \"ftp_files\": null, \"space_to_tab\": null, \"to_posix_lines\": \"Yes\", \"url_paste\": null, \"uuid\": null}]", | ||
| "file_count": "\"auto\"", | ||
| "file_type": "\"vcf\"" | ||
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| "inputs": {}, | ||
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| "output0": { | ||
| "id": "e3277c38cc450a3b", | ||
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| "uuid": "22e10a34-0d21-431c-85b6-c57a5f085d4c" | ||
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| "dependencies": [], | ||
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| } |
48 changes: 48 additions & 0 deletions
48
reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/errors/54c9b5a658b55aba.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "54c9b5a658b55aba", | ||
| "history_id": "42754f3568e7f6b9", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/samtools_slice_bam/samtools_slice_bam/2.0.1", | ||
| "state": "error", | ||
| "exit_code": null, | ||
| "create_time": "2024-08-31T18:51:46.671041", | ||
| "update_time": "2024-08-31T18:51:52.612178", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-59b5j", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "ln -s '/galaxy/server/database/objects/b/3/0/dataset_b30ed270-42d6-405d-ae94-6f9e851269b7.dat' temp_input.bam && ln -s '/galaxy/server/database/objects/_metadata_files/e/b/1/metadata_eb10331b-31d0-4b70-a72e-1d9e25b49e81.dat' temp_input.bam.bai && samtools view -@ ${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam \"chrM\" && samtools sort -O bam -T sorted -@ ${GALAXY_SLOTS:-1} -o '/galaxy/server/database/objects/c/5/2/dataset_c52783b6-902d-414c-88ba-67ec6bf0699b.dat' unsorted_output.bam", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"bam\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "slice_method": "{\"__current_case__\": 1, \"refs\": \"chrM\", \"slice_method_selector\": \"chr\"}" | ||
| }, | ||
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| "id": "af7a0a1c2f849bdf", | ||
| "src": "hda", | ||
| "uuid": "b30ed270-42d6-405d-ae94-6f9e851269b7" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "output_bam": { | ||
| "id": "edcb10450d886174", | ||
| "src": "hda", | ||
| "uuid": "c52783b6-902d-414c-88ba-67ec6bf0699b" | ||
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| "copied_from_job_id": null, | ||
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| "tool_stdout": "", | ||
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| "stdout": "", | ||
| "stderr": "", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
48 changes: 48 additions & 0 deletions
48
reports/anvil-edge/tool-tests/edge-24-08-31-18-14-1/errors/5aeb7a388ee67e41.json
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Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| { | ||
| "model_class": "Job", | ||
| "id": "5aeb7a388ee67e41", | ||
| "history_id": "42754f3568e7f6b9", | ||
| "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/anndata_inspect/anndata_inspect/0.7.5+galaxy1", | ||
| "state": "error", | ||
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| "create_time": "2024-08-31T19:00:49.573554", | ||
| "update_time": "2024-08-31T19:00:55.377048", | ||
| "galaxy_version": "24.1", | ||
| "external_id": "gxy-dbxv4", | ||
| "handler": null, | ||
| "job_runner_name": null, | ||
| "command_line": "cat '/galaxy/server/database/jobs_directory/000/118/configs/tmp4kthkkxk' && python '/galaxy/server/database/jobs_directory/000/118/configs/tmp4kthkkxk'", | ||
| "user_email": "tests@fake.org", | ||
| "command_version": null, | ||
| "params": { | ||
| "__input_ext": "\"h5ad\"", | ||
| "dbkey": "\"?\"", | ||
| "chromInfo": "\"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len\"", | ||
| "inspect": "{\"__current_case__\": 7, \"info\": \"varm\", \"varm_info\": \"PCs\"}" | ||
| }, | ||
| "inputs": { | ||
| "input": { | ||
| "id": "a55a27d6a4e40c5a", | ||
| "src": "hda", | ||
| "uuid": "ff3cdd74-6ea0-447c-b630-a972220254d3" | ||
| } | ||
| }, | ||
| "outputs": { | ||
| "varm_PCs": { | ||
| "id": "4792aab3e3e68708", | ||
| "src": "hda", | ||
| "uuid": "ab578fc1-44b6-4d67-bad8-3e442bb9cf78" | ||
| } | ||
| }, | ||
| "copied_from_job_id": null, | ||
| "output_collections": {}, | ||
| "tool_stdout": "\n\nimport anndata as ad\n \n \nimport pandas as pd\nfrom scipy import io\n\npd.options.display.precision = 15\n\nadata = ad.read('/galaxy/server/database/objects/f/f/3/dataset_ff3cdd74-6ea0-447c-b630-a972220254d3.dat')\n\npd.DataFrame(adata.varm['PCs']).to_csv(\"/galaxy/server/database/objects/a/b/5/dataset_ab578fc1-44b6-4d67-bad8-3e442bb9cf78.dat\", sep=\"\\t\", index = False)\n\n", | ||
| "tool_stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", | ||
| "job_stdout": null, | ||
| "job_stderr": null, | ||
| "stdout": "\n\nimport anndata as ad\n \n \nimport pandas as pd\nfrom scipy import io\n\npd.options.display.precision = 15\n\nadata = ad.read('/galaxy/server/database/objects/f/f/3/dataset_ff3cdd74-6ea0-447c-b630-a972220254d3.dat')\n\npd.DataFrame(adata.varm['PCs']).to_csv(\"/galaxy/server/database/objects/a/b/5/dataset_ab578fc1-44b6-4d67-bad8-3e442bb9cf78.dat\", sep=\"\\t\", index = False)\n\n", | ||
| "stderr": "Observation names are not unique. To make them unique, call `.obs_names_make_unique`.\n", | ||
| "job_messages": null, | ||
| "dependencies": [], | ||
| "job_metrics": [] | ||
| } |
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