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broadinstitute / PANOPLY

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
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Following tutorial with V1.3, run_panda() does not populate data #42

Closed sooheon closed 5 months ago

sooheon commented 6 months ago

Followed tutorial at https://github.com/broadinstitute/PANOPLY/wiki/PANOPLY-Tutorial step by step, the only change being to use PANOPLY_Production_Pipelines_v1_3 workspace and broadcptac/panda:1_3 as the VM image. At the end of the run, the Data tab looks like the following, only sample_set table generated, and no data populated.

image

It does not take a few hours, as the tutorial notes, but finishes within a minute or two.

wcorinne commented 6 months ago

The PANOPLY v1_4 release— which has now been made public— contains a number of Startup-Notebook patches. If the same issue still occurs in a v1_4 workspace, we can troubleshoot further with the logfile, which can be accessed from the terminal: image The logfile can be copied from the notebook VM to the workspace Data File folder with the following command: gsutil cp $WORKSPACE_NAME/edit/runspace/logfile_mn.txt $WORKSPACE_BUCKET

image image

Also, the shorter runtime of run_panda() is normal and should only take 5-10 minutes to complete successfully. The function was heavily re-optimized after v1_2, cutting the runtime from a few hours to a few minutes-- but the tutorial documentation still reflects v1_0.

sooheon commented 6 months ago

I've now tried with published V1_4, and sample_set is populated (though not multiple tables as indicated in tutorial, I assume this is due to version difference?)

However, moving on to the workflow, all 5 tasks in panoply_main failed.

workflow level failures image

Execution log: workflow.151a5dfa-f5b2-478a-bf0f-be053843e850.log

panoply_rna_protein_correlation.log: ``` 2024/03/22 16:03:10 Starting container setup. 2024/03/22 16:03:11 Done container setup. 2024/03/22 16:03:13 Starting localization. 2024/03/22 16:03:26 Localization script execution started... 2024/03/22 16:03:26 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_rna_protein_correlation/script -> /cromwell_root/script 2024/03/22 16:03:30 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml 2024/03/22 16:03:31 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/rna-subset.gct -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/rna-subset.gct 2024/03/22 16:03:31 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct Copying gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/rna-subset.gct to file:///cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/rna-subset.gct Copying gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct to file:///cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct .. Average throughput: 135.1MiB/s 2024/03/22 16:03:33 Localization script execution complete. 2024/03/22 16:03:39 Done localization. 2024/03/22 16:03:40 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash broadcptac/panoply_rna_protein_correlation@sha256:8db7abb9fd4a43be0c233e885e7b9a38b2cdab5390426a543a03e0b120ce4a14 /cromwell_root/script NULL NULL Error in source("config.r") : config.r:300:1: unexpected '}' 299: min.numratio <- 300: } ^ Execution halted 2024/03/22 16:03:43 Starting delocalization. 2024/03/22 16:03:43 Delocalization script execution started... 2024/03/22 16:03:43 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_rna_protein_correlation/memory_retry_rc 2024/03/22 16:03:46 Delocalizing output /cromwell_root/rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_rna_protein_correlation/rc 2024/03/22 16:03:47 Delocalizing output /cromwell_root/stdout -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_rna_protein_correlation/stdout 2024/03/22 16:03:49 Delocalizing output /cromwell_root/stderr -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_rna_protein_correlation/stderr 2024/03/22 16:03:50 Delocalizing output /cromwell_root/panoply_rna_protein_correlation-output.tar -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_rna_protein_correlation/panoply_rna_protein_correlation-output.tar Required file output '/cromwell_root/panoply_rna_protein_correlation-output.tar' does not exist. ```
subsea_rna.log 2024/03/22 16:02:42 Starting container setup. 2024/03/22 16:02:43 Done container setup. 2024/03/22 16:02:44 Starting localization. 2024/03/22 16:02:52 Localization script execution started... 2024/03/22 16:02:52 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_rna/script -> /cromwell_root/script 2024/03/22 16:02:55 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/rna-subset.gct -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/rna-subset.gct 2024/03/22 16:02:56 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml 2024/03/22 16:02:56 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt Copying gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml to file:///cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml Copying gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt to file:///cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt Average throughput: 9.8MiB/s 2024/03/22 16:02:58 Localization script execution complete. 2024/03/22 16:03:02 Done localization. 2024/03/22 16:03:03 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash broadcptac/panoply_ssgsea@sha256:5bdb529bb513f986dd0786ade226e13a2e71b65b06abffd583803851861448f9 /cromwell_root/script parsing command line parameters: ------------------------------------------------------------ --- gct_str /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/rna-subset.gct ; prefer yaml? FALSE --- level gc ; prefer yaml? FALSE --- id_type NA ; prefer yaml? TRUE --- id_type_out NA ; prefer yaml? TRUE --- acc_type_in NA ; prefer yaml? TRUE --- seqwin_column NA ; prefer yaml? TRUE --- gene_symbol_column NA ; prefer yaml? TRUE --- humanize_gene_names NA ; prefer yaml? TRUE --- sgt_column NA ; prefer yaml? TRUE --- localized NA ; prefer yaml? TRUE --- mode NA ; prefer yaml? TRUE --- residue NA ; prefer yaml? TRUE --- ptm NA ; prefer yaml? TRUE --- preprocess_gct NA ; prefer yaml? TRUE --- libdir /home/pgdac/src ; prefer yaml? FALSE --- yaml_file /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml ; prefer yaml? FALSE --- help FALSE ; prefer yaml? FALSE Updating parameter file with command line parameters: ------------------------------------------------------------ level : gc -> gc ------------------------------------------------------------ importing gct file: /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/rna-subset.gct ... parsing as GCT v1.3 /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/rna-subset.gct 15800 rows, 77 cols, 1 row descriptors, 13 col descriptors Error in if (humanize.gene.names) genes <- toupper(genes) : argument is not interpretable as logical Calls: preprocessGCT Execution halted 2024/03/22 16:03:13 Starting delocalization. 2024/03/22 16:03:14 Delocalization script execution started... 2024/03/22 16:03:14 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_rna/memory_retry_rc 2024/03/22 16:03:16 Delocalizing output /cromwell_root/rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_rna/rc 2024/03/22 16:03:18 Delocalizing output /cromwell_root/stdout -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_rna/stdout 2024/03/22 16:03:19 Delocalizing output /cromwell_root/stderr -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_rna/stderr 2024/03/22 16:03:21 Delocalizing output /cromwell_root/tutorial-proteome.tar.gz -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_rna/tutorial-proteome.tar.gz Required file output '/cromwell_root/tutorial-proteome.tar.gz' does not exist.
ssgsea_ome.log 2024/03/22 16:04:42 Starting container setup. 2024/03/22 16:04:45 Done container setup. 2024/03/22 16:04:48 Starting localization. 2024/03/22 16:05:08 Localization script execution started... 2024/03/22 16:05:08 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_ome/script -> /cromwell_root/script 2024/03/22 16:05:14 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct 2024/03/22 16:05:18 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml 2024/03/22 16:05:18 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt Copying gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml to file:///cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml Copying gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt to file:///cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt . Average throughput: 1.0MiB/s 2024/03/22 16:05:21 Localization script execution complete. 2024/03/22 16:05:31 Done localization. 2024/03/22 16:05:32 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash broadcptac/panoply_ssgsea@sha256:5bdb529bb513f986dd0786ade226e13a2e71b65b06abffd583803851861448f9 /cromwell_root/script parsing command line parameters: ------------------------------------------------------------ --- gct_str /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct ; prefer yaml? FALSE --- level gc ; prefer yaml? FALSE --- id_type NA ; prefer yaml? TRUE --- id_type_out NA ; prefer yaml? TRUE --- acc_type_in NA ; prefer yaml? TRUE --- seqwin_column NA ; prefer yaml? TRUE --- gene_symbol_column NA ; prefer yaml? TRUE --- humanize_gene_names NA ; prefer yaml? TRUE --- sgt_column NA ; prefer yaml? TRUE --- localized NA ; prefer yaml? TRUE --- mode NA ; prefer yaml? TRUE --- residue NA ; prefer yaml? TRUE --- ptm NA ; prefer yaml? TRUE --- preprocess_gct NA ; prefer yaml? TRUE --- libdir /home/pgdac/src ; prefer yaml? FALSE --- yaml_file /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml ; prefer yaml? FALSE --- help FALSE ; prefer yaml? FALSE Updating parameter file with command line parameters: ------------------------------------------------------------ level : gc -> gc ------------------------------------------------------------ importing gct file: /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct ... parsing as GCT v1.3 /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct 10569 rows, 77 cols, 15 row descriptors, 17 col descriptors Error in if (humanize.gene.names) genes <- toupper(genes) : argument is not interpretable as logical Calls: preprocessGCT Execution halted 2024/03/22 16:05:51 Starting delocalization. 2024/03/22 16:05:52 Delocalization script execution started... 2024/03/22 16:05:52 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_ome/memory_retry_rc 2024/03/22 16:05:58 Delocalizing output /cromwell_root/rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_ome/rc 2024/03/22 16:06:01 Delocalizing output /cromwell_root/stdout -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_ome/stdout 2024/03/22 16:06:04 Delocalizing output /cromwell_root/stderr -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_ome/stderr 2024/03/22 16:06:07 Delocalizing output /cromwell_root/tutorial-proteome.tar.gz -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-ssgsea_ome/tutorial-proteome.tar.gz Required file output '/cromwell_root/tutorial-proteome.tar.gz' does not exist.
assoc.log 2024/03/22 16:03:52 Starting container setup. 2024/03/22 16:03:54 Done container setup. 2024/03/22 16:03:54 Starting localization. 2024/03/22 16:04:03 Localization script execution started... 2024/03/22 16:04:03 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_association_workflow/assoc_workflow.panoply_association_workflow/a1f65b46-1697-4527-aaf0-f8e0a892776a/call-assoc/script -> /cromwell_root/script 2024/03/22 16:04:06 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/groups-subset.csv -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/groups-subset.csv 2024/03/22 16:04:07 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml 2024/03/22 16:04:07 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct Copying gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml to file:///cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml Copying gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct to file:///cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/proteome-subset.gct . Average throughput: 45.8MiB/s 2024/03/22 16:04:09 Localization script execution complete. 2024/03/22 16:04:13 Done localization. 2024/03/22 16:04:13 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash broadcptac/panoply_association@sha256:ae088ec96a1325101c5e05601c571a26682fa30d285cc60f44c5eeb9280b1056 /cromwell_root/script NULL NULL Error in source("config.r") : config.r:300:1: unexpected '}' 299: min.numratio <- 300: } ^ Execution halted 2024/03/22 16:04:16 Starting delocalization. 2024/03/22 16:04:17 Delocalization script execution started... 2024/03/22 16:04:17 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_association_workflow/assoc_workflow.panoply_association_workflow/a1f65b46-1697-4527-aaf0-f8e0a892776a/call-assoc/memory_retry_rc 2024/03/22 16:04:19 Delocalizing output /cromwell_root/rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_association_workflow/assoc_workflow.panoply_association_workflow/a1f65b46-1697-4527-aaf0-f8e0a892776a/call-assoc/rc 2024/03/22 16:04:21 Delocalizing output /cromwell_root/stdout -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_association_workflow/assoc_workflow.panoply_association_workflow/a1f65b46-1697-4527-aaf0-f8e0a892776a/call-assoc/stdout 2024/03/22 16:04:22 Delocalizing output /cromwell_root/stderr -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_association_workflow/assoc_workflow.panoply_association_workflow/a1f65b46-1697-4527-aaf0-f8e0a892776a/call-assoc/stderr 2024/03/22 16:04:23 Delocalizing output /cromwell_root/panoply_association-output.tar -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-panoply_association_workflow/assoc_workflow.panoply_association_workflow/a1f65b46-1697-4527-aaf0-f8e0a892776a/call-assoc/panoply_association-output.tar Required file output '/cromwell_root/panoply_association-output.tar' does not exist.
panoply_ssgsea.log 2024/03/22 16:44:55 Starting container setup. 2024/03/22 16:44:56 Done container setup. 2024/03/22 16:44:57 Starting localization. 2024/03/22 16:45:07 Localization script execution started... 2024/03/22 16:45:07 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-panoply_ssgsea/script -> /cromwell_root/script 2024/03/22 16:45:09 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml 2024/03/22 16:45:11 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt Copying gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt to file:///cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/msigdb_v7.0_h.all.v7.0.symbols.gmt 2024/03/22 16:45:13 Localizing input gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-postprocess/glob-11ddd39ddf44cd39f6d839871aee5c17/tutorial-proteome_proteome_K3_W_rowNorm_combined_signed_n3x7198.gct -> /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-postprocess/glob-11ddd39ddf44cd39f6d839871aee5c17/tutorial-proteome_proteome_K3_W_rowNorm_combined_signed_n3x7198.gct 2024/03/22 16:45:15 Localization script execution complete. 2024/03/22 16:45:19 Done localization. 2024/03/22 16:45:20 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash broadcptac/panoply_ssgsea@sha256:5bdb529bb513f986dd0786ade226e13a2e71b65b06abffd583803851861448f9 /cromwell_root/script parsing command line parameters: ------------------------------------------------------------ --- gct_str /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-postprocess/glob-11ddd39ddf44cd39f6d839871aee5c17/tutorial-proteome_proteome_K3_W_rowNorm_combined_signed_n3x7198.gct ; prefer yaml? FALSE --- level NA ; prefer yaml? TRUE --- id_type NA ; prefer yaml? TRUE --- id_type_out NA ; prefer yaml? TRUE --- acc_type_in NA ; prefer yaml? TRUE --- seqwin_column NA ; prefer yaml? TRUE --- gene_symbol_column NA ; prefer yaml? TRUE --- humanize_gene_names NA ; prefer yaml? TRUE --- sgt_column NA ; prefer yaml? TRUE --- localized NA ; prefer yaml? TRUE --- mode abs.max ; prefer yaml? FALSE --- residue NA ; prefer yaml? TRUE --- ptm NA ; prefer yaml? TRUE --- preprocess_gct NA ; prefer yaml? TRUE --- libdir /home/pgdac/src ; prefer yaml? FALSE --- yaml_file /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/sample_sets/all/master-parameters_tutorial.yaml ; prefer yaml? FALSE --- help FALSE ; prefer yaml? FALSE Updating parameter file with command line parameters: ------------------------------------------------------------ mode : median -> abs.max ------------------------------------------------------------ importing gct file: /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-postprocess/glob-11ddd39ddf44cd39f6d839871aee5c17/tutorial-proteome_proteome_K3_W_rowNorm_combined_signed_n3x7198.gct ... parsing as GCT v1.3 /cromwell_root/fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-postprocess/glob-11ddd39ddf44cd39f6d839871aee5c17/tutorial-proteome_proteome_K3_W_rowNorm_combined_signed_n3x7198.gct 7198 rows, 3 cols, 9 row descriptors, 0 col descriptors Error in if (humanize.gene.names) genes <- toupper(genes) : argument is not interpretable as logical Calls: preprocessGCT Execution halted 2024/03/22 16:45:30 Starting delocalization. 2024/03/22 16:45:31 Delocalization script execution started... 2024/03/22 16:45:31 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-panoply_ssgsea/memory_retry_rc 2024/03/22 16:45:34 Delocalizing output /cromwell_root/rc -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-panoply_ssgsea/rc 2024/03/22 16:45:36 Delocalizing output /cromwell_root/stdout -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-panoply_ssgsea/stdout 2024/03/22 16:45:38 Delocalizing output /cromwell_root/stderr -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-panoply_ssgsea/stderr 2024/03/22 16:45:39 Delocalizing output /cromwell_root/tutorial-proteome_proteome.tar.gz -> gs://fc-1fc25f57-17bc-442f-a03a-6359a27a1f08/submissions/9bae57da-2431-4314-89ca-64714a8070e2/panoply_main/151a5dfa-f5b2-478a-bf0f-be053843e850/call-so_nmf/nmf_wdl.panoply_nmf_internal_workflow/00a87914-1254-4baa-a402-e59efcb803be/call-panoply_ssgsea/tutorial-proteome_proteome.tar.gz Required file output '/cromwell_root/tutorial-proteome_proteome.tar.gz' does not exist.
wcorinne commented 5 months ago

The majority of these errors look to be from parameter-mismatches. If this is occurring with the tutorial dataset (tutorial-brca-input.zip), it is likely that the master-parameters_tutorial.yaml in that zip file has not yet been updated to reflect v1_4. We are working on regenerating that tutorial zip-- but in the meantime, excluding the master-parameters_tutorial.yaml from the zip file (or, perhaps more simply, declaring master-parameters_tutorial.yaml as some other dummy file-category with 0 when running panda_input() in the notebook) will cause the notebook to generate a master-parameters.yaml file with the appropriate defaults for PANOPLY v1.4.

Update: The tutorial and tutorial-brca-input.zip have been updated to reflect PANOPLY v1.4 (2024-04-05)