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[ERROR] [normalize] Error Message #18

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naity2 opened this issue Apr 28, 2022 · 5 comments
Open

[ERROR] [normalize] Error Message #18

naity2 opened this issue Apr 28, 2022 · 5 comments

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@naity2
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naity2 commented Apr 28, 2022

Hi @polyactis,

First, thank you for this great tool.

I aligned my reads to the reference genome included in hs38d1 provided by Accucopy and sorted the bam files with duplicates marked. However, I am having the error as shown below when trying to run the main.py file.

Please let me know if you have any suggestions! Thank you very much!

[2022-04-28T20:45:05.792488] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr4' to master workflow
  [2022-04-28T20:45:05.792738] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr5' to master workflow
  [2022-04-28T20:45:05.792866] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr6' to master workflow
  [2022-04-28T20:45:05.792992] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr7' to master workflow
  [2022-04-28T20:45:05.793113] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr8' to master workflow
  [2022-04-28T20:45:05.793232] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr9' to master workflow
  [2022-04-28T20:45:05.793362] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr10' to master workflow
  [2022-04-28T20:45:05.793481] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr11' to master workflow
  [2022-04-28T20:45:05.793596] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr12' to master workflow
  [2022-04-28T20:45:05.794122] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr13' to mast' to master workflow
  [2022-04-28T20:45:05.793481] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr11' to master workflow
  [2022-04-28T20:45:05.793596] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr12' to master workflow
  [2022-04-28T20:45:05.794122] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr13' to master workflow
  [2022-04-28T20:45:05.794601] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr14' to master workflow
  [2022-04-28T20:45:05.795005] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr15' to master workflow
  [2022-04-28T20:45:05.795131] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr16' to master workflow
  [2022-04-28T20:45:05.795248] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr17' to master workflow
  [2022-04-28T20:45:05.795368] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr18' to master workflow
  [2022-04-28T20:45:05.795483] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr19' to master workflow
  [2022-04-28T20:45:05.795597] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr20' to master workflow
  [2022-04-28T20:45:05.795710] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr21' to master workflow
  [2022-04-28T20:45:05.795840] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'segment_chr22' to master workflow
  [2022-04-28T20:45:05.795961] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'reduce_all_segments' to master workflow
  [2022-04-28T20:45:05.796443] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'rm_individual_seg_files' to master workflow
  Last step time span: 0:00:00.007164
  step 5: Infer tumor purity and ploidy.
  	start time: 2022-04-29 04:45:05.796882
  [2022-04-28T20:45:05.797097] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'infer' to master workflow
  Last step time span: 0:00:00.000715
  step 6: Make plots.
  	start time: 2022-04-29 04:45:05.797597
  [2022-04-28T20:45:05.797682] [1d46eeca3e55] [8_1] [WorkflowRunner] Adding command task 'plot_cnv' to master workflow
  Last step time span: 0:00:00.000146
  End time: 2022-04-29 04:45:05.797743
  [2022-04-28T20:45:05.797779] [1d46eeca3e55] [8_1] [TaskRunner:masterWorkflow] Finished task specification for master workflow
  [2022-04-28T20:45:59.922904] [1d46eeca3e55] [8_1] [TaskManager] Completed command task: 'indexTumorBam' launched from master workflow
  [2022-04-28T20:46:00.087241] [1d46eeca3e55] [8_1] [TaskManager] Completed command task: 'indexNormalBam' launched from master workflow
  [2022-04-28T20:46:00.087753] [1d46eeca3e55] [8_1] [TaskManager] Launching command task: 'strelka_prepare' from master workflow
  [2022-04-28T20:46:00.088045] [1d46eeca3e55] [8_1] [TaskManager] Launching command task: 'normalize' from master workflow
  [2022-04-28T20:46:00.090603] [1d46eeca3e55] [8_1] [TaskRunner:strelka_prepare] Task initiated on local node
  [2022-04-28T20:46:00.091298] [1d46eeca3e55] [8_1] [TaskRunner:normalize] Task initiated on local node
  [2022-04-28T20:46:00.151922] [1d46eeca3e55] [8_1] [TaskManager] [ERROR] Failed to complete command task: 'normalize' launched from master workflow, error code: 101, command: 
  [2022-04-28T20:46:00.151960] [1d46eeca3e55] [8_1] [TaskManager] [ERROR] [normalize] Error Message:
  [2022-04-28T20:46:00.151972] [1d46eeca3e55] [8_1] [TaskManager] [ERROR] [normalize] Last 0 stderr lines from task (of 0 total lines):
  [2022-04-28T20:46:00.151983] [1d46eeca3e55] [8_1] [TaskManager] [ERROR] Shutting down task submission. Waiting for remaining tasks to complete.
  [2022-04-28T20:46:00.366062] [1d46eeca3e55] [8_1] [TaskManager] Completed command task: 'strelka_prepare' launched from master workflow
  [2022-04-28T20:46:08.952897] [1d46eeca3e55] [8_1] [WorkflowRunner] [ERROR] Worklow terminated due to the following task errors:
  [2022-04-28T20:46:08.952995] [1d46eeca3e55] [8_1] [WorkflowRunner] [ERROR] Failed to complete command task: 'normalize' launched from master workflow, error code: 101, command: 
  [2022-04-28T20:46:08.953010] [1d46eeca3e55] [8_1] [WorkflowRunner] [ERROR] [normalize] Error Message:
  [2022-04-28T20:46:08.953019] [1d46eeca3e55] [8_1] [WorkflowRunner] [ERROR] [normalize] Last 0 stderr lines from task (of 0 total lines):
@fanxinping
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@naity2
Hi, Can you provide us with the log folder (under the folder pyflow.data)?

@naity2
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naity2 commented Apr 29, 2022

Thank you @fanxinping. Does information below help?

[2022-04-29T20:27:48.359275] [42b46c09263b] [8_1] [pyflowTaskWrapper:indexNormalBam] Task: 'indexNormalBam' exit code: '0'
[2022-04-29T20:27:48.361815] [42b46c09263b] [8_1] [pyflowTaskWrapper:indexNormalBam] Task: 'indexNormalBam' complete. elapsedSec: 39 elapsedCoreSec: 39
[2022-04-29T20:28:38.423703] [42b46c09263b] [8_1] [pyflowTaskWrapper:indexTumorBam] Task: 'indexTumorBam' exit code: '0'
[2022-04-29T20:28:38.426481] [42b46c09263b] [8_1] [pyflowTaskWrapper:indexTumorBam] Task: 'indexTumorBam' complete. elapsedSec: 89 elapsedCoreSec: 89
[2022-04-29T20:28:38.560864] [42b46c09263b] [8_1] [pyflowTaskWrapper:normalize] Task: 'normalize' exit code: '101'
[2022-04-29T20:28:38.764306] [42b46c09263b] [8_1] [pyflowTaskWrapper:strelka_prepare] Task: 'strelka_prepare' exit code: '0'
[2022-04-29T20:28:38.766839] [42b46c09263b] [8_1] [pyflowTaskWrapper:strelka_prepare] Task: 'strelka_prepare' complete. elapsedSec: 0 elapsedCoreSec: 0

thread 'main' panicked at 'called `Option::unwrap()` on a `None` value', src/main.rs:26:63
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Successfully created workflow run script.
To execute the workflow, run the following script and set appropriate options:

@fanxinping
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@naity2
An error occurred when executing normalize subcommand according to the information you provided, but I cannot find the detailed reason why this error occurred with the partial logs. Can you zip and upload the folder pyflow.data? This folder only contains the logs generated by Accucopy.

@WuRAFY
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WuRAFY commented May 4, 2023

@fanxinping
I have the same error as mentioned above. pyflow.data is shared using onedrive at https://1drv.ms/u/s!AoDQLeCux6IamRtfv3ycAsa871K7?e=BecSRc. Hope this will help.

@polyactis
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@WuRAFY the error was due to 1) a bug in handling UID inside a container (fixed and updated in the dockerhub image); 2) the bam header contains contig IDs that are missing in our pre-packaged reference genome, which can be solved by making a custom reference genome package https://www.yfish.org/display/PUB/Accucopy#Accucopy-3.7Makeyourownreferencegenomepackage.

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@polyactis @fanxinping @WuRAFY @naity2