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polyactis / Accucopy

Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.
https://www.yfish.org/software/Accucopy
GNU General Public License v3.0
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[ERROR] [normalize] Error Message #18

Open naity2 opened 2 years ago

naity2 commented 2 years ago

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 commented 2 years ago

@naity2 Hi, Can you provide us with the log folder (under the folder pyflow.data)?

naity2 commented 2 years ago

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 commented 2 years ago

@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 commented 1 year ago

@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 commented 1 year ago

@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.