[ERROR] [normalize] Error Message about accucopy

[fanxinping]

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

[naity2]

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

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[fanxinping]

@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]

@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]

@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.