Open naity2 opened 2 years ago
@naity2
Hi, Can you provide us with the log folder (under the folder pyflow.data
)?
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:
@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.
@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.
@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.
Hi @polyactis,
First, thank you for this great tool.
I aligned my reads to the reference genome included in
hs38d1
provided byAccucopy
and sorted the bam files with duplicates marked. However, I am having the error as shown below when trying to run themain.py
file.Please let me know if you have any suggestions! Thank you very much!