Comments (5)
@naity2
Hi, Can you provide us with the log folder (under the folder pyflow.data
)?
from accucopy.
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:
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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.
from 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.
from accucopy.
@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.
from accucopy.
Related Issues (20)
- Licensing issues HOT 8
- Run on long reads data? HOT 2
- Lacking python3 packages in docker HOT 5
- Suggestion on input bams? HOT 2
- Empty Output HOT 3
- The meaning of minus cp HOT 11
- maestre: libbz2.so.1.0 not found HOT 2
- Bug at "--period" option HOT 4
- caller_path HOT 1
- unable to infer tumour purity HOT 4
- input to pyclone-vi HOT 1
- unable to open file: name = '/data/modif_genome_test1/model_selection_l og/model_selection.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0 HOT 7
- CNV.output.tsv not generated HOT 3
- https://www.yfish.org/display/PUB/Accucopy is missing (404) HOT 2
- can accucopy support create a baseline by normal samples and then use tumor only samples? HOT 1
- unmatched chromosome name get error HOT 6
- Failed to complete command task: 'rm_individual_seg_files' launched from master workflow, HOT 11
- Stuck at reduce_all_segments HOT 1
- Exception in thread TaskFileWriter-Thread: HOT 7
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