Open AdrianS85 opened 5 years ago
Hi @AdrianS85 - I am not familiar with Singularity or snakemake, but we can try to help. A few things to check:
[samtools] <defunct>
- please verify the version of samtools you're using matches the recommended versions on our main page. (note the --old-samtools flag is required for old samtools versions)-T
option)echo
to determine whether the loop exits as expected. (Can you provide the parallel command you issued here for inspection?)Dear mlovci,
nudup.py: error: Must be able to make named pipes in temp directory. See
man mkfifofor named pipe info.
. Exactly the same command issued moment later starts without problem.I also tried to run only 5 files in parallel in case of RAM issues, but it still seems to work/fail randomly, sometimes after producing 16 files, sometimes after single one.
Best, Adrian
Dear all,
I was trying to run 20 bam files through nudup.py in parallel inside Singularity container. I used parallel processing as implemented in snakemake, nextflow and parallel GNU. The effect was always the same: some of the files were processed, while others ran (or just stay hanged?) forever. I have logged the paralell's GNU stdout/err during execution of nudup script - https://github.com/AdrianS85/varia/blob/master/nudup_raport.txt. Please notice that the same jobs are issued over and over again. For comparison, the strip script, which is run before nudup.py, runs in parallel properly - https://github.com/AdrianS85/varia/blob/master/strip_raport.txt
I will be thankful for any help, Adrian
EDIT: Program also hangs when running it in parallel outside the container. Ive also produced another raport for failed jobs: https://github.com/AdrianS85/varia/blob/master/nudup_errors_more
https://github.com/nugentechnologies/nudup/blob/468c62e948b87fa8a3231355d26cc37e1d0717d5/nudup.py#L1