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Hello @sbslee, I hope you are well.
I'm trying to run a WGS sample that was run using Dragen 3.9 for the prepare-depth-of-coverage and have the below error:
$ docker run -v "$PWD":/data pypgx:v0.15.0 pypgx prepare-depth-of-coverage /data/sample/sample_WGS-depth-of-coverage.zip /data/sample_WGS/sample_WGS-contigs.bam --assembly GRCh38
ERROR conda.cli.main_run:execute(33): Subprocess for 'conda run ['pypgx', 'prepare-depth-of-coverage', '/data/sample_WGS/sample_WGS-depth-of-coverage.zip', '/data/sample_WGS/sample_WGS-contigs.bam', '--assembly', 'GRCh38']' command failed. (See above for error)
Traceback (most recent call last):
File "/opt/conda/envs/myenv/bin/pypgx", line 10, in <module>
sys.exit(main())
File "/opt/conda/envs/myenv/lib/python3.8/site-packages/pypgx/__main__.py", line 33, in main
commands[args.command].main(args)
File "/opt/conda/envs/myenv/lib/python3.8/site-packages/pypgx/cli/prepare_depth_of_coverage.py", line 90, in main
archive = utils.prepare_depth_of_coverage(
File "/opt/conda/envs/myenv/lib/python3.8/site-packages/pypgx/api/utils.py", line 1232, in prepare_depth_of_coverage
cf = pycov.CovFrame.from_bam(bams, regions=regions, zero=True)
File "/opt/conda/envs/myenv/lib/python3.8/site-packages/fuc/api/pycov.py", line 261, in from_bam
results += pysam.depth(*(bams + args + ['-r', region]))
File "/opt/conda/envs/myenv/lib/python3.8/site-packages/pysam/utils.py", line 69, in __call__
raise SamtoolsError(
pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=samtools depth: cannot parse region "chr22_KI270879v1_alt:267307-281486"\n'
I think it is happening because the contig name is different:
I have removed the reads in these random contigs because I'm trying to use a sample already aligned instead of aligning it again without the contigs. Do you think there is any other way of solving it? Maybe creating the sample_WGS-depth-of-coverage.zip file out of pypgx?
Thank you.
The text was updated successfully, but these errors were encountered:
This is a GRCh38-specific issue. One of the genes with SV is GSTT1 and it is located in the contig chr22_KI270879v1_alt, which is missing in your BAM file. That's why the prepare-depth-of-coverage command is complaining. For more details, please read GRCh37 vs. GRCh38.
In any case, the solution is to exclude the GSTT1 gene when running the command:
Hello @sbslee, I hope you are well.
I'm trying to run a WGS sample that was run using Dragen 3.9 for the
prepare-depth-of-coverage
and have the below error:I think it is happening because the contig name is different:
I have removed the reads in these random contigs because I'm trying to use a sample already aligned instead of aligning it again without the contigs. Do you think there is any other way of solving it? Maybe creating the
sample_WGS-depth-of-coverage.zip
file out of pypgx?Thank you.
The text was updated successfully, but these errors were encountered: