Run without errors but failed to produce the site list #64
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I don't know if it will solve your problem, but we recently released a bugfix to the script that might not be available on bioconda. The newest version of the script is available via the mgibio/bam_readcount_helper-cwl:1.1.1 docker container. I would appreciate it, if you could run the latest version of the script to confirm whether or not the problem still persists there. |
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Unfortunately, I can not run docker on my server |
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You can download the latest version from GitHub as well (https://raw.githubusercontent.com/genome/docker-bam_readcount_helper-cwl/1.1.1/bam_readcount_helper.py). |
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@susannasiebert It did not work. Same message and no output files |
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But it ran to completion or did you have to abort it? You might be running out of memory and the process that runs bam readcount gets killed but that's just a wild guess. Without being able to reproduce the error I don't have much to go on. |
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It runs to completion. I would expect a message with termination signal if the subprocess is killed. I will rerun in a safer environment with high allocated resources to see. |
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It just a status messages indicating that you haven't set a minimum mapping quality threshold in your command so it defaulted to 0. |
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I have the same issue running on docker: most of them are snp positions(rows with "#N/A" values in ref column): |
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I am using the script "bam_readcount_helper.py" to run bam-readcount (installed from bioconda) to generate site list. The input VCF has ~1million line. The script runs without errors except a massage that says
b'Minimum mapping quality is set to 0\n'however fails to produce to produce any output files.When I tried to run the script with a small subset of the input VCF (only 5000 lines), everything worked fine and I got the expected tsv output files
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