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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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a same command fails in the first time #672

Open asmlgkj opened 2 years ago

asmlgkj commented 2 years ago

Dear pfrofessor, Thanks a lot fot providing such a powerful tool for cnv. I found a very strange error, a same command in cnvkit fails in the first time, but success in the second time. it is a rare mistate, maybe 1%%， does some random seed in code will lead to this?

cnvkit version 0.9.9
I found the error log is like this Cannot convert non-finite values (NA or inf) to integer
because of this error fails to generate sort_dedup.cns but when I rerun, it ends successfully

5039537143c9b6b818f591fd3eb4c98

etal commented 2 years ago

Strange, it looks like in the coverage command, there are rows in the output of samtools depth (or pysam/htslib equivalent) that are parsed as in NA or Inf values. Are you using the most recent versions of CNVkit and pysam?

asmlgkj commented 2 years ago

thanks a lot, I am using the latest. this problem has occured several times, and rerun is ok.

cnvkit.py version 0.9.9