etal
a same command fails in the first time
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
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?
thanks a lot, I am using the latest. this problem has occured several times, and rerun is ok.
cnvkit.py version 0.9.9