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CollectReadCounts in process Germline copy number variants.

ElliothuiElliothui HZAUMember
We have fully understood the workflow of Germline copy number variants and we have previously followed the workflow using hg38 successfully. We now want to repeat the process using hg19, yet we found the following mistakes in CollectReadCounts:
A USER ERROR has occurred: Couldn't write file //RDPYD17082173_A.tsv because : The output file is not writeable.
we were unable to find similar mistakes in the forum.


  • asmirnovasmirnov BroadMember, Broadie, Dev

    Hi @Elliothui , could you provide your command line with the full stack trace?

  • ElliothuiElliothui HZAUMember
    Hi we have already had some hg19 samples, so I wrote a .sh file to realize the circulation so that I can read each bam file. And this is my file command line:

    while (($i < 54))
    bampath=$(cat /hg19.log | head -$i | tail -1)
    tsvname=$(cat /sample2.log | head -$i | tail -1)
    /PANEL/gatk/gatk- CollectReadCounts -L /PANEL/try-hg19/hg19chrall.interval_list -R hg19.fa -imr OVERLAPPING_ONLY -I $bampath --format TSV -O/PANEL/hg19-try/$tsvname.tsv
    let i++

    This is the information after I input my command line.
    A USER ERROR has occurred: Couldn't write file
    PANEL/hg19-try/RDPYD17082173_A.tsv because : The output file is not writeable.

    I have used similar command in hg38 and it is successful, but when I try to use the program in hg19, it occurs this mistake.
  • sleeslee Member, Broadie, Dev ✭✭✭

    @Elliothui it looks like you might be missing a space in your command line---perhaps -O/PANEL/hg19-try/$tsvname.tsv should be -O /PANEL/hg19-try/$tsvname.tsv?

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