Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

CollectReadCounts in process Germline copy number variants.

ElliothuiElliothui HZAUMember
Hi!
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.
Thanks!

Answers

  • asmirnovasmirnov BroadMember, Broadie, Dev ✭✭

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

  • ElliothuiElliothui HZAUMember
    @asmirnov
    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:

    i=1
    while (($i < 54))
    do
    bampath=$(cat /hg19.log | head -$i | tail -1)
    tsvname=$(cat /sample2.log | head -$i | tail -1)
    /PANEL/gatk/gatk-4.1.2.0/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++
    done

    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?

Sign In or Register to comment.