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PrintReads out of space on device

I'm running PrintReads and gettting the "There is no space left on the device, so writing failed" error message, but we have 1.7TB free disk space. Is PrintReads using temporary space and if so how much does it needed? I couldn't find any documentation on it.

Could the error message be altered to give information on which device ran out of space?

Program Args: -T PrintReads -R ../../ref/taeGut1.bamorder.fasta -I ../indel_realigner_B/173.realigned.bam -BQSR 173.recal.grp -o 173.recal.bam



Best Answer


  • I am also getting the same error.

    @Geraldine_VdAuwera said:
    Otherwise I'm not sure what your error could be. You could try checking the tmp dir used by java. You can change that from cmd line if necessary.

    How would you do this exactly?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    To change the java tmp dir from cmd-line, add -Djava.io.tmpdir=<your_directory_path> (replacing <your_directory_path> by the path to the directory you want to use for temp files) to your command line before the -jar bit.

  • Sweet. Thanks!

  • williamw827williamw827 North CarolinaMember

    i had this same problem with the reducereads walker, and changing this parameter fixed it. However I was wondering, if the reads in the input bam file are already sorted, does the walker really need to sort them on the fly? I was looking through the source code (gatk v. 2.8) and it looks like the walker treats unsorted and sorted input the same. It seems like you should be able to get a fair amount of speed up on this if your incoming reads are already sorted ( and reduce the runtime memory requirements). I know this tools is unsupported in gatk 3 , but being able to reduce the storage requirement for the files still makes the tools pretty useful.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @williamw827‌,

    I'm not sure what you mean -- the GATK engine itself requires that input reads be sorted. It's possible that this tool may do some additional sorting, but that sounds like it might be a development oversight. In any case we will not be putting any more resources towards improving a deprecated tool, sorry...

  • williamw827williamw827 North CarolinaMember

    oh I didn't realize the input reads had to be sorted already. Must be that the reads generated to write out aren't guaranteed to be sorted... No worries I understand why they quit developing it given the way GATK is now handling the multicalling, but we still think its useful to reduce in house storage space ( and speed up other parts of our pipeline).


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