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Running out of disk space with BWA, wrong CMD line?

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  • Running out of disk space with BWA, wrong CMD line?

    Hi!
    I keep getting "out of disk space" errors , even with 800gb free space.

    This is my code:

    bwa samse -n4 reference.fa x.sai x.fastq.gz > x.sam

    Somebody knows?

  • #2
    Have you checked to see if your /tmp is filling up? Are these very large files?

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    • #3
      Thats probably it..

      All files is about 2-3gb. The x.sam file will be 16gb I guess..

      Could I compress the sam to bam like this?

      bwa samse -n4 reference.fa x.sai x.fastq.gz > x.sam | samtools view -Sb > x.bam
      Last edited by sindrle; 11-26-2013, 08:07 AM.

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      • #4
        See this thread for examples of piping: http://www.biostars.org/p/43677/

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