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  • Samtools pileup filesize limit

    Is there a file size limitation for samtools pileup command? I converted a 82GB sam file (output from bowtie) into a 25 GB compressed bam and then sorted it using samtools. Now when I try running samtools pileup on the sorted file (25GB), samtools quits saying memory leak. If samtools cannot handle large file, is there a way to split the sorted bam, analyze it with samtools pileup separately and then merge the output.
    Thanks.

  • #2
    what is your computer config ? how much RAM ?

    Comment


    • #3
      Hi Nicobxl,
      I am running samtools on a 16 core 64 bit linux server with 256 GB RAM. Going through the samtools manual, I did not notice any performance related command/options. Please let me know if you have any suggestions.
      Thanks,

      Comment


      • #4
        error message? I am sure 200GB BAMs have no problems. Pileup only uses tiny amount of memory.

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        • #5
          Hi Ih3,
          I am using this command to generate a txt file.
          samtools pileup -vcf filename.fas filename_sorted.bam > rawsnp.txt

          I ran samtools on a 1.7 GB file under 32 bit linux system and it worked fine. When I tried running the same file on the 64 bit server, samtools quits saying memory leak 1. continue anyway and then quits.

          Can you suggest some solution to this.
          Thanks,

          Comment


          • #6
            I also had a memory leak, I could solve this by sorting my bam files.

            (this was highest hit when googeling memory leak of mpileup and this is a common mistake)

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