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  • shawpa
    Member
    • Aug 2011
    • 73
    #1

    samtool sort: truncated file error?

    I was trying to sort a bam file using samtools. The original bam file is about 34.4GB. After I ran the sorting, the output file was only 12.9GB. If it worked correctly I don't see where over half the data went. I checked a log and it says

    [bam_sort_core] truncated file. Continue anyway.
    [bam_sort_core] merging from 103 files...

    I'm not sure what this means. I think it might be a memory issue and its creating tmp dir where there isn't enough space maybe. I wasn't able to find any posts with this error already.
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