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  • featureCounts Error: SAM_pairer_osr_next_name: Assertion `rlen < 1024' failed

    I get this error when I run featureCounts on an output file generated by STAR as BAM SortedByCoordinate:

    || Process BAM file xxx... ||
    || Paired-end reads are included. ||
    || Assign fragments (read pairs) to features... ||
    featureCounts: input-files.c:3377: SAM_pairer_osr_next_name: Assertion `rlen < 1024' failed.
    Aborted

    Interestingly, if I run STAR again and I choose BAM Unsorted as the output parameters, featureCounts does not fail. Out of 20 samples that I'm analyzing only one gave me this error. What I would like to know is what the error means (in the code I see that rlen is the buffer for fread(), but I don't understand what would make it be more than 1024 bytes), and if I there is an easy way to identify what's causing it.

    Thanks

  • #2
    Hi @nachocab,

    Could you send us your bam file offline so that we can figure out what caused the problem? Could you show us your command as well?

    Wei

    Comment


    • #3
      Hi Shi,
      Sure, no problem. How and where do I send it? It's 2.1GB

      Comment


      • #4
        Could you send it via CloudStor?

        Comment


        • #5
          Hmm, I don't think so. I don't belong to any of those universities

          Comment


          • #6
            Sure. Maybe via dropbox? Or you can put it somewhere on internet and then we can download it.

            Comment

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