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  • bowtie memory warning

    Hi

    I'm mapping solid reads using bowtie and received the following warnings for MANY reads. Mapping % is very low as well.
    Am I running out of memory?

    command line:
    bowtie -C -S -k 3 --best --un unmapped_list genome_index -f seq.csfasta -Q seq.qual bowtie.sam



    Warning: Exhausted best-first chunk memory for read 301_728_1008_F3 (patid 11858997); skipping read

    # reads processed: 19323816
    # reads with at least one reported alignment: 4408352 (22.81%)
    # reads that failed to align: 14915464 (77.19%)
    Reported 5326165 alignments to 1 output stream(s)

    Thanks

    charles

  • #2
    I get similar warnings when I use paired end data. But if I align read1 and read2 separately, I do not get any warnings. Solutions/pointers are appreciated.
    Thanks,
    Vishal

    Comment


    • #3
      Yes, I believe you are running out of memory. If you use --chunkmbs 200 you should stop getting the warning. This may help improve your alignment statistics.

      Comment


      • #4
        In fact, I have tried using --chunkmbs 1000 and still managed to get these errors ... only for paired-end data though.

        Comment


        • #5
          Try higher I guess. 200 worked for me when working with non-paired end data.

          Comment


          • #6
            bowtie memory warning

            All

            Thanks for the advice:

            Using --chunkmbs 200 eliminated the memory warnings.

            I'm still not mapping a significant fraction of the reads. I'm going to trim the unmapped colorspace reads from 3'end to see if I can get any of these to map - other suggestions?

            bowtie -C -S -k 3 --best


            # reads processed: 19323816
            # reads with at least one reported alignment: 4408352 (22.81%)
            # reads that failed to align: 14915464 (77.19%)
            Reported 5326165 alignments to 1 output stream(s)

            Comment


            • #7
              Bowtie: Memory error warning

              Same as the quoted question. When I run the Bowtie command as below to generate SAM with the 1 best hit from fasta input, it has such warning messages,

              $ bowtie -f -S -m 1 -k 1 --best h_sapiens_37_asm Input.fa > Output.sam
              ------------------
              Warning: Exhausted best-first chunk memory for read seq_5023_1 (patid 5023); skipping read
              Warning: Exhausted best-first chunk memory for read seq_5041_1 (patid 5041); skipping read
              Warning: Exhausted best-first chunk memory for read seq_20071_1 (patid 20071); skipping read
              ......
              ------------------

              Which flag options should I use?

              Many thanks.

              Ben


              Originally posted by crh View Post
              Hi

              I'm mapping solid reads using bowtie and received the following warnings for MANY reads. Mapping % is very low as well.
              Am I running out of memory?

              command line:
              bowtie -C -S -k 3 --best --un unmapped_list genome_index -f seq.csfasta -Q seq.qual bowtie.sam



              Warning: Exhausted best-first chunk memory for read 301_728_1008_F3 (patid 11858997); skipping read

              # reads processed: 19323816
              # reads with at least one reported alignment: 4408352 (22.81%)
              # reads that failed to align: 14915464 (77.19%)
              Reported 5326165 alignments to 1 output stream(s)

              Thanks

              charles

              Comment


              • #8
                I had this problem as well. I tried --chunkmbs 200 as well, and it didn't help, but --chunkmbs 2000 seems like it might have fixed the bug being reported, but I am still getting very low alignmment proportions (5% of reads).

                Comment

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