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  • about the pipe from bowtie2 to samtools view

    Hi, dears.
    Last night I ran the code:
    nohup bowtie2 -x Ref_index -U ER172.fastq --local -D 20 -R 3 -N 1 -L 21 -i S,1,0.75 -p 15 | samtools view -bS -t Ref.fa.fai - > ER172.bam
    Unfortunately,I got:
    [sam_read1] reference ' 1482179 (26.27%) aligned 0 times' is recognized as '*'.Parse error at line 5645986: invalid CIGAR character

    I tried to view the line 5645986 from fastq, but I failed to find the reason. Maybe I need to view it from .sam file, but I used the pipe with no .sam file.
    Can you help me ?

  • #2
    from bowtie manual:
    Alignment summmary

    When Bowtie 2 finishes running, it prints messages summarizing what happened. These messages are printed to the "standard error" ("stderr") filehandle. For datasets consisting of unpaired reads, the summary might look like this:

    20000 reads; of these:
    20000 (100.00%) were unpaired; of these:
    1247 (6.24%) aligned 0 times
    18739 (93.69%) aligned exactly 1 time
    14 (0.07%) aligned >1 times
    93.77% overall alignment rate

    For datasets consisting of pairs, the summary might look like this:

    10000 reads; of these:
    10000 (100.00%) were paired; of these:
    650 (6.50%) aligned concordantly 0 times
    8823 (88.23%) aligned concordantly exactly 1 time
    527 (5.27%) aligned concordantly >1 times
    ----
    650 pairs aligned concordantly 0 times; of these:
    34 (5.23%) aligned discordantly 1 time
    ----
    616 pairs aligned 0 times concordantly or discordantly; of these:
    1232 mates make up the pairs; of these:
    660 (53.57%) aligned 0 times
    571 (46.35%) aligned exactly 1 time
    1 (0.08%) aligned >1 times
    96.70% overall alignment rate

    The indentation indicates how subtotals relate to totals.

    ---

    I guess you are capturing this because of the nohup command....

    Comment


    • #3
      Thanks,sphil.
      how about the error :.Parse error at line 5645986: invalid CIGAR character

      Comment


      • #4
        The error is caused by redirecting stderr to samtools. Don't do that.

        Comment


        • #5
          Thank you!
          maybe it's best to me that I will not use the pipe.

          Comment

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