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  • How to store bowtie log?

    Hello there:

    Under windows 7, I am trying to align reads by Bowtie like this
    bowtie -t hg19 -S -p4 -m 1 -q XXXXXX.fastq > XXXXXX.sam

    And after the alignment, the screen showed:

    Time loading forward index: 00:00:15
    Time loading mirror index: 00:00:14
    Seeded quality full-index search: 01:26:49
    # reads processed: 37763608
    # reads with at least one reported alignment: 26849716 (71.10%)
    # reads that failed to align: 3594644 (9.52%)
    # reads with alignments suppressed due to -m: 7319248 (19.38%)
    Reported 26849716 alignments to 1 output stream(s)
    Time searching: 01:27:18
    Overall time: 01:27:18

    Is there a way to store the above log? I saw tophat got logs, but I cannot find any log file after the alignment.

    Thanks!

  • #2
    Hello vixensjlin,

    At least this works for me in unix
    bowtie -t hg19 -S -p4 -m 1 -q XXXXXX.fastq > XXXXXX.sam 2>&1 | tee hg19.XXX.log
    Kindly check if there is a 'tee' unix command in windows.

    HTH

    MBandi

    Comment


    • #3
      Similar to what Apexy said, you can use 2> to redirect stdout to a file (bowtie writes the summary log files to stdout). But it isn't necessary to pipe into tee for this.

      So your command would just be:
      bowtie -t hg19 -S -p4 -m 1 -q XXXXXX.fastq > XXXXXX.sam 2> XXXXXX.log

      This is how I store the bowtie logs on my unix machine - I believe stdout redirection works the same on windows, so should work there too.

      Comment

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