alignPacBio.py edited online with Bitbucket

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Author
  1. Ratnesh Singh
Reviewers
Description

alignPacBio.py edited online with Bitbucket 'cat' was causing error on run. changed to 'cat ' (space before end quote)

Comments (2)

  1. luping

    [luping@centos sample1-consensus]$ /disk/luping/tools/comp_bio-tapis-44cc05ebc78c/axiba/bin/alignPacBio.py /disk/luping/bam/iso-bam/cluster/FG FG FG.RR.32.genome.fa consensus.fasta cat: write error: Broken pipe /bin/sh: convertSam.py: command not found

  2. luping
    [luping@centos sample1-consensus]$ /disk/luping/tools/comp_bio-tapis-44cc05ebc78c/axiba/bin/alignPacBio.py /disk/luping/bam/iso-bam/cluster/FG FG FG.RR.32.genome.fa consensus.fasta 
    cat: write error: Broken pipe
    /bin/sh: convertSam.py: command not found
    rm: cannot remove `filtered/temp_dir/consensus_r1.bam.bai': No such file or directory
    /bin/sh: cleanAlignments.py: command not found
    Traceback (most recent call last):
      File "/disk/luping/tools/comp_bio-tapis-44cc05ebc78c/axiba/bin/alignPacBio.py", line 75, in <module>
        if os.path.getsize(gmapIn) == 0:
      File "/disk/luping/tools/Python-2.7.14/lib/python2.7/genericpath.py", line 57, in getsize
        return os.stat(filename).st_size
    OSError: [Errno 2] No such file or directory: 'filtered/temp_dir/consensus_fixed_r1.fa'