Continued problems with Support step: PBJelly in PBSuite

2014-03-21
2014-03-21
  • Matt MacManes

    Matt MacManes - 2014-03-21

    Hello,

    Using the test dataset included in the package, I have continued problems:

    Mapping seems to work: produces alignments that look like this:

    m130724_230321_00121_c100518582550000001823079209281361_s1_p0/116034/3824_6124 lambda_NEB3011_1|ref0000001 -720 72.7848 0 6 278 2300 1 2128 2423 28380 50
    

    When I run support, I get no error, but it fails:

    *~/pb-jelly-code-0/pbsuite/jelly/Jelly.py support Protocol.xml*
    2014-03-21 07:35:39,065 [INFO] Running /home/macmanes/pb-jelly-code-0/pbsuite/jelly/Jelly.py support Protocol.xml
    [WARNING] Couldn't find /home/macmanes/pb-jelly-code-0/docs/jellyExample/data/reference/lambda.qual...
    assuming there isn't a quality file for the reference
    2014-03-21 07:35:39,067 [INFO] Executing Stage: support
    2014-03-21 07:35:39,210 [INFO] Finished Running Stage: support
    

    looking inside support/ my .gml file contains:

    graph [
    ]
    

    and my *err file has:

    2014-03-21 07:35:39,196 [INFO] Running
    /home/macmanes/pb-jelly-code-0//bin//Support.py /home/macmanes/pb-jelly-code-0/docs/jellyExample/mapping/filtered_subreads.fastq.m4
    /home/macmanes/pb-jelly-code-0/docs/jellyExample/data/reference/lambda.gapInfo.bed
    /home/macmanes/pb-jelly-code-0/docs/jellyExample/support/filtered_subreads.fastq.gml
    2014-03-21 07:35:39,197 [INFO] Building Helper Objects
    2014-03-21 07:35:39,197 [INFO] Connecting Alignments
    2014-03-21 07:35:39,200 [INFO] Classifying Alignments' Support
    2014-03-21 07:35:39,200 [INFO] Saving Support Graph
    2014-03-21 07:35:39,201 [INFO] Finished
    

    So, something is amiss, but I'm not sure what..

    FWIW, I have the right networkx installed:

    pip show networkx
    ---
    Name: networkx
    Version: 1.1
    Location: /usr/local/lib/python2.7/dist-packages
    

    The Protocol.xml file is unchanged from what is distributed:

    <jellyProtocol>
    
    <reference>/home/macmanes/pb-jelly-code-0/docs/jellyExample/data/reference/lambda.fasta</reference>
        <outputDir>/home/macmanes/pb-jelly-code-0/docs/jellyExample/</outputDir>
        <blasr>-minMatch 8 -minPctIdentity 70 -bestn 5 -nCandidates 20
    -maxScore -500 -nproc 32 -noSplitSubreads</blasr>
        <input
    baseDir="/home/macmanes/pb-jelly-code-0/docs/jellyExample/data/reads/">
            <job>filtered_subreads.fastq</job>
        </input>
    </jellyProtocol>
    

    Thanks, Matt

     
    Last edit: Matt MacManes 2014-03-21
  • Adam English

    Adam English - 2014-03-21

    Hey Matt,

    Sorry you're having trouble. I'm unsure of a potential fix based on the information you've given me. Could you please re-run Support.py with --debug. Perhaps the verbose logs will give us a better indication of what's happening.

      /home/macmanes/pb-jelly-code-0//bin//Support.py /home/macmanes/pb-jelly-code-0/docs/jellyExample/mapping/filtered_subreads.fastq.m4 /home/macmanes/pb-jelly-code-0/docs/jellyExample/data/reference/lambda.gapInfo.bed /home/macmanes/pb-jelly-code-0/docs/jellyExample/support/filtered_subreads.fastq.gml --debug
    
     

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