pbjelly assembly error

crd1859
2014-02-19
2015-02-13
  • crd1859

    crd1859 - 2014-02-19

    I'm working with pacbio data. Everything seems fine up to the assembly stage, at which point I get the following error:

    2014-02-19 04:54:29,715 [INFO] Executing Stage: assembly
    Traceback (most recent call last):
    File "../bin/Jelly.py", line 254, in <module>
    prog.run()
    File "../bin/Jelly.py", line 239, in run
    self.options.extras)
    File "/home/peter/bioinformatics/pbjelly/pbsuite/jelly/Stages.py", line 179, in assembly
    size = gapInfo["%s_%d_%d" % (ref, ca, cb)].length
    KeyError: 'ref0000008_101_102'

    I dealing with a large number of css files (which I didn't generate) so I wouldn't be too surprised if this were a formatting error in the files. Any advice would be greatly appreciated.

     
  • Adam English

    Adam English - 2014-03-21

    The first thing to check is that you have networkx v1.1 installed.

    From there, look in your reference.fasta and see if you can find the tag ref0000008. Also look in your gapInfo.bed file (beside your reference) and see if you can find ref0000008_101_102 in one of the entry's 4th column (the name column). If you can't find both of those, are you certain that A) You're pointing to the correct reference and B) That you've run the setup stage?

    --
    Have a good day,
    ~/Adam English

     
  • Steph

    Steph - 2015-02-13

    Hi there,

    After on year from this post I am sorry to say i'm facing the same error.

    File "/PBjelly/PBSuite_14.9.9/bin/Jelly.py", line 263, in <module>
        prog.run()
      File "/PBjelly/PBSuite_14.9.9/bin/Jelly.py", line 249, in run
        self.options.extras)
      File "/PBjelly/PBSuite_14.9.9/pbsuite/jelly/Stages.py", line 179, in assembly
        size = gapInfo["%s_%d_%d" % (ref, ca, cb)].length
    KeyError: 'ref0000001_0_1'
    

    I am running Networkx 1.9.1 and i patched it with this:

    https://sourceforge.net/p/pb-jelly/discussion/pbjtiks/thread/82fc47c6/

    I did not do this:
    https://sourceforge.net/p/pb-jelly/discussion/pbjtiks/thread/d32d4be0/

    because i think you fixed it in the source code right after that ticket and it would have been redundant.

    Here I am by the way. I checked the files you suggested to crd1859

    cat ../refer.fasta | grep ref0000001
    >scaffold_108|ref0000060|ref0000048|ref0000043|ref0000026|ref0000001|ref0000057|ref0000030|ref0000001
    >scaffold_011|ref0000017|ref0000087|ref0000088|ref0000037|ref0000076|ref0000001|ref0000040|ref000001
    ~~~~~~
    
    etc...etc...
    

    cat ../refer.gapInfo.bed | grep ref0000001
    scaffold_108|ref0000060|ref0000048|ref0000043|ref0000026|ref0000001|ref0000057|ref0000030|ref0000001 na na ref0000001_0_0 3
    scaffold_011|ref0000017|ref0000087|ref0000088|ref0000037|ref0000076|ref0000001|ref0000040|ref0000010 904303 904669 ref0000010_0_1 1
    scaffold_011|ref0000017|ref0000087|ref0000088|ref0000037|ref0000076|ref0000001|ref0000040|ref0000010 1272366 1272912 ref0000010_1_2 2
    ~~~~

    etc... etc....

    cat ../refer.gapInfo.bed | grep ref0000001_0_1
    

    nothing

    i'd be glad if i could get a suggestion.
    thanks for your time.

    Stef

     

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