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#5 Error in REDItoolDnaRna.py

New
Ernesto Picardi
error (2) python (1) index out of range (1)
Medium
Defect
2016-02-12
2016-02-10
antonio
No

What steps will reproduce the problem?
REDItoolDnaRna.py:
python /usr/.../REDItools-1.0.4/reditools/REDItoolDnaRna.py -i /.../RNA.bam -j /.../DNA.bam -f /.../Hs_GRCh37.MT.fa -o output

What is the expected output? What do you see instead?
Don't generate an output. It work only in chr X and Y.

What version of the product are you using? On what operating system?
REDItools-1.0.4, Centos

Please provide any additional information below.

Script time --> START: 09/02/2016 17:15:39
Analysis ID: 739449241
Analysis on 25 regions.
Started analysis on region: ChrY:1-59373566 --> Process-1 pid: 11565
Job completed for region: ChrY:1-59373566
Started analysis on region: ChrX:1-155270560 --> Process-1 pid: 11565
Process Process-1:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/local/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(self._args, self._kwargs)
File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 1133, in do_work
exploreBAM(x)
File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 876, in exploreBAM
gs,gq,gt,gqq=pileupread.alignment.seq[pileupread.qpos].upper(),ord(pileupread.alignment.qual[pileupread.qpos])-gQVAL,'',pileupread.alignment.qual[pileupread.qpos]
IndexError: string index out of range
Merging Tables.
Results saved on Z715_rna_editing/DnaRna_739449241/outTable_739449241
Script time --> END: 09/02/2016 17:42:47

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Tickets: #5

Discussion

  • Ernesto Picardi

    Ernesto Picardi - 2016-02-10

    Hi,
    the error is in the pysam version. You should use 0.6 or 0.7.
    Best,
    Ernesto

    Il giorno 10 feb 2016, alle ore 12:27, antonio agraz@users.sf.net ha scritto:

    [tickets:#5] Error in REDItoolDnaRna.py

    Status: New
    Labels: error python index out of range
    Created: Wed Feb 10, 2016 11:27 AM UTC by antonio
    Last Updated: Wed Feb 10, 2016 11:27 AM UTC
    Owner: Ernesto Picardi

    What steps will reproduce the problem?
    REDItoolDnaRna.py:
    python /usr/.../REDItools-1.0.4/reditools/REDItoolDnaRna.py -i /.../RNA.bam -j /.../DNA.bam -f /.../Hs_GRCh37.MT.fa -o output

    What is the expected output? What do you see instead?
    Don't generate an output. It work only in chr X and Y.

    What version of the product are you using? On what operating system?
    REDItools-1.0.4, Centos

    Please provide any additional information below.

    Script time --> START: 09/02/2016 17:15:39
    Analysis ID: 739449241
    Analysis on 25 regions.
    Started analysis on region: ChrY:1-59373566 --> Process-1 pid: 11565
    Job completed for region: ChrY:1-59373566
    Started analysis on region: ChrX:1-155270560 --> Process-1 pid: 11565
    Process Process-1:
    Traceback (most recent call last):
    File "/usr/local/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
    File "/usr/local/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(self._args, self._kwargs)
    File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 1133, in do_work
    exploreBAM(x)
    File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 876, in exploreBAM
    gs,gq,gt,gqq=pileupread.alignment.seq[pileupread.qpos].upper(),ord(pileupread.alignment.qual[pileupread.qpos])-gQVAL,'',pileupread.alignment.qual[pileupread.qpos]
    IndexError: string index out of range
    Merging Tables.
    Results saved on Z715_rna_editing/DnaRna_739449241/outTable_739449241
    Script time --> END: 09/02/2016 17:42:47

    Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/reditools/tickets/5/

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  • antonio

    antonio - 2016-02-12

    HI, thanks for your answer. I unistalled pysam and I returned to install pysam 0.7.5.

    pysam versioning information

    version = "0.7.5"

    samtools_version = "0.1.19"

    tabix_version = "0.2.6"

    However, I continue having the same problem:

    Script time --> START: 11/02/2016 17:27:28
    Analysis ID: 128228463
    Analysis on 25 regions.
    Started analysis on region: ChrY:1-59373566 --> Process-1 pid: 6340
    Job completed for region: ChrY:1-59373566
    Started analysis on region: ChrX:1-155270560 --> Process-1 pid: 6340
    Process Process-1:
    Traceback (most recent call last):
    File "/usr/local/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
    File "/usr/local/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(self._args, self._kwargs)
    File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 1133, in do_work
    exploreBAM(x)
    File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 876, in exploreBAM
    gs,gq,gt,gqq=pileupread.alignment.seq[pileupread.qpos].upper(),ord(pileupread.alignment.qual[pileupread.qpos])-gQVAL,'    ',pileupread.alignment.qual[pileupread.qpos]
    IndexError: string index out of range
    Merging Tables.
    Results saved on Z715_rna_editing/DnaRna_128228463/outTable_128228463
    Script time --> END: 11/02/2016 17:54:32

    Do you know how i can repair this? Thanks. Antonio Agraz

     

    • Ernesto Picardi

      Ernesto Picardi - 2016-02-12

      Hi
      Using 0.7.4 works fine. Please try also one of 0.6.x

      I'm working to fix pysam version issuses.
      Best,
      Ernesto

      Il giorno 12 feb 2016, alle ore 10:15, antonio agraz@users.sf.net ha scritto:

      HI, thanks for your answer. I unistalled pysam and I returned to install pysam 0.7.5.

      pysam versioning information

      version = "0.7.5"

      samtools_version = "0.1.19"

      tabix_version = "0.2.6"

      However, I continue having the same problem:

      Script time --> START: 11/02/2016 17:27:28
      Analysis ID: 128228463
      Analysis on 25 regions.
      Started analysis on region: ChrY:1-59373566 --> Process-1 pid: 6340
      Job completed for region: ChrY:1-59373566
      Started analysis on region: ChrX:1-155270560 --> Process-1 pid: 6340
      Process Process-1:
      Traceback (most recent call last):
      File "/usr/local/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
      self.run()
      File "/usr/local/lib/python2.7/multiprocessing/process.py", line 114, in run
      self._target(self._args, self._kwargs)
      File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 1133, in do_work
      exploreBAM(x)
      File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 876, in exploreBAM
      gs,gq,gt,gqq=pileupread.alignment.seq[pileupread.qpos].upper(),ord(pileupread.alignment.qual[pileupread.qpos])-gQVAL,'',pileupread.alignment.qual[pileupread.qpos]
      IndexError: string index out of range
      Merging Tables.
      Results saved on Z715_rna_editing/DnaRna_128228463/outTable_128228463
      Script time --> END: 11/02/2016 17:54:32

      Do you know how i can repair this? Thanks. Antonio Agraz

      [tickets:#5] Error in REDItoolDnaRna.py

      Status: New
      Labels: error python index out of range
      Created: Wed Feb 10, 2016 11:27 AM UTC by antonio
      Last Updated: Wed Feb 10, 2016 11:27 AM UTC
      Owner: Ernesto Picardi

      What steps will reproduce the problem?
      REDItoolDnaRna.py:
      python /usr/.../REDItools-1.0.4/reditools/REDItoolDnaRna.py -i /.../RNA.bam -j /.../DNA.bam -f /.../Hs_GRCh37.MT.fa -o output

      What is the expected output? What do you see instead?
      Don't generate an output. It work only in chr X and Y.

      What version of the product are you using? On what operating system?
      REDItools-1.0.4, Centos

      Please provide any additional information below.

      Script time --> START: 09/02/2016 17:15:39
      Analysis ID: 739449241
      Analysis on 25 regions.
      Started analysis on region: ChrY:1-59373566 --> Process-1 pid: 11565
      Job completed for region: ChrY:1-59373566
      Started analysis on region: ChrX:1-155270560 --> Process-1 pid: 11565
      Process Process-1:
      Traceback (most recent call last):
      File "/usr/local/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
      self.run()
      File "/usr/local/lib/python2.7/multiprocessing/process.py", line 114, in run
      self._target(self._args, self._kwargs)
      File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 1133, in do_work
      exploreBAM(x)
      File "/usr/local/biotools/REDItools-1.0.4/reditools/REDItoolDnaRna.py", line 876, in exploreBAM
      gs,gq,gt,gqq=pileupread.alignment.seq[pileupread.qpos].upper(),ord(pileupread.alignment.qual[pileupread.qpos])-gQVAL,'',pileupread.alignment.qual[pileupread.qpos]
      IndexError: string index out of range
      Merging Tables.
      Results saved on Z715_rna_editing/DnaRna_739449241/outTable_739449241
      Script time --> END: 09/02/2016 17:42:47

      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/reditools/tickets/5/

      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

       

      Related

      Tickets: #5

      alternate

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