For Viral Recombination Identification

Question

[bandanaschapagain]

Hi all, I am trying to trace the recombination event of plant virus. I am trying to use ViReMa as the tool. Is there any better option to try ? Thank you for your time. Regards, Bandana

[bandanaschapagain]

ViReMa is giving some error which I am not able to fix.

Error:
Last modified 6/6/2014
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Output File already exists!  Appending time to directory name to prevent overwrite.
Begining alignments
10000 reads in input file.
Traceback (most recent call last):
  File "ViReMa.py", line 538, in <module>
    IterateAlignments(cfgvars.File1)
  File "ViReMa.py", line 451, in IterateAlignments
    Alignment(File, '-q', cfgvars.Seed)
  File "ViReMa.py", line 342, in Alignment
    call(['bowtie', ReadType, '-n', str(cfgvars.Mismatches), '-l', str(Seed), '-e', '100000', '--quiet', '--mm', '-p', cfgvars.Threads, '--best', '-S', '--sam-nohead', cfgvars.Lib1, ReadsIn, 'TEMPSAM1'])
  File "/usr/local/lib/python2.7/subprocess.py", line 522, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/usr/local/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/local/lib/python2.7/subprocess.py", line 1335, in _execute_child
    raise child_exception