String index out of range.

[mquijano1]

Hi!

I managed to run AfterQC succesfully the first time I used it with one of my libraries with the following command line:

pypy /home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/after.py

I tried to use the exact same command to run AfterQC on my second pair of libraries (from/in a different directory wheres these libraries are) and this error appeared:

specify current dir as input dir
l4i2-unpaired_R1.fastq
l4i2-trimmo_R1.fastq
Process Process-1:
Traceback (most recent call last):
File "/usr/lib/pypy/lib-python/2.7/multiprocessing/process.py", line 267, in _bootstrap
self.run()
File "/usr/lib/pypy/lib-python/2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/after.py", line 175, in processOptions
filter.run()
File "/home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/preprocesser.py", line 249, in run
self.r1qc_prefilter.statFile(self.options.read1_file)
File "/home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/qualitycontrol.py", line 350, in statFile
self.statRead(read)
File "/home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/qualitycontrol.py", line 107, in statRead
if seq[j] != seq[j+1]:
IndexError: string index out of range
Process Process-2:
Traceback (most recent call last):
File "/usr/lib/pypy/lib-python/2.7/multiprocessing/process.py", line 267, in _bootstrap
self.run()
File "/usr/lib/pypy/lib-python/2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/after.py", line 175, in processOptions
filter.run()
File "/home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/preprocesser.py", line 249, in run
self.r1qc_prefilter.statFile(self.options.read1_file)
File "/home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/qualitycontrol.py", line 350, in statFile
self.statRead(read)
File "/home/pop_manuel/proyecto_transcriptoma_rhizophagus/software/AfterQC-master/qualitycontrol.py", line 107, in statRead
if seq[j] != seq[j+1]:
IndexError: string index out of range
Time used: 0.0947189331055

I tried executing the program with pypy and python2, but it returns the same error.

Thank you for your help!

[joneson]

I have seen this question asked multiple times, but haven't yet seen a response. Did you find a solution to this issue?