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OpenGene / AfterQC

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
MIT License
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String index out of range. #43

Open mquijano1 opened 2 years ago

mquijano1 commented 2 years ago

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 commented 10 months ago

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