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optimuscoprime / autoadapt

Automatic quality control for FASTQ sequencing files
GNU General Public License v2.0
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Showing error when trying with compressed fastq files "Can't open FastQC report at autoadapt line 378" #8

Open snijesh opened 7 years ago

snijesh commented 7 years ago

perl autoadapt.pl first.fastq.gz clean.fastq.gz Can't open FastQC report at autoadapt line 378

snijesh commented 7 years ago

The problem is with the regexp which is creating the $nameWithoutExtension at line 368. '$' makes it match and substitute only at the end of the string but if you have a gzipped fastq file then it will only get rid of .gz and not the .fastq. So removing the '$' has solved the problem

rotifergirl commented 5 years ago

I get this same error now, but it says line 376, I am not using a gzipped file, so I'm not sure where this is coming from or how to fix it

renagel2 commented 5 years ago

@rotifergirl did you find a solution to this problem? I am getting the same error.

rotifergirl commented 5 years ago

@renagel2 I didn't find a solution sorry, I ended up using bbduk instead

renagel2 commented 5 years ago

@rotifergirl too bad. But thank you!