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optimuscoprime / autoadapt

Automatic quality control for FASTQ sequencing files
GNU General Public License v2.0
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getting error with fastqc #3

Open vrutantshah opened 10 years ago

vrutantshah commented 10 years ago

the error i am getting is here: ./autoadapt.pl --minimum-length=16 MiR1_NoIndex_L006_R1_001.fasta mir184_trim.fa

/home/ubuntu/softwares/autoadapt-master/tools/fastqc --threads 1 --outdir /home/ubuntu/softwares/autoadapt-master/autoadapt.tmp.4CkfuyRX /home/ubuntu/mir_gast_analysis/MiR1_NoIndex_L006_R1_001.fasta Can't open FastQC report at /home/ubuntu/softwares/autoadapt-master/./autoadapt.pl line 378. I am not sure why it is not taking path correctly.

evalang commented 9 years ago

Hi, I was getting the same error. The problem was with the regexp that was 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 for me.