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Old 12-03-2013, 12:46 PM   #1
arcolombo698
Senior Member
 
Location: Los Angeles

Join Date: Nov 2013
Posts: 142
Default Tophat Error

Hello,.

I received this error


I submitted this request for Tophat alignment

#!/bin/tcsh
#PBS -m abe -M
#PBS -j oe
tophat2 --GTF /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Annotation/Archives/archive-2013-03-06-11-23-03/Genes/genes.gtf --num-threads 16 --library-type fr-firststrand --mate-inner-dist 100 --output-dir Sample_CHLA-122_output /auto/rcf-proj/sa1/data/Homo_sapiens1/UCSC/hg19/Sequence/Bowtie2Index/genome paired_trimmed_Sample_C-122_R1.fastq.gzpaired_trimmed_Sample_-122_R2.fastq.gz


Notice the job had inputs for GZIPPED files, which reading the forums should be handled by Tophat.

The error produced was
"could not open pipe gzip -cd < paired_trimmed_Sample_.fastq.gz"


I unzipped the files and am re-running it... awaiting the results.

However, why didn't Tophat accepted the Zipped files?

Thank you.

P.S. I also submitted the job from the workding directory, so I know the submission was in the correct directory.

TY
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