Piping a GZipped File
 

Hello

I received this error message

could not open pipe gzip -cd < paired_trimmed_Sample_.fastq.gz

and am not sure what this means.

advice?

What is the full command that is generating that message?

Does the file paired_trimmed_Sample_.fastq.gz exist in that location?

Tophat alignment
 

Hello. THank you for the response.

Here is the full job submission

#!/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_.fastq paired_trimmed_Sample_R2.fastq


I am not sure what else you would need?

Hmmm... it is not at all clear how that "job" relates to the error message from your first post.

So your error is not really about piping a gzipped file, it is about the internals of your application.

I would guess that somewhere in the code that gets executed it uses a pipe on the gunzipped data and that pipe is broken or fails to open. It would be impossible to say what is happening without some familiarity with the application and maybe access to the code. But certainly beyond the scope of this question.

If you are in a work environment I would suggest asking someone familiar with the application - they will likely have seen the message before and can tell you what parameters need to be changed to get past it. Otherwise, recheck all the parameters that you are passing from the shell.

And re-ask yourself the unanswered question from my first post - does the file paired_trimmed_Sample_.fastq.gz actually exist?