Cuffdiff problems

nr23

Member

Join Date: Oct 2012
Posts: 42

08-15-2013, 02:02 AM

I'm running Cuffdiff v2.1.1 and am running into problems:

My script is:

Code:

cuffdiff -p 12 -o ./diff_out -b /ichec/work/nglif015b/nick/bowtie/bowtie-indexes/Laevis_7/Xl7.fasta -L con,smo 
/ichec/work/nglif015b/cufflinks/Laevis7/six1.mo/merged_asm/merged.gtf 
/ichec/work/nglif015b/nick/tophat_out/control/rep1/control.1.bam,/ichec/work/nglif015b/nick/tophat_out/control/rep2/control.2.bam
/ichec/work/nglif015b/nick/tophat_out/six1.mo/rep1/six1.mo.1.bam,/ichec/work/nglif015b/nick/tophat_out/six1.mo/rep2/six1.mo.2.bam

The job refuses to run, with the error messages:

Code:

cuffdiff: /lib64/libz.so.1: no version information available (required by cuffdiff)
cuffdiff v2.1.1 (4046M)

/var/spool/torque/mom_priv/jobs/1417075.stokes-svcs.ice.ichec.ie.SC: line 21: /ichec/work/nglif015b/cufflinks/Laevis7/six1.mo/merged_asm/merged.gtf: Permission denied
/var/spool/torque/mom_priv/jobs/1417075.stokes-svcs.ice.ichec.ie.SC: line 23: /ichec/work/nglif015b/nick/tophat_out/control/rep1/control.1.bam,/ichec/work/nglif015b/nick/tophat_out/
control/rep2/control.2.bam: No such file or directory

I've run the exact same pipeline before with no problems - does anyone know what's causing this?

Tags: cuffdiff 2.1.1, rna-seq tophat illumina

rboettcher

Member

Join Date: Oct 2010

Posts: 71
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#2

08-15-2013, 02:22 AM

There seems to be a related thread on SEQanswers already, see:

Just a moment...

http://seqanswers.com/forums/showthread.php?t=8042
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