error in Cufflinks v2.0.2 when using Cuffmerge

mattanswers

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Join Date: Oct 2009

Posts: 65
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#1

error in Cufflinks v2.0.2 when using Cuffmerge

02-04-2013, 02:47 PM

When I run Cuffmerge, I receive the following error:
You are using Cufflinks v2.0.2, which is the most recent release.
Error creating output file tmp_meta_asm.stats!
[FAILED]
Error: could not execute cuffcompare

No merged.gtf file is being produced, but genes.fpkm_tracking, isoforms.fpkm_tracking, skipped.gtf and transcritps.gtf are all being produced.

I am running on SUSE Linxux, Linux version 2.6.32.59-0.3-default.
Tags: cuffcompare, cufflinks 2.0.2, cuffmerge
sbpo

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Join Date: Mar 2013

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#2

04-01-2013, 10:06 PM

I had the same problem when I used the option -o to specify a path to the output folder.. If I changed to the wished directory before running cuffmerge it worked (i.e. I omitted the -o option)

Soren
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mattanswers

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Join Date: Oct 2009

Posts: 65
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#3

07-11-2014, 02:40 PM

Thanks. I had the same problem again, and I just re-ran the cuffmerge command in the cuffmerge output folder it had created in the first try.
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