Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
XLOC identifiers from cufflinks/cuffmerge/cuffdiff AdamB RNA Sequencing 4 01-24-2016 07:12 PM
cufflinks GTF files incompatible with cuffmerge? shurjo Bioinformatics 21 09-23-2013 04:47 PM
ERROR: cufflinks, cuffmerge, cuffdiff syintel87 Bioinformatics 0 01-19-2013 07:20 AM
cuffmerge on cufflinks denovo or with -g secda1 RNA Sequencing 0 10-09-2012 05:46 PM
Thoughts on running cufflinks with cuffmerge output? hcosta Bioinformatics 0 03-23-2012 06:43 PM

Thread Tools
Old 02-04-2013, 01:47 PM   #1
Location: Boston

Join Date: Oct 2009
Posts: 65
Default error in Cufflinks v2.0.2 when using Cuffmerge

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!
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
mattanswers is offline   Reply With Quote
Old 04-01-2013, 10:06 PM   #2
Junior Member
Location: Aarhus, Denmark

Join Date: Mar 2013
Posts: 1

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)

sbpo is offline   Reply With Quote
Old 07-11-2014, 02:40 PM   #3
Location: Boston

Join Date: Oct 2009
Posts: 65

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.
mattanswers is offline   Reply With Quote

cuffcompare, cufflinks 2.0.2, cuffmerge

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:29 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO