Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Segmentation fault, cuffdiff labrat73 Bioinformatics 12 03-22-2018 12:00 PM
Cufflinks cufflinks v1.0.3 - segmentation fault bias correction chrNT annotations adrian Bioinformatics 0 06-08-2011 02:28 PM
Segmentation fault when running Cufflinks doggysaywhat RNA Sequencing 0 03-30-2011 11:48 AM
Maq: Segmentation Fault mrxcm3 Bioinformatics 2 03-21-2011 03:43 PM
SOAP:segmentation fault Mansequencer Bioinformatics 1 11-19-2010 11:47 AM

Thread Tools
Old 06-29-2011, 09:32 AM   #1
Location: Ireland

Join Date: Jun 2011
Posts: 14
Default cufflinks segmentation fault help please


I get the output below when I run cufflinks using the command

cufflinks -g /data/shared/genomes/Btau_4.0/Bos_taurus.Btau_4.0.62.gtf --frag-len-mean 201 --frag-len-std-dev 81 accepted_hits.bam

I've tried -G and without any annotation file and I've also tried leaving it to use default frag-len-mean/std-dev values but it's the same each time and no output files are generated. Any help would be appreciated.



here's the output

cufflinks: /lib64/ no version information available (required by cufflinks)
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (
[17:24:11] Loading reference annotation.
[17:24:14] Inspecting reads and determining fragment length distribution.
> Processed 271810 loci. [*************************] 100%
> Map Properties:
> Total Map Mass: 12341530.00
> Read Type: 36bp single-end
> Fragment Length Distribution: Truncated Gaussian (user-specified)
> Default Mean: 201
> Default Std Dev: 81
Segmentation fault
seq_newbie is offline   Reply With Quote
Old 06-29-2011, 12:52 PM   #2
Location: Florida

Join Date: Jan 2011
Posts: 15

This error could be due to insufficient memory
sunkorner is offline   Reply With Quote

cufflinks, segmentation fault

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 06:50 AM.

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