Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Ray : Segmentation fault (11) Nagesh De novo discovery 3 02-02-2017 05:22 AM
Cuffdiff 2.2.0 segmentation fault blancha Bioinformatics 7 04-28-2014 02:24 AM
segmentation fault with cisGenome aquleaf Bioinformatics 0 10-03-2012 08:31 AM
cufflinks segmentation fault help please seq_newbie Bioinformatics 1 06-29-2011 12:52 PM
Newbler segmentation fault flobpf Bioinformatics 4 04-18-2011 12:45 PM

Thread Tools
Old 08-28-2016, 11:17 PM   #21
Location: Sydney, Australia

Join Date: Jan 2012
Posts: 61

Originally Posted by shi View Post
What is the version of featureCounts you use?
Rsubread_1.20.6 or command line version subread-1.5.0-p1-Linux-x86_64
dvanic is offline   Reply With Quote
Old 08-28-2016, 11:23 PM   #22
Wei Shi
Location: Australia

Join Date: Feb 2010
Posts: 235

Can you update to Subread 1.5.1 and try again?
shi is offline   Reply With Quote
Old 11-09-2016, 06:45 AM   #23
Junior Member
Location: Groningen, Netherlands

Join Date: Nov 2016
Posts: 2

I'm also getting a segmentation error.

I use featureCount on 33k files and only 3 of them return this error. I'm getting no stdout or err on these 3 files, just:
44818 Segmentation fault (core dumped)

The query I use:
featureCounts -s 1 -T 8 -t exon -g gene_id -a Homo_sapiens.GRCh37.75.gtf bamfile.bam

Version: 1.5.1
Platform: Linux-x86_64

Link to one of the problem bam files:

Any help would be highly appreciated

Last edited by hbrugge; 11-15-2016 at 01:48 AM.
hbrugge is offline   Reply With Quote
Old 01-10-2017, 08:38 AM   #24
Junior Member
Location: Groningen, Netherlands

Join Date: Nov 2016
Posts: 2

It would be really nice if anyone could look into this problem
hbrugge is offline   Reply With Quote
Old 12-30-2017, 11:24 PM   #25
Junior Member
Location: Beijing

Join Date: Mar 2011
Posts: 3

I also encounter similar problem:

SAM_pairer_run: Assertion `1 != corrected_run'
But after I sort the bam file using PICARD, featureCounts worked fine.
japrin is offline   Reply With Quote

countdata, featurecounts

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 12:27 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO