featureCounts segmentation fault, Is there any solution yet ?
2
0
Entering edit mode
8.9 years ago
EagleEye 7.6k

http://seqanswers.com/forums/showthread.php?t=50353

featureCounts -Q 10 -F GTF -a MY_ANNOTATION.gtf -t exon -g gene_id -o mypath/out_counts.txt mypath/celline1.bam

========== _____ _ _ ____ _____ ______ _____ 
===== / ____| | | | _ \| __ \| ____| /\ | __ \ 
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.4.5-p1

//========================== featureCounts setting ===========================\\
|| ||
|| Input files : 1 BAM file ||
Segmentation fault (core dumped)
RNA-Seq error software • 4.7k views
ADD COMMENT
1
Entering edit mode

They have already told you that there is a bug and you need to wait for a new release.

ADD REPLY
0
Entering edit mode

Thanks Istvan, I am waiting. But meanwhile looking into different solutions to this problem, if someone has.

ADD REPLY
1
Entering edit mode

In the mean time just use htseq-count. It's slower but it'll presumably work too.

ADD REPLY
1
Entering edit mode
8.9 years ago
EagleEye 7.6k

Great there is a new patched version for Subread (subread-1.5.0-p1-source) released today. It works perfectly :-)

Thanks a lot for all your suggestions and help.... See you with some other issue.

ADD COMMENT
0
Entering edit mode
8.9 years ago
kanika.151 ▴ 130

It worked for me when I called it in R.

I followed this protocol:

http://bioinf.wehi.edu.au/RNAseqCaseStudy/

ADD COMMENT
0
Entering edit mode

Hi Kanika,

Thanks for your reply, please let me know in which R version you installed Rsubread?

ADD REPLY
0
Entering edit mode

R version 3.2.2 on Fedora

ADD REPLY
0
Entering edit mode

Thanks again for the suggestion, but I get the same issue using R. I guess I should wait for the next patched version.

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 1.20.2

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||

 *** caught segfault ***
address 0x3020002fa, cause 'memory not mapped'

Segmentation fault (core dumped)
ADD REPLY
0
Entering edit mode

I think this should help you. It is because of the size of GTF file. :/

https://stat.ethz.ch/pipermail/bioconductor/2014-May/059512.html

ADD REPLY
0
Entering edit mode

My GTF file is very small with just 3,000 genes in it. I think it is the problem with larger BAM as mentioned by Wei Shi. You can see his comments on seqanswers link on my first post.

ADD REPLY
0
Entering edit mode

Have you tried using HTSeq instead? Both give you the same results.

ADD REPLY
0
Entering edit mode

I have not tried. I just waited for the update from featureCount. Since I wanted to maintain the consistancy with my analysis pipeline, I did not try it. But it is an interesting question.

ADD REPLY
0
Entering edit mode

Don't do that. All the analysis pipeline need one count module which can be done by either featureCount or HTSeq the difference is only of the platforms. I did both :)

ADD REPLY
0
Entering edit mode

No, I haven't done yet. I am already done with all analysis part.

How much correlation did you get between these two methods? It will be nice if you can share it.

ADD REPLY
2
Entering edit mode

The difference you get in counts is incredibly small if it even still exists. Originally, the only difference was due to an off-by-one error in htseq-count (see the featureCounts paper for a figure on this).

ADD REPLY

Login before adding your answer.

Traffic: 1737 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6