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)
2 answers
It worked for me when I called it in R.
I followed this protocol:
R version 3.2.2 on Fedora
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)
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
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kanika.151
Have you tried using HTSeq instead? Both give you the same results.
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kanika.151
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 :)
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).
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They have already told you that there is a bug and you need to wait for a new release.
Thanks Istvan, I am waiting. But meanwhile looking into different solutions to this problem, if someone has.
In the mean time just use htseq-count. It's slower but it'll presumably work too.