cufflinks segmentation fault help please

seq_newbie · 06-29-2011, 09:32 AM

Hi,

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.

Regards,

K.

here's the output

cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks)
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
[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

sunkorner · 06-29-2011, 12:52 PM

This error could be due to insufficient memory

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06-29-2011, 09:32 AM	#1
seq_newbie Member Location: Ireland Join Date: Jun 2011 Posts: 14	cufflinks segmentation fault help please Hi, 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. Regards, K. here's the output cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks) Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). [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

06-29-2011, 12:52 PM	#2
sunkorner Member Location: Florida Join Date: Jan 2011 Posts: 15	This error could be due to insufficient memory