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

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Default 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
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Old 06-29-2011, 12:52 PM   #2
sunkorner
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This error could be due to insufficient memory
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