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Old 01-25-2011, 07:13 AM   #1
Location: california

Join Date: Jan 2011
Posts: 26
Question cufflinks error


I am getting the following errors in cufflinks.

./cufflinks: /usr/lib64/ no version information available (required by ./cufflinks)
[bam_header_read] EOF marker is absent.
File /data/ms2374/accepted_hits.sam doesn't appear to be a valid BAM file, trying SAM...

But after printing the errors it seems to be producing the output correctly without any errors as follows

[10:17:24] Inspecting reads and determining fragment length distribution.
> Processed 217449 loci. [*************************] 100%
> Map Properties:
> Total Map Mass: 18001680.04
> Read Type: 75bp single-end
> Fragment Length Distribution: Gaussian (default)
> Estimated Mean: 209.55
> Estimated Std Dev: 70.54
[10:19:30] Assembling transcripts and estimating abundances.
> Processed 217449 loci. [*************************] 100%

I would like to know if the errors I received earlier is something that I should worry about or just move on with the output?

madsaan is offline   Reply With Quote
Old 01-26-2011, 02:50 PM   #2
Location: Berkeley, CA

Join Date: Jul 2010
Posts: 71

This error is output by samtools (which Cufflinks calls) if you are using a SAM instead of a BAM. However, Cufflinks recognizes this and switches to SAM support, so there is no issue.

adarob is offline   Reply With Quote

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