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Old 10-01-2010, 05:18 PM   #1
Location: los angeles, ca

Join Date: Aug 2010
Posts: 11
Default Error with cuffdiff, version 0.9.0

Hi, I am running the newest version of cufflinks with cuffdiff and am getting the error:
"Error: this SAM file doesn't appear to be correctly sorted!
current hit is at chr3:3018707, last one was at chr2:181747854
You may be able to fix this by running:
$ LC_ALL="C" sort -k 3,3 -k 4,4n input.sam > fixed.sam"
I have used the sort command as suggested as well as sorting through samtools and continue to get the error.
I can successfully split up the chromosomes per bam file and this works. But is anyone else getting this error?
The same files worked with the previous version of cufflinks.
ae_ucla is offline   Reply With Quote
Old 10-01-2010, 11:14 PM   #2
Senior Member
Location: Durham, NH

Join Date: Sep 2009
Posts: 108

yep, I am having the exact same error! I, too, have tried the various sort commands mentioned in the error output, as well as in the other post concerning v0.9.0.

For now, Im back to an older version.
peromhc is offline   Reply With Quote
Old 10-02-2010, 02:24 AM   #3
Location: Sydney

Join Date: Nov 2009
Posts: 14

Same here

Error: this SAM file doesn't appear to be correctly sorted!
current hit is at chr2:12738, last one was at chr19:59117053

Also tried to sort the SAM files without success.
ChrisL is offline   Reply With Quote
Old 10-04-2010, 09:05 AM   #4
Location: Berkeley, CA

Join Date: Jul 2010
Posts: 71

The newest update should fix this issue.
adarob is offline   Reply With Quote
Old 10-05-2010, 04:44 AM   #5
Location: Australia

Join Date: May 2010
Posts: 36

The newer version (v0.9.1) fixes the sorting errors with SAM. However, SAM files still need to be sorted with samtools. Cole has a suggestion on how to do this in this thread.
Balat is offline   Reply With Quote
Old 11-17-2010, 03:37 PM   #6
Senior Member
Location: USA

Join Date: Aug 2010
Posts: 103

based on my experience, the latest version of Tophat1.12 output accepted_hits.BAM instead of SAM. And the newest cufflinks, cuffdiff allows BAM directly. Inputing BAM files to cuffdiff might avoid the problem.
mrfox is offline   Reply With Quote

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