Error with cuffdiff, version 0.9.0

[ae_ucla]

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.
Thanks!

[peromhc]

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.

[ChrisL]

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.

[adarob]

The newest update should fix this issue.

[Balat]

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.

http://seqanswers.com/forums/showthread.php?t=7128

[mrfox]

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.