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Old 03-02-2011, 11:15 AM   #1
endether
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Location: St. Louis

Join Date: Feb 2011
Posts: 11
Default Cuffdiff sqrt(det(cov))==0) error

Hi All,

I encountered several error messages during cuffdiff run. The error message is as follows:


[13:43:11] Loading reference and sequence.
No fasta index found for ../ref/all.fa. Rebuilding, please wait..
Fasta index rebuilt.
[13:44:04] Inspecting maps and determining fragment length distributions.
[13:46:04] Calculating initial abundance estimates.
> Processed 23484 loci. [*************************] 100%
[13:51:17] Learning bias parameters.
[13:53:15] Testing for differential expression and regulation in locus.
> Processing Locus chr1:5441872-5445261 [ ] 2%Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
> Processing Locus chr10:18647262-18648745 [**** ] 17%Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
> Processing Locus chr10:19656777-19663522 [**** ] 17%Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
> Processing Locus chr10:20340517-20356103 [**** ] 18%Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Error: sqrt(det(cov)) == 0, 0.000000 after rounding.


This error did not halt the program and cuffdiff actually kept running until all results were output. I am not sure what did those errors mean? Are they fatal errors that might lead to the error in my result.

Here is what I did before running cuffdiff.

I ranthe Tophat to get my alignment results "sample_X/accepted_hits.bam" (I have 10 samples here, so X = 1..10). I ran Cufflinks to get the "sample_X/transcripts.gtf". Then I use Cuffcompare using all transcripts.gtf files output by cufflinks to get a combined gtf file. At the end, I feed this combined gtf file into cuffdiff and two samples from my sample pool to do the diff-express analysis.

Thanks,
Zheng
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Old 04-18-2011, 06:49 AM   #2
Enrico Palazzo
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Location: Hamburg, Germany

Join Date: Jul 2010
Posts: 9
Default

Hi Zheng,

I have got the same problem. Did you hear sth. about this problem yet?

Regards,
Christian

Quote:
Originally Posted by endether View Post
Hi All,

I encountered several error messages during cuffdiff run. The error message is as follows:


[13:43:11] Loading reference and sequence.
No fasta index found for ../ref/all.fa. Rebuilding, please wait..
Fasta index rebuilt.
[13:44:04] Inspecting maps and determining fragment length distributions.
[13:46:04] Calculating initial abundance estimates.
> Processed 23484 loci. [*************************] 100%
[13:51:17] Learning bias parameters.
[13:53:15] Testing for differential expression and regulation in locus.
> Processing Locus chr1:5441872-5445261 [ ] 2%Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
> Processing Locus chr10:18647262-18648745 [**** ] 17%Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
> Processing Locus chr10:19656777-19663522 [**** ] 17%Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
> Processing Locus chr10:20340517-20356103 [**** ] 18%Error: sqrt(det(cov)) == 0, 0.000000 after rounding.
Error: sqrt(det(cov)) == 0, 0.000000 after rounding.


This error did not halt the program and cuffdiff actually kept running until all results were output. I am not sure what did those errors mean? Are they fatal errors that might lead to the error in my result.

Here is what I did before running cuffdiff.

I ranthe Tophat to get my alignment results "sample_X/accepted_hits.bam" (I have 10 samples here, so X = 1..10). I ran Cufflinks to get the "sample_X/transcripts.gtf". Then I use Cuffcompare using all transcripts.gtf files output by cufflinks to get a combined gtf file. At the end, I feed this combined gtf file into cuffdiff and two samples from my sample pool to do the diff-express analysis.

Thanks,
Zheng
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Old 06-16-2011, 12:18 AM   #3
altodor
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Location: Sweden

Join Date: Nov 2009
Posts: 12
Default

And I have the same problem now.
Does anyone hear something from the authors or solve the problem?
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Old 07-13-2011, 12:58 AM   #4
seeker
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Location: Zurich

Join Date: Jan 2011
Posts: 26
Default

I have the same error (pasted below) when running cuffcompare in a local instance of Galaxy




An error occurred running this job: cuffcompare v1.0.3 (2401)
cuffcompare -o cc_output -s ref.fa ./input1 ./input2
Error running cuffcompare. You are using Cufflinks v1.0.3, which is the most recent release.
No fasta index found for ref.fa. Rebuilding, please wait..
Fasta index rebuilt.
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