Cuffdiff sqrt(det(cov))==0) error

endether · 03-02-2011, 11:15 AM

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

Enrico Palazzo · 04-18-2011, 06:49 AM

Hi Zheng,

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

Regards,
Christian

Quote:

Originally Posted by endether

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

altodor · 06-16-2011, 12:18 AM

And I have the same problem now.
Does anyone hear something from the authors or solve the problem?

seeker · 07-13-2011, 12:58 AM

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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03-02-2011, 11:15 AM	#1
endether Member Location: St. Louis Join Date: Feb 2011 Posts: 11	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

06-16-2011, 12:18 AM	#3
altodor Member Location: Sweden Join Date: Nov 2009 Posts: 12	And I have the same problem now. Does anyone hear something from the authors or solve the problem?

07-13-2011, 12:58 AM	#4
seeker Member Location: Zurich Join Date: Jan 2011 Posts: 26	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.