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03022011, 11:15 AM  #1 
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 chr1:54418725445261 [ ] 2%Error: sqrt(det(cov)) == 0, 0.000000 after rounding. Error: sqrt(det(cov)) == 0, 0.000000 after rounding. > Processing Locus chr10:1864726218648745 [**** ] 17%Error: sqrt(det(cov)) == 0, 0.000000 after rounding. Error: sqrt(det(cov)) == 0, 0.000000 after rounding. > Processing Locus chr10:1965677719663522 [**** ] 17%Error: sqrt(det(cov)) == 0, 0.000000 after rounding. Error: sqrt(det(cov)) == 0, 0.000000 after rounding. > Processing Locus chr10:2034051720356103 [**** ] 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 diffexpress analysis. Thanks, Zheng 
04182011, 06:49 AM  #2  
Junior Member
Location: Hamburg, Germany Join Date: Jul 2010
Posts: 9

Hi Zheng,
I have got the same problem. Did you hear sth. about this problem yet? Regards, Christian Quote:


06162011, 12:18 AM  #3 
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? 
07132011, 12:58 AM  #4 
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. 
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