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

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  • 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

  • #2
    Hi Zheng,

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

    Regards,
    Christian

    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

    Comment


    • #3
      And I have the same problem now.
      Does anyone hear something from the authors or solve the problem?

      Comment


      • #4
        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.

        Comment

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