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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And I have the same problem now.
Does anyone hear something from the authors or solve the problem?Leave a comment:
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Hi Zheng,
I have got the same problem. Did you hear sth. about this problem yet?
Regards,
Christian
Originally posted by endether View PostLeave a comment:
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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
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
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