Question: Cuffmerge error for large number of samples
gravatar for Satyajeet Khare
2.8 years ago by
Satyajeet Khare1.5k
Pune, India
Satyajeet Khare1.5k wrote:


I am trying cuffmerge using following command

cuffmerge -o cuffmerge_out -g gene.GTF -s genome.fa -p 10 assembly_list.txt

The command ends with following error

[17:56:54] Inspecting reads and determining fragment length distribution.
Processed 40099 loci.                       
> Map Properties:
>   Normalized Map Mass: 1975849.00
>   Raw Map Mass: 1975849.00
>   Fragment Length Distribution: Truncated Gaussian (default)
>                 Default Mean: 200
>              Default Std Dev: 80
[17:57:04] Assembling transcripts and estimating abundances.
Processed 40099 loci.                       
[Sat Dec 24 17:59:32 2016] Comparing against reference file gene.GTF
You are using Cufflinks v2.2.1, which is the most recent release.
Error (GFaSeqGet): subsequence cannot be larger than 1346
Error getting subseq for CUFF.1401.1 (1..1350)!
Error: could not execute cuffcompare

But if run cuffmerge without the fasta file, it works.

cuffmerge -o cuffmerge_out -g gene.GTF -p 10 assembly_list.txt

Any idea whats going on?

P.S. I am merging 48 samples.


cuffmerge rna-seq cufflinks • 809 views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Satyajeet Khare1.5k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1599 users visited in the last hour