Question: Cuffmerge error for large number of samples
2.8 years ago by
Satyajeet Khare • 1.5k
Satyajeet Khare • 1.5k 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)! [FAILED] 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.
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