Cuffmerge error for large number of samples

Question

[Satyajeet Khare]

Biostars,

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.

Best,