Cuffmerge can't execute gtf_to_sam

[thickrick99]

Hi Everyone,

I am having some issues with cuff merge right now because it is giving me an error that it could not execute gtf_to_sam. I have seen other questions posted about this but couldn't find a solution that worked for me. I am using cufflinks version 2.1.1 and here is the command I used:

cuffmerge -g Homo_sapiens.knownGene.hg19.sorted.withGenes.gtf -s hg19.fa -p 2 assemblies.txt

I tried to run gtf_to_sam separately and it gave me a segmentation fault: 11 error. I am not sure if this is a regular error in cuffmerge or if there is something wrong with the program. I am thinking it may be a problem with my GTF file but I am not sure.

Thanks in advance!!

[thickrick99]

I also tried this with a newer version of cufflinks and it did not work.. still giving me the same error.