Cuffmerge_Error: could not execute gtf_to_sam

[cnova1126]

Hi All,

I am having an issue merging my transcript.gtf files using Cuffmerge (cufflinks version 2.1.1). However, this only occurs when I use the UCSC_knownGene.gtf file, and when ran with the genes.gtf provided by iGenome it works fine. I do not like using the iGenome genes.gtf file as I have noticed the gene names provided with the Cuffdiff output do not completely match the UCSC gene names (i.e ~6500 off when compared to UCSC kgxref). While most of the genes are lincRNA, etc I would still like to run using my provided gtf file.



The command and error are as follows:

cuffmerge -g /Volumes/Untitled/MD_Anderson/Programs/Homo_sapiens_UCSC_hg19/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2015-07-17-14-32-32/Genes/genes2.gtf -s /Volumes/Untitled/MD_Anderson/Programs/Homo_sapiens_UCSC_hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa -p 8 /Volumes/Untitled2/BRCA_UBR7/BRCA_UBR7_RNA-SEQ/Cufflinks_BRCA_UBR7_3/Sh4_assemblies.txt



[Thu Jun 23 11:35:07 2016] Beginning transcriptome assembly merge

-------------------------------------------



[Thu Jun 23 11:35:07 2016] Preparing output location ./merged_asm/

[Thu Jun 23 11:35:25 2016] Converting GTF files to SAM

[11:35:25] Loading reference annotation.

[FAILED]

Error: could not execute gtf_to_sam



Any help would be greatly appreciated!

Thanks!!!