TopHat2 failed to read known junctions from GTF file (from ensembl or UCSC)

[Alex234]

Hello, I've seen similar problems with gtf files posted elsewhere, where the problems seem to be due to differences in the naming of the chomosomes (e.g. Chr22 vs. 22) between the gtf file and indexed genome. But my chromosomes are both called 'chr_' in my index and gtf files (I have tried gft files from both ensembl and UCSC'. Could anyone suggest a solution?

The error I get is as follows:

[2013-08-05 09:54:38] Beginning TopHat run (v2.0.9)
[2013-08-05 09:54:38] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-08-05 09:54:38] Checking for Samtools
Samtools version: 0.1.19.0
[2013-08-05 09:54:38] Checking for Bowtie index files (genome)..
[2013-08-05 09:54:38] Checking for reference FASTA file
[2013-08-05 09:54:38] Generating SAM header for /lmb/home/alexsc/bowtie2-2.1.0/indexes/genome
format: fastq
quality scale: phred33 (default)
[2013-08-05 09:54:41] Reading known junctions from GTF file
[FAILED]
[Errno 8] Exec format error

My input line is: /lmb/home/alexsc/tophat-2.0.9.OSX_x86_64/tophat2 -p 12 -G /lmb/home/alexsc/genes.gtf --b2-very-sensitive /lmb/home/alexsc/bowtie2-2.1.0/indexes/genome /lmb/home/alexsc/fqfiles/FCC2B5BACXX-HUMgvmNAARAAPEI-26_L7_1.fq


Thanks!

Alex

[dpryan]

Generally, it's easiest to just use the GTF file from whichever source you got your reference genome. So, Ensembl GTF with the Ensembl genome, UCSC with UCSC, etc. If you're using one of the standard genomes, just download the premade indexes and annotation files from igenomes.

[Alex234]

Thanks for the suggestion but I'm already using the matching UCSC files from iGenomes.

Any other ideas what might be going wrong?

[dpryan]

I'd forgotten that that's actually an OS error. It (tophat) is probably running gtf_juncs there (check tophat's run log in the log directory), so you might try directly running that yourself to see if you get the same error.

[Alex234]

Thanks, it was an OS problem in the end - I was running a version of TopHat2 for OS instead of Linux!