[ensembl-dev] Problem with gtf2vep.pl

[Harris, Ronald Alan]

Hi,

I have been trying to use gtf2vep.pl to generate a cache file based on RhesusBase (http://www.rhesusbase.org/) gene annotations on the UCSC rheMac2/Ensembl MMUL_1 assembly. I downloaded their rb2 gene predictions as a gtf file through their UCSC mirror, changed the source column to "protein_coding", added "exon_number" and the appropriate number in the description field, and sorted the annotations by chromosome position. The gtf file can be downloaded from here:

https://bigfile.bcm.edu/download.php?claimID=tnwUAesf9rRRH3u5&claimPasscode=B8mm8RNVZG4Ub6Xy&fid=52811&emailAddr=rharris1@bcm.edu

When I run gtf2vep.pl I get this error:

Can't call method "start" on an undefined value at gtf2vep.pl line 376.

This error occurs after generating some of the cache files in the .vep directory. I tried to run gtf2vep.pl using gtf files with only a single chromosome and it looks like the error consistently occurs when trying to generate the 1-1000000 cache file. Oddly, if I just run gtf2vep.pl on the annotations from 1-1000000 on a single chromosome I do not get this error.

I don't think this is due to chr in chromosome names because the fasta file I am using has chr in the chromosome names.

I would appreciate any help you could give me with this.

Thanks,

Alan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140107/f97c0b47/attachment.html>