Segmentation Fault when Processing annotations GTF

[RRodgers]

Hi,

I have been trying to generate a genome index using an annotations file in GFF3 format.  Here is the command and the output I get:

STAR --runThreadN 8 --runMode genomeGenerate --genomeDir /home/dduvernell/Desktop/fhet_index/ --genomeFastaFiles /home/dduvernell/Desktop/Fhet_Files/killifish20130322asm.fa --sjdbGTFfile /home/dduvernell/Desktop/Fhet_Files/killifish20130322asm.chr.gff --sjdbOverhang 99 --sjdbGTFtagExonParentTranscript Name

Jun 17 16:09:52 ..... Started STAR run
Jun 17 16:09:52 ... Starting to generate Genome files
Jun 17 16:10:36 ... starting to sort  Suffix Array. This may take a long time...
Jun 17 16:10:53 ... sorting Suffix Array chunks and saving them to disk...
Jun 17 16:17:00 ... loading chunks from disk, packing SA...
Jun 17 16:17:38 ... Finished generating suffix array
Jun 17 16:17:38 ... starting to generate Suffix Array index...
Jun 17 16:22:55 ..... Processing annotations GTF
Segmentation fault (core dumped)

Unfortunately I don't know enough about STAR to understand what's happening.  When I remove the annotation file and it's corresponding commands, the process runs fine.  Is there anything I can do to remedy this issue, as I'd prefer to use the annotation file if at all possible.

Thanks

[Alexander Dobin]

Hi Rachel,

could you post a few "exon" lines from the gff file. Typically, gff files denote the "transcrpt" which the exon belongs to with the "Parent=" attribute, so you would need to use 
--sjdbGTFtagExonParentTranscript Parent option.

Cheers

Alex