Cufflinks cufflinks v1.0.3 - segmentation fault bias correction chrNT annotations

[adrian]

Hi:

I am using:

bowtie-0.12.5.
tophat-1.2.0
cufflinks v1.0.3


while running:

cufflinks -p 4 -N -G Homo_sapiens.NCBI36.52.fixed.gtf -b hg18.fa -M masked.gtf accepted_hits.bam

I always hit segmentation fault while cufflinks tried to bias correct chrNT contigs in ensembl GTF file. I teased this on cluster, standalone and other machines.

After removing chrNT contig annotations from GTF file, finally cufflinks progressed further.

why would chrNT contigs help segementation fault in cufflinks?

Could you please share your opinion or reasons why this could be? Also is there a danger removing chrNT contigs from GTF file.

thanks for you time.