tophat segment-search failed with err=-11 segmentation fault

[webappl]

Hello all.

I am using tophat 2.0.6 to map pair end reads of 60 bp length. The command is:

tophat -p 8 -r 240 -G ~/index/hg19.knownGene.gtf --transcriptome-index=~/index/hg19.knownGene -o tophat_out ~/ucsc/hg19 hm_1.fastq hm_2.fastq

However, the job failed and printed the following error:


segment_juncs v2.0.6 (3670M)
---------------------------
[samopen] SAM header is present: 84 sequences.
Loading reference sequences...
Loading chr1...done
Loading chr2...done
Loading chr3...done
Loading chr4...done
Loading chr5...done
Loading chr6...done
Loading chr7...done
Loading chr8...done
Loading chr9...done
Loading chr10...done
Loading chr11...done
Loading chr12...done
Loading chr13...done
Loading chr14...done
Loading chr15...done
Loading chr16...done
Loading chr17...done
Loading chr18...done
Loading chr19...done
Loading chr20...done
Loading chr21...done
Loading chr22...done
Loading chrX...done
Loading chrY...done
Loading chrM...done
Loading ...done
>> Performing segment-search:
Loading left segment hits...
Segmentation fault (core dumped)

I googled but could not find any help.


Any ideas on how to solve this?

Thanks,

Alex

[webappl]

I found out that the problem was caused by using a wrong reference genome sequence file.