Segmentation fault (core dumped)

[hhx037]

Hi,

I'm trying to map a paired-end exome sequence, but get a segmentation fault.
I've redownloaded the source code, used scons to install, everything completed successfully.

Our cluster is running under Scientific Linux. Any idea?

/hpg-aligner-x86_64-src-1.0.1/bin/hpg-aligner dna --bwt-index /share/panosscratch/REPOSITORY/Reference_genomes/Homo_sapiens.GRCh37.73/HPG_index/ --fastq ./fastq/11167_5_71.end1.fq --fastq2 ./fastq/11167_5_71.end2.fq --outdir /share/panosscratch/hhx037/GreekMI/BAM/HPG/ --prefix 11167_71 --paired-mode 1 --time --report-only-paired

+--------------------------------------------------------------------------------------+
| PARAMETERS CONFIGURATION |
+--------------------------------------------------------------------------------------+
General parameters
Mode: DNA
Input FastQ filename, pair #1: ./fastq/11167_5_71.end1.fq
Input FastQ filename, pair #2: ./fastq/11167_5_71.end2.fq
BWT index directory name: /share/panosscratch/REPOSITORY/Reference_genomes/Homo_sapiens.GRCh37.73/HPG_index/
Output directory name: /share/panosscratch/hhx037/GreekMI/BAM/HPG/

Architecture parameters
Number of cpu threads 32
Batch size: 20000 bytes

Report parameters
Report all hits: Disable
Report n best hits: 0
Report n hits: 0
Report best hits: Enable
Report unpaired reads: Disable

Seeding and CAL parameters
Number of seeds: 10
Seed size: 20
Min seed size: 16
Min CAL size: 30
Min. number of seeds in a CAL: the maximun
Seeds max distance: 100
Flank length: 5

Mapping filters
For reads: 50 mappings maximum, otherwise discarded
For seeds: 500 mappings maximum, otherwise discarded

Pair-mode parameters
Pair mode: 1
Min. distance: 50
Max. distance: 800

Smith-Waterman parameters
Min score : 0.6000
Match : 5.0000
Mismatch : -4.0000
Gap open : 10.0000
Gap extend : 0.5000

+--------------------------------------------------------------------------------------+
Segmentation fault (core dumped)

Cheers,

Stephane