Has anyone found any solution to this problem? I've just tried this C program, which seems to work well, but I am still getting the segmentation fault. I have 32GB of RAM on my system, so again its not memory.
[p@c0-0]$ bwa samse /share/apps/genome/human/bowtie/hg18/hg18.fa /data/Mk/FpMb.sai /data/Mk/FpMb.part1.fastq > /data/Mk/FpMb.2.sam
[bwa_aln_core] convert to sequence coordinate... 5.31 sec
[bwa_aln_core] refine gapped alignments... Segmentation fault
[p@c0-0]$ bwa samse /share/apps/genome/human/bowtie/hg18/hg18.fa /data/Mk/FpMb.sai /data/Mk/FpMb.part1.fastq > /data/Mk/FpMb.2.sam
[bwa_aln_core] convert to sequence coordinate... 5.31 sec
[bwa_aln_core] refine gapped alignments... Segmentation fault
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