Hi everyone,
I'm running bwa in the sampe mode and, after successfully processing >10M reads it fails with a segmentation fault (as follows) on what appears like a set of poorly-alignable reads. Any suggestions on what can be done to overcome this problem would be much appreciated. Many thanks!
#chunk processed ok
[bwa_read_seq] 2.8% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (492, 529, 561)
[infer_isize] low and high boundaries: 354 and 699 for estimating avg and std
[infer_isize] inferred external isize from 55618 pairs: 523.901 +/- 55.549
[infer_isize] skewness: -0.798; kurtosis: 0.914; ap_prior: 2.38e-04
[infer_isize] inferred maximum insert size: 897 (6.71 sigma)
[bwa_sai2sam_pe_core] time elapses: 9.46 sec
[bwa_sai2sam_pe_core] changing coordinates of 9766 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 76039 out of 91346 Q17 singletons are mated.
[bwa_paired_sw] 5151 out of 16392 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 52.09 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 4.60 sec
[bwa_sai2sam_pe_core] print alignments... 1.93 sec
[bwa_sai2sam_pe_core] 11010048 sequences have been processed.
# failed chunk
[bwa_read_seq] 3.1% bases are trimmed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] fail to infer insert size: too few good pairs
[bwa_sai2sam_pe_core] time elapses: 11.07 sec
[bwa_sai2sam_pe_core] changing coordinates of 0 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 0 out of 0 Q17 singletons are mated.
[bwa_paired_sw] 68090 out of 140740 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 63.65 sec
[bwa_sai2sam_pe_core] refine gapped alignments...
/spool/1339511835.1833481: line 8: 9921 Segmentation fault (core dumped)
../../bwa-0.6.1/bwa sampe -a 2000 ../myGenome.fa myReads.PE500.4.1.sai myReads.PE500.4.2.sai myReads.PE500.4.1.fq myReads.PE500.4.2.fq > myReads.PE500.4.bwape.sam
