Nextera Expanded Exome BWA aln

[gmarco]

Hello,

I'm trying to align Nextera Expanded Exome (62Mb) samples from HiSeq 2000 (Paired end ~99bp insert size) with BWA aln.

I'm having some troubles. Calculate SA coordinate seems to take a lot more time than for TruSeq 71Mb exome. More than 24 hours at this moment to align R1 and still has not finished. All my R1 and R2 are split in 4M reads (output from Illumina CASSAVA software).

Some aligns are stuck here:

[bwa_aln_core] calculate SA coordinate...

Others have advanced a bit more bit still unusually slow for more than 24 hours:

[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 6.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 61080.65 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 262144 sequences have been processed.
[bwa_read_seq] 6.7% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 60561.20 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 524288 sequences have been processed.
[bwa_read_seq] 7.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 59024.93 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 786432 sequences have been processed.
[bwa_read_seq] 7.8% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 58316.68 sec
[bwa_aln_core] write to the disk... 0.07 sec
[bwa_aln_core] 1048576 sequences have been processed.
[bwa_read_seq] 8.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 57773.30 sec
[bwa_aln_core] write to the disk... 0.08 sec
[bwa_aln_core] 1310720 sequences have been processed.
[bwa_read_seq] 5.5% bases are trimmed.
[bwa_aln_core] calculate SA coordinate...

Thanks

Thank you