[Bio-bwa-help] fail to infer insert size

[Fantine M. <fan...@en...>]

Dear Bwa users,

I have a question concerning the sampe step of Bwa aligner.
I tried to map 2 000 000 SOLiD paired-end reads and I get the following
warning in the log:

[bwa_sai2sam_pe_core] 1835008 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] fail to infer insert size: too few good pairs

My problem is that it seems to prevent Bwa from processing the remaining
sequences. Is that normal? The sam file generated contains errors and is not
complete (most of times, samtools fails to transform it to a bam file).
Besides the job error output indicates a segmentation fault.

I am using version 0.5.9

Did anyone come across the same problem?
Any suggestion or help would be greatly appreciated.

Cheers,
-- 
Fantine Mordelet, PhD
Statistical machine learning and modelling of biological systems
Inserm u900/Institut Curie/Mines ParisTech
26 rue d'Ulm
75005 Paris - France

Email : fan...@mi...
Tél : 01 56 24 69 88