Bfast localalign error
 

I am Pooja working as an intern in Ganit labs in Bangalore, on NGS .

I was trying to run bfast for paired end alignment using bfast (bfast+bwa-0.6.4e) and I am getting the following error in the localalign step

The error looks like this:

bfast: AlignNTSpace.c:165: AlignNTSpaceGappedConstrained: Assertion `0 <= endRowStepOne && 0 <= endColStepOne' failed.

command used for localalign was:

/Apps/serial/bfast+bwa/bin/bfast localalign -f hg_18.fa -n 8 -M 1280 -A 0 -O bfast.bwaaln_20-T_3_3_1_sequence.fastq.bmf -T bfast.bwaaln_20T_3_3_2_sequence.bmf > bfast.la_20-T_3_3_sequence_te.baf

I have all the files like .brg file and all the indexed(.bif) files present in the working directory.
Also I have used bwaaln to generate the match (.bmf) files.

Thank you

Can you add -U and try again?