Bfast localalign error

dg.pooja · 01-31-2011, 05:53 PM

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

drio · 01-31-2011, 06:35 PM

Can you add -U and try again?

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01-31-2011, 05:53 PM	#1
dg.pooja Junior Member Location: India Join Date: Nov 2010 Posts: 2	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

01-31-2011, 06:35 PM	#2
drio Senior Member Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008 Posts: 323	Can you add -U and try again? __________________ -drd