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Old 11-08-2010, 03:16 AM   #1
Junior Member
Location: Nottingham

Join Date: Oct 2010
Posts: 9
Question Maq: Segmentation Fault


I am trying to map my SOLiD reads in Maq. I have converted my reads from .csfasta and .qual to .fastq using ''. I then generated a binary file using 'maq fastq2bfq'. I turned my reference genome (GRCh37) from .fa to .csfa using 'maq fasta2csfa' and made this binary using 'fasta2bfa'.

When I use 'maq map' I get a segmentation fault. There is no other information. Here is my command;

maq map -c ref.csbfa reads.bfq 2> aln.log

Does anyone have any ideas what could be causing this? I am currently using v0.7.1, but have tried the same command on earlier versions and get the same. I am wondering is the 'maq fasta2csfa' accepts reference in '.fa'?
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