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Old 11-08-2010, 04:16 AM   #1
Junior Member
Location: Nottingham

Join Date: Oct 2010
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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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Old 03-21-2011, 12:48 PM   #2
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I have recently experienced a similar problem. I am also attempting to use MAQ to map my SOLiD reads.

I had recieved the .fastq files from a collaborator so I first used "maq fastq2bfq" and "maq fasta2csfa" and then ran the following the command:

maq map -c ref.csbfa reads_1.bfq reads_2.bfq 2

I got back the following error:

-- maq-0.7.1
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 1.
[ma_load_reads] set length of the second read as 1.
maq: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `strncmp(name, lr->name[j], tl-1) == 0' failed.

I then tried to go back a step and use the .csfasta and _QV.qual files to create the .fastq files using This ran with no error, howvever, the output files are empty!

I am stuck. Can anyone offer any advice??

Sincere thanks,

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Old 03-21-2011, 03:43 PM   #3
Nils Homer
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@TenchBB: Please do not double-post in two different forums (or here for that matter). Thank-you!
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.fasta, maq problem, reference sequence, segmentation fault

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