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Old 03-21-2011, 11:48 AM   #2
TenchBB
Junior Member
 
Location: Washington DC

Join Date: Mar 2011
Posts: 1
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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 out.cs.map 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: read.cc:61: 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 solid2fastq.pl. This ran with no error, howvever, the output files are empty!

I am stuck. Can anyone offer any advice??

Sincere thanks,

Tench
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