[maq-help] error with illumina

[Girish B <bg...@he...>]

Hi there,

I am trying to align some short reads to the human genome using maq .  My forward fastq file is about 400 Megs big and consists of 4,255,242 short reads. As a result, I wrote a python code which would select 50,000 short reads. The same thing was done to the reverse sequence. For some reason, after generating the file and running maq map out.map file1.bfq file2.bfq , i get the following error :

irish@girish-Kdesktop:~/maq-0.6.8_x86_64-linux$ ./maq map lane1_s1.map ref1.bfa lane_1_f.bfq lane_1_r.bfq
-- maq-0.6.8
[ma_load_reads] loading reads...
[ma_load_reads] set length of the first read as 36.
[ma_load_reads] set length of the second read as 36.
maq: read.cc:58: longreads_t* ma_load_reads(void*, int, void*, int): Assertion `l >= size_r' failed.
Aborted
 I cannot see where I went wrong. Can anyone advise? Many thanks,Girish B