Question about MAQ Easyrun

[cliff]

Hey, all

I am new to MAQ and am frustrated about the easyrun function. I tried the following command on a single-end fastq file:

maq.pl easyrun -d /..../usr chr1.fa s_1_1_sequence.fastq

It took about 5 hours to finish this run and the below is the report:
-- == statmap report ==
-- # single end (SE) reads: 18980757 (because I just used read)
-- # mapped SE reads: 1772399 (/ 18980757 = 9.33%)
-- # paired end (PE) reads: 0
-- # mapped PE reads: 0 (/ 0 = NA%)
-- # reads that are mapped in pairs: 0 (/ 0 = NA%)
-- # Q>=30 reads that are moved to meet mate-pair requirement: 0 (/ 0 = NA%)
-- # Q<30 reads that are moved to meet mate-pair requirement: 0 (NA%)

Since our expriment design is paired-end, I tried again for two fastq files.

maq.pl easyrun -d /..../usr chr1.fa -p s_1_1_sequence.fastq s_1_2_sequence.fastq

I specified "-p" here because there are two input read sequence files. But this time, the run failed.

I can't figure it out why this can't work. Can anybody here help me on this?

All your help will be greatly appreciated!