MAQ - Segmentation fault

[dukevn]

Hi all,

I just started with the DNA sequencing and analysis area and everything is all new to me. So please be easy on me.

Now I am trying to learn how to align and analyze data. I downloaded MAQ, compiled it (in PowerPC G5 computer), copied maq, maq.pl etc to runfiles director, and try to run with a test data file as suggested in MAQ

maq.pl demo ref.fasta calib-36.dat

Calib-36.dat came together with the MAQ package, and ref.fasta is as simple as

>D86934(D86934)probable sugar-nucleotide dehydratase [imported] - Mycobacterium leprae
MYGEPVRALVTGAAGFIGSTLVDRLLADGHTVVGLDNFATGHAANLEHLASTPALAFVEA
DIVTADLQTILDEHRPEVVFHLAAQIDVRHSVVDPQFDASVNVIGTVRLAEAARHTGVRK
IVHTSSGGSIYGTPSQYPTPETVPTDPTSPYAAGKVAGEIYLNTFRHLCGLDCSHIAPAN
VYGPRQDPYGEAGVVAIFVQALLSDRPTKVFGDGTHTRDYVFVDDVVDAFIKASGDAGGG
QRFNIGTGIETSDRQLHTAVSAAVGGPDDPEFHPPRLGDLKRSCLDIGLATTVLGWSPQV
QLDDGVRRTVEYFRAAQRS

After a while, I got Segmentation fault error:

-- CMD: mkdir -p maqdemo
-- CMD: /usr/local/bin/maq simulate -N 1000000 maqdemo/r1.fq maqdemo/r2.fq ref.fasta calib-36.dat > maqdemo/true.snp
-- 1 sequences, total length: 319
sh: line 1: 37110 Segmentation fault      /usr/local/bin/maq simulate -N 1000000 maqdemo/r1.fq maqdemo/r2.fq ref.fasta calib-36.dat > maqdemo/true.snp
** fail to run command '/usr/local/bin/maq simulate -N 1000000 maqdemo/r1.fq maqdemo/r2.fq ref.fasta calib-36.dat > maqdemo/true.snp' at /usr/local/bin/maq.pl line 842.

What I am doing wrong, or is this any missing step that I forget? Anybody help please!

[nilshomer]

Hi all,

>D86934(D86934)probable sugar-nucleotide dehydratase [imported] - Mycobacterium leprae
MYGEPVRALVTGAAGFIGSTLVDRLLADGHTVVGLDNFATGHAANLEHLASTPALAFVEA
DIVTADLQTILDEHRPEVVFHLAAQIDVRHSVVDPQFDASVNVIGTVRLAEAARHTGVRK
IVHTSSGGSIYGTPSQYPTPETVPTDPTSPYAAGKVAGEIYLNTFRHLCGLDCSHIAPAN
VYGPRQDPYGEAGVVAIFVQALLSDRPTKVFGDGTHTRDYVFVDDVVDAFIKASGDAGGG
QRFNIGTGIETSDRQLHTAVSAAVGGPDDPEFHPPRLGDLKRSCLDIGLATTVLGWSPQV
QLDDGVRRTVEYFRAAQRS

That doesn't look any DNA I have seen before!