[Bioperl-l] about exonerate

Dimitar Kenanov dimitark at bii.a-star.edu.sg
Thu Apr 29 21:04:09 EDT 2010


Hi guys,
im sorry for bothering you so much but i found some strange thing for 
exonerate. I wrote to Guy Slater about it as well.

So, i downloaded Exonerate 2.2.0 and built it myself on Slackware 
13(64). It went without problem and is working.

Now i am trying to use exonerate through Perl but i got a problem. I 
first used BioPerl's modules to try and run it but no luck. I only get 
three lines of output:
----------------
Command line: [exonerate --model protein2genome --showalignment FALSE 
--showvulgar FALSE --showcigar FALSE --showquerygff TRUE --showtargetgff 
TRUE wdr5_human.fa tmp_fa.out]
Hostname: [darkstar]
-- completed exonerate analysis
----------------

Then i tried to run it myself with the lines  below. It ran with no 
complain but again i got only the three lines above :)
---------------
my @ex_args=("$prog --model protein2genome --showalignment FALSE 
--showvulgar FALSE --showcigar FALSE --showquerygff TRUE --showtargetgff 
TRUE $prot_fa $tmp_fa > $outf");
system(@ex_args) == 0 or die "system @ex_args failed: $!";
---------------

Now when i use exactly the same code but on the terminal everything is 
working just fine. But i need it automatic. Could you please help me? Am 
i missing something?

Thank you for your time.

Best wishes
Dimitar

-- 
Dimitar Kenanov
Postdoctoral research fellow
Protein Sequence Analysis Group
Bioinformatics Institute
A*STAR, Singapore
email: dimitark at bii.a-star.edu.sg
tel: +65 6478 8514



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