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perl script 'blast_rod_finder.pl' not giving output but no errors either
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2.3 years ago
Lau • 0

Hi, I apologize about this question in case its easy answer, I have been trying to run this script written in perl blast_rod_finder.pl (https://github.com/aleimba/bac-genomics-scripts/tree/master/rod_finder), which finds regions of difference between two genomes. It should be pretty straight forward but when I run it nothing happens. It should give back a folder with the results but that's not the case and is not giving me any errors so not sure how to figure out whats going wrong. I checked and all my bioperl modules are there... any tips greatly appreciated.

This is the script I am using:

perl blast_rod_finder.pl -q CarnobacteriummaltaromaticumSKLD3.gbk -r CarnobacteriummaltaromaticumSKLD3_blastout -m 2000

-q is GBK file of the query -r blast output between query and a reference genome![enter image description here -m is size

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Entering edit mode
2.0 years ago
YaGalbi ♦ 1.4k
Biocomputing, MRC Harwell Institute, Ox…

Did you check your home or in the folder that contains the script? Some programs print output there unless you give a full output path

This looks like where you choose output folder location:

### Create results directory, where output files are written to
my $out_dir = './results/'; if (-e$out_dir) {
print "\n\n###Directory \'$out_dir\' already exists! Replace the directory and all its contents? [y|n] "; my$user_ask = <STDIN>;
if ($user_ask =~ /y/i) { unlink glob$out_dir."*"; # remove all files in results directory
rmdir $out_dir; # remove the empty directory } else { die "Script abborted!\n"; } } mkdir$out_dir or die "Can't create directory \"$out_dir\":$!\n";


Are you getting any of the messages here printed to your terminal?

Try:

    my \$out_dir = 'full/path/to/results/';

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Thanks, for the tips, I think the script must not be running because I added a message and is not showing up, even if I run the script alone it doesn't do anything. Sorry I am not used to perl so not sure how to tackle this

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I tried this change, but I think the problem is the script is not running because there are no messages appearing in the terminal

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I just realized what was happening, it was really simple, thanks!

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Entering edit mode

I just realized what was happening, it was really simple, thanks!

And what was solution, to provide closure to this question?