[Bio-Linux] Fwd: Re:Help in running PanFunPro stand alone tool

[Tony Travis]

On 18/08/15 15:24, amanjain at imtech.res.in wrote:
> Hi,
> 
>       I am  having difficulty in running PanFunPro  stand alone tool 
> used to compare core and pan genes. I have installed all the required
> tools and after which I am running PanFunPro2profiles.pl file. No error
> is shown but "Queue: 1" starts printing and it does not end even after 1
> day (snapshot attached). How should I go about it.
> 
> Link to ARTICLE: http://f1000research.com/articles/2-265/v1
> 
> Links to the software : "https://zenodo.org/record/7583#.vcyaflokvc0"   
> "http://www.cbs.dtu.dk/~oksana/phd_thesis/panfunpro/"

Hi, Aman.

It looks like "PanFunPro2profiles.pl" is stuck in this loop because
"InterProScan" is not creating the output file that it's looking for:

> 	for (my $i=0;$i<=$#CF || @queue > 0;) {
> 		if (@queue < $num2scan && $i <= $#CF) {
> 			my $file_in = $CF[$i];
> 			system "cp $file_in $interpro_path";
> 			system "$interpro_path/interproscan.sh -ms 1 -f TSV --iprlookup --goterms --pathways -appl PfamA,TIGRFAM,SuperFamily -i $file_in -b $file_in.Interpro";
> 			push (@queue, $file_in);
> 			sleep 10;
> 			$i++;
> 			next;
> 		} 
> 		print "Queue: ". at queue."\n";
> 		for (my $j=0;$j<=$#queue;) {
> 			my $filename = $interpro_path."/".$queue[$j].".Interpro.tsv";
> 			if (-e $filename) {
                        ^^^^^^^^^^^^^^^^^
> 				splice (@queue, $j, 1);
> 				last;
                                ^^^^^
> 			} 
> 			$j++;
> 		}
> 		sleep 10;
> 	

I would check that your "InterProScan" installation is working properly
before debugging the script. However, you can use the Perl debugger:

  perl -d PanFunPro2profiles.pl ...

HTH,

  Tony.

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