Amphora2: Illegal division by zero at Phylotyping.pl line 132

Question

[sanzeev.dahal]

I am using AMPHORA2 for phylotyping. And I am stuck at the third script because the counter does not increase at all because it possibly cannot find a match.

my $count = 0;
open (IN, "$marker.aln") ||die "cant open $marker.aln";
    while (<IN>) {
        $count++ if /REF-/; 
    }
close IN;

$count is always 0. and this counter is used for division purpose later on. Therefore, the run is stuck. Anyone encountered the same problem? And/or solved this issue?

Answer 1

[Claire]

Old post but replying for anyone else stuck here.

I was experiencing the same problem, and then noticed in the documentation for Part 2: Marker sequence alignment and trimming:

It is important to know that in order to run the Phylotyping.pl script properly, the MarkerAlignTrimp.pl needs to be run using '-WithReference -OutputFormat phylip' options.

When I added -WithReference to the MarkerAlignTrim.pl command, it worked.

Example, MarkerAlignTrim:

perl /Users/cgib0389/bioinf/Programs/AMPHORA2/Scripts/MarkerAlignTrim.pl \
    -Directory /Users/cgib0389/bioinf/Montana36/assemblies/amphora2 \
    -WithReference \
    -Trim

Then Phylotyping:

perl /Users/cgib0389/bioinf/Programs/AMPHORA2/Scripts/Phylotyping.pl > phylotype.result