Error in gene prediction

[Xiaojun928]

Hi Simon,

I'm getting errors running the gene prediction As no *_nett_filtered.fasta can be found, I ran Step1 independently. The command is: perl Step_1_contigs_cleaning_and_gene_prediction.pl VIRSorter ./fasta input_sequences.fna 2

but I got this output

Internal error in autodie/Fatal processing CORE::open: Unknown warnings category 'experimental::smartmatch' at (eval 50) line 6. BEGIN failed--compilation aborted at (eval 50) line 6. at Step_1_contigs_cleaning_and_gene_prediction.pl line 37.

I cannot find solutions by searching online. Your help is really appreciated!

Best, Xiaojun

[simroux]

Hi Xiaojun,

The error seems to be specifically with the "autodie" module from perl, maybe it would be worth installing it as part of the conda installation (https://anaconda.org/bioconda/perl-autodie) if you are running VirSorter in a conda environment ?

[Xiaojun928]

Hi Simon,

Thanks for your reply! I've installed perl-autodie in the using conda. Here is a snapshot.

But I got the same output

Internal error in autodie/Fatal processing CORE::open: Unknown warnings category 'experimental::smartmatch' at (eval 50) line 6. BEGIN failed--compilation aborted at (eval 50) line 6. at Step_1_contigs_cleaning_and_gene_prediction.pl line 37.

Is there something I am missing? Your help is really appreciated!

Best, Xiaojun

[simroux]

I just realized your error is thrown at l. 37, which is where the script tries to read the contig file. Does the file "input_sequences.fna" exists, and is readable by the script ?

[Xiaojun928]

Yes, "input_sequences.fna" is in fasta/ directory, I also tried perl Step_1_contigs_cleaning_and_gene_prediction.pl VIRSorter ./fasta ./fasta/input_sequences.fna 2

And I got the same output.

[Xiaojun928]

It is readable too.

[simroux]

This is really weird.. was the file "input_sequences.fna" created by VirSorter ?

[Xiaojun928]

I use part of scripts in wrapper_phage_contigs_sorter_iPlant.pl to generate "input_sequences.fna". Here are the scripts.

#!/usr/bin/perl -w 
use File::Spec::Functions;
use File::Path 'mkpath';

my $wdir = "./";
my $input_file = "/home-user/xjwang/Minglei/double_check190731/genome_info/Roseovarius_sp_xm-a-104.genome";
my $code_dataset    = 'VIRSorter';
my $fastadir = catdir($wdir, 'fasta');
if ( !-d $fastadir ) {
    mkpath($fastadir);
    my $fna_file = catfile($fastadir, 'input_sequences.fna');
    open my $fa, '<', $input_file;
    open my $s1, '>', $fna_file;

    while (<$fa>) {
        chomp($_);
        if ( $_ =~ /^>(.*)/ ) {
            my $id = $1;
            $id =~ s/[\/\.,\|\s?!\*%]/_/g;
            my $new_id = $code_dataset . "_" . $id;
            say $s1 ">$new_id";
        }
        else {
            say $s1 $_;
        }

    }
    close $fa;
    close $s1;
}

[simroux]

Interesting.. I've never seen anything like this, and no user ever reported this type of error, so I'm not sure what's going on, but it's likely specific to your system / the way VirSorter is run with these separate scripts.

[Xiaojun928]

Ok, maybe I can try it on another system to see what happen. Thanks a lot!