Argument "1.7.7" isn't numeric in numeric

[tseemann]

Argument "1.7.7" isn't numeric in numeric lt (<) at /home/tseemann/git/prokka/bin/prokka line 259.

[MatthewRalston]

Hello @tseemann , I noticed a similar error with a recent release of blastp (2.10) isn't being recognized as properly sufficient (>2.2 is required). Could this be a similar string comparison error?

[hydong113]

The same situation. What can I do to solve it?

[JAnsede]

Is there any solution since September?

[wolfgangrumpf]

I am also getting this error. I simply can't get Prokka to run!

[ghost]

Hi, I am getting the same error message, any recommendation?

[ghost]

Hello,

It could be resolved doing this --> https://github.com/tseemann/prokka/issues/448

follow --> cabrerad commented on 13 Jan, I'll quote him

Try this: $ conda create -n prokka_env -c conda-forge -c bioconda prokka $ conda activate prokka_env

It worked for me! I had the same problem as you.

You can check your environment list with: $ conda env list

Hope this can help!

[wolfgangrumpf]

This approach finally worked for me. It's bizarre - I TRIED doing a Conda install previously, but it too failed - until I wiped everything and started again with this approach. Thanks, JuanMartinezV!

[arif-tanmoy]

Hi, faced this Bioperl version issue a few months back. solved it by modifying a few lines of code.

Here's how I solved it on v1.14.5. Pretty sure, it will work on v1.14.6 too.

Need this module. use Perl::Version;

Changed the code a bit on those specific lines (starts from line 259)

my $minbpver = "1.006002"; # for Bio::SearchIO::hmmer3
my $bpver0 = Perl::Version->new($Bio::Root::Version::VERSION);
my $bpver = $bpver0->numify;
msg("You have BioPerl $bpver");
err("Please install BioPerl $minbpver or higher") if $bpver < $minbpver;

[minhtrung1997]

I can solve it with a pre-code : prokka --setupdb

[neelam19051]

Hi, I have tried all the suggestion regarding this error on this page but still unable to resolve it. please help me if anyone know anything about this error.

This is prokka 1.14.6 [09:35:51] Written by Torsten Seemann torsten.seemann@gmail.com [09:35:51] Homepage is https://github.com/tseemann/prokka [09:35:51] Local time is Tue Sep 27 09:35:51 2022 [09:35:51] You are bvs [09:35:51] Operating system is linux [09:35:51] You have BioPerl 1.7.8 Argument "1.7.8" isn't numeric in numeric lt (<) at /home/bvs/anaconda3/envs/prokka_env/bin/prokka line 259. [09:35:51] System has 96 cores. [09:35:51] Will use maximum of 10 cores. [09:35:51] Annotating as >>> Bacteria <<< [09:35:51] Please supply a contig FASTA file on the command line. /home/bvs/neelam/plasmid_cp/P_aeruginosa_KB-PA_F19-3.fna

Thank you!

[MHassanSaeed]

I can solve it with a pre-code : prokka --setupdb

How?

I am unable to resolve this issue.

[Veroman]

prokka --setupdb did not work, but @arif-tanmoy solution worked for me.

[saras224]

Hi, faced this Bioperl version issue a few months back. solved it by modifying a few lines of code.

Here's how I solved it on v1.14.5. Pretty sure, it will work on v1.14.6 too.

Need this module. use Perl::Version;

Changed the code a bit on those specific lines (starts from line 259)

my $minbpver = "1.006002"; # for Bio::SearchIO::hmmer3
my $bpver0 = Perl::Version->new($Bio::Root::Version::VERSION);
my $bpver = $bpver0->numify;
msg("You have BioPerl $bpver");
err("Please install BioPerl $minbpver or higher") if $bpver < $minbpver;

Hi @arif-tanmoy I tried to change the code in prokka script but it shows me this error now:

Can't locate object method "new" via package "Perl::Version" (perhaps you forgot to load "Perl::Version"?) at /home/rsharma/anaconda3/envs/prokka/bin/prokka line 257

Kindly help me resolve this error! Thanks in Advance!!

[joelwwh]

Hi, faced this Bioperl version issue a few months back. solved it by modifying a few lines of code. Here's how I solved it on v1.14.5. Pretty sure, it will work on v1.14.6 too. Need this module. use Perl::Version; Changed the code a bit on those specific lines (starts from line 259)

my $minbpver = "1.006002"; # for Bio::SearchIO::hmmer3
my $bpver0 = Perl::Version->new($Bio::Root::Version::VERSION);
my $bpver = $bpver0->numify;
msg("You have BioPerl $bpver");
err("Please install BioPerl $minbpver or higher") if $bpver < $minbpver;

Hi @arif-tanmoy I tried to change the code in prokka script but it shows me this error now:

Can't locate object method "new" via package "Perl::Version" (perhaps you forgot to load "Perl::Version"?) at /home/rsharma/anaconda3/envs/prokka/bin/prokka line 257

Kindly help me resolve this error! Thanks in Advance!!

This link (https://github.com/tseemann/prokka/pull/619) fixed it for me as of today. I had the same problem as you

[arif-tanmoy]

Hi @joelwwh you just need to add the module I mentioned in the text.

use Perl::Version;

Add this in the script (in the module calling section) and it should be fine too.

[joelwwh]

@arif-tanmoy I actually tried that but got the same error as @saras224. Not sure why. Perhaps others have better luck. Thanks for your help though

[saras224]

Hi @joelwwh you just need to add the module I mentioned in the text.

use Perl::Version;

Add this in the script (in the module calling section) and it should be fine too.

Hi @arif-tanmoy Thanks for responding but I have a doubt, what do you mean when you are saying " use Perl::Version; "? What I am doing is that I am going to the prokka script in the bin and changing the lines from 259. Is it not what we should do? And even after doing that, I am getting the same error.

Thanks!

[arif-tanmoy]

Hi @joelwwh you just need to add the module I mentioned in the text. use Perl::Version; Add this in the script (in the module calling section) and it should be fine too.

Hi @arif-tanmoy Thanks for responding but I have a doubt, what do you mean when you are saying " use Perl::Version; "? What I am doing is that I am going to the prokka script in the bin and changing the lines from 259. Is it not what we should do? And even after doing that, I am getting the same error.

Thanks!

Hi @saras224 - yes, you have to change the codes in/from line 259. However, you are using a different module there, named "Perl::Version" and it's not in the script by default. So, you have call that module from the script. You can add that module calling part use Perl::Version; in line 41. Now, with the changes in line 41 and few lines near 259, the script should run without an error.

[brilliant2643]

Hi @joelwwh you just need to add the module I mentioned in the text. use Perl::Version; Add this in the script (in the module calling section) and it should be fine too.

Hi @arif-tanmoy Thanks for responding but I have a doubt, what do you mean when you are saying " use Perl::Version; "? What I am doing is that I am going to the prokka script in the bin and changing the lines from 259. Is it not what we should do? And even after doing that, I am getting the same error. Thanks!

Hi @saras224 - yes, you have to change the codes in/from line 259. However, you are using a different module there, named "Perl::Version" and it's not in the script by default. So, you have call that module from the script. You can add that module calling part use Perl::Version; in line 41. Now, with the changes in line 41 and few lines near 259, the script should run without an error.

Hi! I use this method to change those code, but I get some new error Bareword "Perl::Version" not allowed while "strict subs" in use at /home/boot/micromamba/envs/prokka/bin/prokka line 41. BEGIN not safe after errors--compilation aborted at /home/boot/micromamba/envs/prokka/bin/prokka line 1612. I'm wondering if I change the wrong line?