Argument "1.7.8" isn't numeric in numeric lt (<) at /home/bvs/anaconda3/envs/prokka_env/bin/prokka line 259.

Question

[Neel]

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 [e-mail]
[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!

[JC]

What is your original command?

[Neel]

Hi, actually i am giving it in to a for loop and the error i had already share above.

#!/bin/bash
    for k in /home/bvs/neel/plasmidCP/*.fna;do

     NAME=$(basename $k .fna)
     echo $k
      prokka --outdir ProkkaA/$k --prefix $k --kingdom Bacteria --cpu 10 
    done

Thank you!

[Mensur Dlakic]

prokka --outdir ProkkaA/$k --prefix $k --kingdom Bacteria --cpu 10

Do you really not see that there is no file name on this line? That is exactly what the error is telling you.

[Neel]

Thank you for pointing out this error, I had fixed this error now as it gives next error, which are given below.

[10:26:58] Will use maximum of 4 cores.
[10:26:58] Annotating as >>> Bacteria <<<
[10:26:58] Generating locus_tag from '/home/bvs/neelam/plasmidCP/P_aeruginosa_1.fna' contents.
[10:26:58] Setting --locustag CGFIGHKM from MD5 c0f201467182fb9550e0d158eb2266c0
[10:26:58] Creating new output folder: ProkkaA//home/bvs/neelam/plasmidCP/P_aeruginosa_1.fna
[10:26:58] Running: mkdir -p ProkkaA\/\/home\/bvs\/neelam\/plasmidCP\/P_aeruginosa_1\.fna
[10:26:58] Using filename prefix: /home/bvs/neelam/plasmidCP/P_aeruginosa_1.fna.XXX
[10:26:58] Setting HMMER_NCPU=1
[10:26:58] Writing log to: ProkkaA//home/bvs/neelam/plasmidCP/P_aeruginosa_1.fna//home/bvs/neelam/plasmidCP/P_aeruginosa_1.fna.log
[10:26:58] **Can't open logfile**
/home/bvs/neelam/plasmidCP/P_aeruginosa_2020HL00861_pPaeWC20_001_02.fna

[Mensur Dlakic]

Your command is set up completely wrong regarding variable names, and you repeatedly refuse to read the screen output which is in front of you. I suggest you read literally each line, word by word, and see if those prefix names and directories make sense to you. It literally tells you what log file it is trying to write to before saying that it can't. There is some basic troubleshooting you must do yourself.

Answer 1

[Mensur Dlakic]

I don't think Perl version is your problem. There is a line at the end:

[09:35:51] Please supply a contig FASTA file on the command line.

It doesn't interpret correctly the file you provided. If you give a complete command line - I think that should be done with any problem - we may be able to troubleshoot. A few lines P_aeruginosa_KB-PA_F19-3.fna could be useful as well.

[Neel]

Thank you so much for your time. Now i had change file name (P_aeruginosa_KB-PA_F19-3.fna to P_aeruginosa_KB_PA_F19-3.fna) still it giving same above error.