amrfinder not working on loop?

Question

[Sapphire]

Hi, i am trying to run amrfinder on multiple genome as in loop, and it gives following error, and whatever input file I am using in this program are also not shown after it run.

    #!/bin/bash

    **for k in /home/bvs/neelam/AMRFINDER_hypo/hyocool/*.fasta;do
            NAME=$(basename $k .fasta)
            echo $k
    amrfinder --protein $k --threads 30  -o $k 
    done**

    sh amrfinder.sh

    /home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta
    Running: amrfinder --protein /home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta --threads 30 -o /home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta
    Software directory: '/home/bvs/neelam/AMRFINDER_hypo/amr/'
    Software version: 3.11.14
    Database directory: '/home/bvs/neelam/AMRFINDER_hypo/amr/data/2023-04-17.1'
    Database version: 2023-04-17.1
    AMRFinder protein-only search
      - include -n NUC_FASTA, --nucleotide NUC_FASTA and -g GFF_FILE, --gff GFF_FILE options to add translated searches
      - include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins

    *** ERROR ***
    Cannot open file '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta' to get file size

    HOSTNAME: ?
    SHELL: /bin/bash
    PWD: /home/bvs/neelam/AMRFINDER_hypo
    PATH: /tmp/home/bvs/neelam/bin:/home/bvs/perl5/bin:/home/bvs/neelam/raxml-ng/build/bin:/home/bvs/neelam/PanFunPro_v1.0/my_interproscan/interproscan-5.61-93.0/interproscan.sh:/home/bvs/neelam/AMRFINDER_hypo/amr:/home/bvs/neelam/bedops/bin:/home/bvs/neelam/annotated/ISCompare:/home/bvs/neelam/snippy/bin/samtools-1.12/samtools:/home/bvs/ksnp/kSNP3:/home/bvs/neelam/annotated/anvio/bin:/home/bvs/hole2/exe:/home/bvs/neelam/rgi/bowtie2/bowtie2:/home/bvs/neelam/mlst/any2fasta:/home/bvs/neelam/mlst/bin:/home/bvs/neelam/staramr/bin:/home/bvs/neelam/mash:/home/bvs/neelam/quicktree:/home/bvs/neelam/gclust:/home/bvs/neelam/bedtools2/bin:/home/bvs/neelam/barrnap/bin:/home/bvs/neelam/mmseqs/bin:/home/bvs/neelam/Prodigal/prodigal:/home/bvs/neelam/ncbi-blast/bin:/tmp/home/bvs/neelam/bin:/home/bvs/perl5/bin:/home/bvs/neelam/raxml-ng/build/bin:/home/bvs/neelam/PanFunPro_v1.0/my_interproscan/interproscan-5.61-93.0/interproscan.sh:/home/bvs/neelam/AMRFINDER_hypo/amr/amrfinder:/home/bvs/neelam/bedops/bin:/home/bvs/neelam/annotated/ISCompare:/home/bvs/neelam/snippy/bin/samtools-1.12/samtools:/home/bvs/ksnp/kSNP3:/home/bvs/neelam/annotated/anvio/bin:/home/bvs/hole2/exe:/home/bvs/neelam/rgi/bowtie2/bowtie2:/home/bvs/neelam/mlst/any2fasta:/home/bvs/neelam/mlst/bin:/home/bvs/neelam/staramr/bin:/home/bvs/neelam/mash:/home/bvs/neelam/quicktree:/home/bvs/neelam/gclust:/home/bvs/neelam/bedtools2/bin:/home/bvs/neelam/barrnap/bin:/home/bvs/neelam/mmseqs/bin:/home/bvs/neelam/Prodigal/prodigal:/home/bvs/neelam/ncbi-blast/bin:/tmp/home/bvs/neelam/bin:/home/bvs/perl5/bin:/home/bvs/neelam/raxml-ng/build/bin:/home/bvs/neelam/PanFunPro_v1.0/my_interproscan/interproscan-5.61-93.0/interproscan.sh:/home/bvs/neelam/AMRFINDER_hypo/amr/amrfinder:/home/bvs/neelam/bedops/bin:/home/bvs/neelam/annotated/ISCompare:/home/bvs/neelam/snippy/bin/samtools-1.12/samtools:/home/bvs/ksnp/kSNP3:/home/bvs/neelam/annotated/anvio/bin:/home/bvs/hole2/exe:/home/bvs/neelam/rgi/bowtie2/bowtie2:/home/bvs/neelam/mlst/any2fasta:/home/bvs/neelam/mlst/bin:/home/bvs/neelam/staramr/bin:/home/bvs/neelam/mash:/home/bvs/neelam/quicktree:/home/bvs/neelam/gclust:/home/bvs/neelam/bedtools2/bin:/home/bvs/neelam/barrnap/bin:/home/bvs/neelam/mmseqs/bin:/home/bvs/neelam/Prodigal/prodigal:/home/bvs/neelam/ncbi-blast/bin:/home/bvs/.local/bin:/home/bvs/bin:/home/bvs/.rbenv/shims:/home/bvs/.rbenv/bin:/home/bvs/miniconda3/envs/crisprcasfinder/condabin:/home/bvs/perl5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/go/bin:/home/bvs/sratoolkit.3.0.0-ubuntu64/bin:/home/bvs/.rvm/bin:/home/bvs/.rvm/bin
    Progam name:  amrfinder
    Command line: amrfinder --protein /home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta --threads 30 -o /home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta
    /home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RW109.fasta
    Running: amrfinder --protein /home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RW109.fasta --threads 30 -o /home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RW109.fasta
    Software directory: '/home/bvs/neelam/AMRFINDER_hypo/amr/'
    Software version: 3.11.14
    Database directory: '/home/bvs/neelam/AMRFINDER_hypo/amr/data/2023-04-17.1'
    Database version: 2023-04-17.1
    AMRFinder protein-only search
      - include -n NUC_FASTA, --nucleotide NUC_FASTA and -g GFF_FILE, --gff GFF_FILE options to add translated searches
      - include -O ORGANISM, --organism ORGANISM option to add mutation searches and suppress common proteins

    *** ERROR ***
    Cannot open file '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RW109.fasta' to get file size

Thank you!

[GenoMax]

Cannot open file '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta'

Looks like either the file path is incorrect or the account you are running this from is not able to read files in that location.

[Pierre Lindenbaum]

what is the output of the following commands:

ls -lah '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta'
file '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta'