Entering edit mode
17 months ago
Sapphire
▴
10
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!
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.
what is the output of the following commands: