I am having trouble getting my for loop to work with prokka, where it keeps throwing the error "Please supply a contig FASTA file on the command line."
I have successfully used this code for other analyses (e.g. with deepARG and ABRicate), so I am unsure as to why it is not working now.
Based on other boards, I also tried to rename the last file in my series to remove any non-alphabetic characters, but this did not appear to do anything.
Hi all,
I am having trouble getting my for loop to work with prokka, where it keeps throwing the error "Please supply a contig FASTA file on the command line."
I have successfully used this code for other analyses (e.g. with deepARG and ABRicate), so I am unsure as to why it is not working now.
Based on other boards, I also tried to rename the last file in my series to remove any non-alphabetic characters, but this did not appear to do anything.
Working in bash:
list1=( $(find /Users/megan/Desktop/R148/ -name "*.fasta" | sort) )
for i in {0..3}
do prokka --locustag ${list1[i]} --outdir ${list1[i]} --prefix ${list1[i]} --compliant --metagenome --coverage 90
done
I have also tried the addition of quotes, as seen here:
list1=( $(find /Users/megan/Desktop/R148/ -name "*.fasta" | sort) )
for i in {0..3}
do prokka --locustag “${list1[i]}” --outdir “${list1[i]}” --prefix “${list1[i]}” --compliant --metagenome --coverage 90
done
If someone could give me suggestions for edits, I would greatly appreciate the help!
Megan