BASH statements execute alone but return "no such file" in for loop.

Answer 1

try without the quotes. and you forgot some slashes.

for i in ${1}/*
do
filename=$(basename $i)
local/ncbi-blast-2.2.23+/bin/psiblast \
 -query "${i}" \
 -db "$db" \
 -out "${outfile}/${filename}.out" \
 -evalue "$e" \
 -num_threads "$threads" \
 -num_iterations "$itnum" \
 -out_pssm "${pssm}/$filename" \
 -out_ascii_pssm "${pssm_txt}/${filename}.txt" \
 -pseudocount "$pseudo" \
 -inclusion_ethresh "$pwa_inclusion"
done

Answer 2

The behavior you're observing will occur if there are spaces in the filenames you're iterating over. For this reason, you'll want to properly quote your filenames, as in the following minimal example:

#!/bin/bash
for i in *
do
  filename="$(basename "$i")"
  command="ls -lah '$filename'"
  echo "filename=$filename"
  echo "Command = $command"
  eval "$command"
done

Answer 3

Adding quotes to filenames will not help when using a for loop. To overcome this, I've always done something similar to the following example whenever I needed to loop over filenames:

ls -1 directory | { while read line; do echo $line; done; }