Another one I can't find an answer for, and it feels like I've gone mad.
I have a BASH script using a for loop to run a complex command (many protein sequence alignments) on a lot of files (~5000). The loop produces statements that will execute when given alone (i.e. copy-pasted from the error message to the command prompt), but which return "no such file or directory" inside the loop. Script below; there are actually several more arguments but this includes some representative ones and the file arguments.

#!/bin/bash

# Pass directory with targets as FASTA sequences as argument.
# Arguments to psiblast
# Common
db=local/db/nr/nr
outfile="/mnt/scratch/psi-blast"
e=0.001
threads=8
itnum=5
pssm="/mnt/scratch/psi-blast/pssm."
pssm_txt="/mnt/scratch/psi-blast/pssm."
pseudo=0
pwa_inclusion=0.002
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

Running this scripts gives "<scriptname> line <last line before 'done'>: <attempted command> : No such file or directory. If I then paste the attempted command onto the prompt it will run.
Each of these commands takes a couple of minutes to run.