writing loop in bash stops after first iteration [duplicate] - bash

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Are shell scripts sensitive to encoding and line endings?
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Read a file line by line assigning the value to a variable [duplicate]
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Closed 2 months ago.
New to coding
I have a very simple loop that Im using to rename files, but it stops after the first iteration.
Im running the loop:
for x in `cat list_genomes.txt`
do
mv -v $x"_busco/run_hypocreales_odb10" "/busco_runs/run_"$x
done
and the error I get is:
‘FV25228_busco/run_hypocreales_odb10’ -> ‘busco_runs/run_FV25228’
mv: cannot stat ‘\r_busco/run_hypocreales_odb10’: No such file or directory
mv: cannot stat ‘FV32968\r_busco/run_hypocreales_odb10’: No such file or directory
mv: cannot stat ‘FV34765\r_busco/run_hypocreales_odb10’: No such file or directory
mv: cannot stat ‘FV-NC-01\r_busco/run_hypocreales_odb10’: No such file or directory
so the first line works, but then it cannot read the rest.
list_genomes.txt looks like:
FV25228
FV32968
FV34765
FV-NC-01
Fc25332

Answer 1

Your input file has originated on a system that is not identical to the one where you are running the script.
The "\r" on the 2nd-5th line indicate that the file came from a Windows-based system. The person who created the file should have chosen a format that is compatible with system on which the data was going to be processed, which in this case appears to be Unix/Linux based.
If the creator of your input file doesn't change the way they do that, you need to massage the file before feeding it to your program logic, using the command dos2unix.
The following would likely provide you with the necessary fix if all else is correct:
#!/bin/bash
dos2unix -n list_genomes.txt list_genomes.fix
while read line
do
mv -v "${line}_busco/run_hypocreales_odb10" "/busco_runs/run_${line}"
done < list_genomes.fix