bash script error to copy files from multiple directories to one directory

Question

[sharmatina189059]

for FILE in home/tinas/MAGs_12_example_data/12_MAGs_seq.fna/dir_extension_checkm/tina/prokka_annotation/**/*.gff
do
        cp $FILE /home/tinas/MAGs_12_example_data/12_MAGs_seq.fna/dir_extension_checkm/tina/prokka_annotation/all_gff_file/
done

This command is working fine in terminal but in bash script this shows No such file or directory. Can anybody help me out with this command?

[Michael]

Hi, not sure why this loop is necessary. cp can copy multiple files at once. cp /home/.../*.gff /home/.../destination works, note you are lacking a single "/" in your source dir.

After you have run this for the first time, if you run it again, you will get an error that you are trying to copy a file onto itself.

[sharmatina189059]

I tried cp **/*.gff /home/tinas/MAGs_12_example_data/12_MAGs_seq.fna/dir_extension_checkm/tina/prokka_annotation/all_gff_file/ in bash script but it was not working.

[fracarb8]

cp */*.gff otherwise you will copy the hidden file .gff

Answer 1

[fracarb8]

home/ -> /home/

[sharmatina189059]

Thank you so much. Now it is working.

[ATpoint]

I moved the comment to answer, please accept it (the checkmark symbol) if it solved the issue.