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

bash
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updated by Ram Ram • written by sharmatina189059 • sharmatina189059

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.

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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

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.

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updated by Ram Ram • written by sharmatina189059 • sharmatina189059

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

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written by fracarb8 fracarb8

1 answer

home/ -> /home/

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written by fracarb8 fracarb8

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

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written by ATpoint ATpoint

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