Merging .fq files per sample using a big loop

Don't use sudo for normal functions as in sudo cat PA001*.fq > PA001m.fq. Following may work. Remove --dry-run to execute the command. Make sure that system has enough resources.

$ parallel --dry-run 'cat {=s/_2//=} {=s/_2/_1/=} {} > {=s/_2.fq//=}_m.fq' ::: *_2.fq

bash loop:

$ for i in $(ls *_2.fq); do echo "cat ${i/_2*/.fq} ${i/_2/_1} $i > ${i/_2/_m}";done

Remove echo after checking the dry-run.

without bash loop:

$ find * -type f -name '*.fq' ! -name '*_*.fq' -exec bash -c 'cat {} ${0/./_1.} ${0/./_2.} > ${0/./_m.}' {} ;

Please take a backup of files before you proceed or try with example files in a test directory.