Snakemake looking for files when try to rerun
This occurs on some data sets, especially those which have been copied or moved. It looks for the files:
mg.se1.trimmed.fq mg.se2.trimmed.fq
The above supposed to be intermediate files and snakemake should not actually look for them. The same happens to the fastqc files. It runs well in a complete run but not when it specific steps are attempted to be rerun.