Subsampling only works, if the file contains enough reads

[VascoElbrecht]

usearch -fastx_subsample "../D_Minmax/_data/GMP-04606)CCDB-S5-0053)CBGMB-00003_cut_minmax.fasta" -fastaout "_data/GMP-04606)CCDB-S5-0053)CBGMB-00003_cut_minmax_N50000.fasta" -sample_size 50000 -sizein -sizeout

Solution, count reads first and then copy the file over if it has fewer reads than should be subsetted