formatdb -i AllBacterias.fasta -p F -o T
formatdb -i vector -p F -o T
/opt/seqclean/seqclean cleanSeqs.fasta -s AllBacterias.fasta,vector -c 2

**************************************************
Sequences analyzed: 200347
—————————————————- valid: 200096 (13 trimmed) trashed: 251 **************************************************
——= Trashing summary =——— by ‘short’: 247 by ‘shortq’: 1 by ‘AllBacterias.fasta’: 3
———————————————
Output file containing only valid and trimmed sequences: cleanSeqs.fasta.clean
For trimming and trashing details see cleaning report : cleanSeqs.fasta.cln

/opt/seqclean/cln2qual cleanSeqs.fasta.cln cleanSeqs.qual