Getting a vector cleaned output file

[chklopp]

After commenting some source code lines I got the assembly and vector cleaning results

-rwxrwxrwx 1 cklopp miat 63 déc. 16 18:24 samtools.stdout
drwxrwxrwx 1 cklopp miat 0 déc. 16 18:24 filtered
-rwxrwxrwx 1 cklopp miat 1392 déc. 16 18:24 BifidoProton.S01_trim_stdout.txt
-rwxrwxrwx 1 cklopp miat 51600 déc. 16 18:24 BifidoProton.S01_contigs.fasta
-rwxrwxrwx 1 cklopp miat 51600 déc. 16 18:24 BifidoProton.S01_scaffolds.fasta
-rwxrwxrwx 1 cklopp miat 172326 déc. 16 18:24 spades_log.txt
-rwxrwxrwx 1 cklopp miat 12673 déc. 16 18:24 BifidoProton.S01.nsq
-rwxrwxrwx 1 cklopp miat 180 déc. 16 18:24 BifidoProton.S01.nin
-rwxrwxrwx 1 cklopp miat 192 déc. 16 18:24 BifidoProton.S01.nhr
-rwxrwxrwx 1 cklopp miat 301 déc. 16 18:24 BifidoProton.S01_endsMapped.tbl
-rwxrwxrwx 1 cklopp miat 144 déc. 16 18:24 potential_fosmid_fragments.tsv
-rwxrwxrwx 1 cklopp miat 8002 déc. 16 18:24 BifidoProton.S01_fosmid_coordinates.tsv
-rwxrwxrwx 1 cklopp miat 7960 déc. 16 18:24 BifidoProton.S01_formatted.fasta
-rwxrwxrwx 1 cklopp miat 52 déc. 16 18:24 BifidoProton.S01_fosmid_end_failures.tsv

The Spades results are OK but the formatted.fasta file does not contain the vector cleaned insert.
I perhaps misunderstood how to provide the bacteria and plamid vector sequences for the cleaning process.
Is there some documentation available on this topic?

[chklopp]

I've found the endsMapped.tbl with the vector alignment results which enable to remove the vector in the assembly but I'm a bit surprise not to find a clean insert fasta file.