fpa error?

[subwaystation]

Running the major script I get:

[ERROR] missing input: please specify a query file to map or option -d to keep the index

real    5m11.866s
user    16m54.474s
sys 0m21.519s
error: Found argument '-l' which wasn't expected, or isn't valid in this context

USAGE:
    fpa [OPTIONS] [SUBCOMMAND]

Actually fpa does not have this option:

[heumos@wave ~]$ fpa --help
fpa 0.5 Krabby
Pierre Marijon <pierre.marijon@inria.fr>
fpa take long read mapping information and filter them

USAGE:
    fpa [OPTIONS] [SUBCOMMAND]

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

OPTIONS:
    -z, --compression-out <compression-out>
            Output compression format, the input compression format is chosen by default [possible values: gzip, bzip2,
            lzma, no]
    -F, --format <format>                                  Force the format used [possible values: paf, m4]
    -i, --input <input>                                    Path to input file, use '-' for stdin [default: -]
        --internal-threshold <internal-match-threshold>
            A match is internal match if overhang length > match length * internal threshold this option set internal
            match [default: 0.8]
    -o, --output <output>                                  Path to output file, use '-' for stdout [default: -]

[subwaystation]

Oh, just discovered there is fpa keep:

[heumos@wave ~]$ fpa keep --help
fpa-keep 
fpa keep only mapping match this constraints

USAGE:
    fpa keep [FLAGS] [OPTIONS] [SUBCOMMAND]

FLAGS:
    -c, --containment      Keep only containment mapping
    -d, --dovetail         Keep only dovetail mapping
    -h, --help             Prints help information
    -i, --internalmatch    Keep only internal mapping
    -m, --same-name        Keep only mapping where reads have same name
    -V, --version          Prints version information

OPTIONS:
    -l, --length-lower <length_lower>                      Keep only mapping with length lower than value
    -L, --length-upper <length_upper>                      Keep only mapping with length upper than value
    -n, --name-match <name_match>                          Keep only mapping where one reads match with regex
    -s, --sequence-length-lower <sequence_length_lower>
            Keep only mapping where one reads have length lower than value

    -S, --sequence-length-upper <sequence_length_upper>
            Keep only mapping where one reads have length upper than value

[AndreaGuarracino]

The working commands:

zcat Sc+Sp.pan.paf.gz | fpa keep -L 10000 | pigz >Sc+Sp.pan.fpal10k.paf.gz
zcat Sc+Sp.pan.paf.gz | fpa keep -L 2000 | pigz >Sc+Sp.pan.fpal2k.paf.gz