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2 hours ago by


I am using pangenome graph builder to align multiple genomes and create make a graph genome using:

pggb -i input.fasta.gz -w 100000 -s 20000 -p 120 -a 70 -n 5 -t 16 -v -l output

It runs the alignment step and generates corresponding PAF output file. However, in the seqwish step, it gives this error:

Passed in argument, but no positional arguments were ready to receive it: 8
  seqwish {OPTIONS}

    seqwish: a variation graph inducer


      -h, --help                        display this help menu
      -a[FILE], --sxs-alns=[FILE]       induce the graph from these .sxs
                                        formatted alignments
      -p[FILE], --paf-alns=[FILE]       induce the graph from these PAF
                                        formatted alignments
      -s[FILE], --seqs=[FILE]           the sequences used to generate the
                                        alignments (FASTA, FASTQ, .seq)
      -b[BASE], --base=[BASE]           build graph using this basename
      -g[FILE], --gfa=[FILE]            write the graph in GFA to FILE
      -m[FILE], --match-list=[FILE]     use the sequence match list in FILE to
                                        subset the input alignments
      -o[BASE], --vgp-out=[BASE]        write the graph in VGP format with
                                        basename FILE
      -t[N], --threads=[N]              use this many threads during parallel
      -r[N], --repeat-max=[N]           limit transitive closure to include no
                                        more than N copies of a given input base
      -k, --keep-temp                   keep intermediate files generated during
                                        graph induction
      -d, --debug                       enable debugging

seqwish -t 16 -s input.fasta.gz -p input.paf -k 8 -g input.gfa -B 1000000 -P

It is not recognizing options -k -B -P and I did give these options in the command line. I think it is automatically coming with some other parameter. I am not sure how to avoid these parameters. Thank you for any help!

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