No L or C lines in gfa from minimap2 paf

[cistarsa]

Hello. I've generated a paf using minimap2 and gfa seqwish (via docker) but the subsequent gfa is missing some important lines and is not read by vg.

$ ./minimap2 -cx asm5 F_Kansas_60.fasta M_MD_60.fasta F_Oregon_60.fasta Ldec_2018LI_60.fasta Mexi_60.fasta -o L5.paf -t 16

$ cat F_Kansas_60.fasta M_MD_60.fasta F_Oregon_60.fasta Ldec_2018LI_60.fasta Mexi_60.fasta > Ldec5.fasta
$ docker run -it -v ${PWD}:/tmp kingcohn1/seqwish:v1 /bin/bash
d:/tmp# seqwish -t 16 -s L5.paf -s Ldec5.fasta -g L5.gfa -P

dockerfile:

FROM ubuntu:20.04

ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get update && apt-get install -y \
  dialog \
  apt-utils \
  build-essential \
  cmake \
  libssl-dev \
  libffi-dev \
  python3-distutils \
  python3-dev \
  git \
  && rm -rf /var/lib/apt/lists/*

RUN git clone --recursive https://github.com/ekg/smoothxg.git

RUN cd smoothxg && cmake -H. -Bbuild && cmake --build build -- -j 4

ENV PATH="/smoothxg/bin:${PATH}"

[AndreaGuarracino]

Hi @cistarsa, could you please explain better what your problem is? What do you mean that vg cannot read your GFA file?

[cistarsa]

Thank you, this has been resolved.