Hi Steffen,
On Sat, Jun 06, 2020 at 03:41:44PM +0200, Steffen Möller wrote:
$ /usr/bin/minimap2 out_pacbio/10-consensus/chunks.fasta
E.coli_PacBio_40x.fasta -x map-pb -t 4 -a -p 0.5 -N 10
--sam-hit-only -L -Q --secondary-seq
[ERROR] unknown option in "E.coli_PacBio_40x.fasta"
Exit code: 1
A look at -h and the .1 suggests that the order of arguments is
unfortunate. Options should be first. Please kindly try
/usr/bin/minimap2 -x map-pb -t 4 -a -p 0.5 -N 10 --sam-hit-only -L
-Q out_pacbio/10-consensus/chunks.fasta E.coli_PacBio_40x.fasta
and then add the "--secondary-seq" argument and see it fail.
At https://github.com/fenderglass/Flye/issues/249 I get the
impression that the --secondary-seq is not an error and at
https://github.com/fenderglass/Flye/blob/b0107d8a4806a42aa8a16667bb1abb93ab9afd56/lib/minimap2/main.c#L69
I see it implemented which I do not see in the original
https://github.com/lh3/minimap2/blob/master/main.c
I do not have an immediate answer to what to do now. Upstream calls
their minimap "flye-minimap". So, maybe embedding that binary with
the flye binary may indeed be an option.
The suspicion that the minimap2 code copy in flye is patched. I have
attached the diff between the Debian packaged minimap2 which actually
introduces --secondary-seq.
I wonder if there is some volunteer to talk to both upstreams to
merge the patch.