Hi Andreas, disclaimer: I don't run minimap2 myself - yet.
On 05.06.20 20:35, Andreas Tille wrote:
... (explicit paths shortened) I tried the very command that is actually run: $ /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. Steffen
