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jts / nanocorrect

Experimental pipeline for correcting nanopore reads
MIT License
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error running HPCdaligner #8

Closed bforde closed 9 years ago

bforde commented 9 years ago

Hi When I run nanocorrect-overlap.make I get the following error perl ~/nanocorrect/nanocorrect-preprocess.pl ../Test_Npore_ReadsPass.2D.fasta > Test_2D.pp.fasta ~/bin/fasta2DB Test_2D Test_2D.pp.fasta ~/bin/DBsplit -s50 Test_2D ~/bin/DBdust Test_2D HPCdaligner -t5 -mdust Test_2D > HPCcommands.txt HPCdaligner: -m is an illegal option make: *\ [HPCcommands.txt] Error 1

When I check the Usage for HPCdaligner I do not see and -m flag

Usage: HPCdaligner [-vbdAI] [-k<int(14)>] [-w<int(6)>] [-h<int(35)>] [-t] [-H] [-e<double(.70)] [-l<int(1000)>] [-s<int(100)] [-M] [-dal<int(4)>] [-mrg<int(25)>] path:db|dam [block:int[-range:int]

Is this a version issue

nickloman commented 9 years ago

Yes, it is - please update your DALIGNER to latest version, e.g. git pull and make