search

tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
136 stars 37 forks source link

tree builder fails #199

Closed prmac closed 6 years ago

prmac commented 6 years ago

Hi Torsten,

nullarbor runs fine for several hours and outputs a folder per isolate plus a roary folder. I am running into the following error and at a loss for how to fix it.

Running make from the run directory gives the following.

aln="core.aln" tree="core.newick" cpus=4 opts="" /home/ubuntu/software/nullarbor/bin/../plugins/treebuilder/iqtree_fast.sh
ERROR: Invalid "-redo" option.
Makefile:128: recipe for target 'core.newick' failed
make: *** [core.newick] Error 2

Makefile for reference

tseemann commented 6 years ago

You need to upgrade iqtree to 1.6.5 version (or a version with -redo option)

Or use --treebuilder fasttree instead.