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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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Pipeline error when snippy starts #189

Closed manuss11 closed 6 years ago

manuss11 commented 6 years ago

Hi everyone! I'm running Nullarbor 2 pipeline, and I have obtained the following error:

ln -f sample2/contigs.gff sample2.gff
aln="core.aln" tree="core.newick" cpus=4 opts="" /home/qiime2/nullarbor/bin/../plugins/treebuilder/iqtree.sh
/home/qiime2/nullarbor/bin/../plugins/treebuilder/iqtree.sh: 4: set: Illegal option -o pipefail
Makefile:130: recipe for target 'core.newick' failed
make: *** [core.newick] Error 2
make: *** Waiting for unfinished jobs....
Found 19 genes in sample2/contigs.fa
make: Leaving directory '/home/qiime2/resultados-efaecium2'

Could you help me? Thanks in advance ;)

manuss11 commented 6 years ago

I tried to reinstall Nullarbor packages since I found my error in a previously published issue. But after re-run I find another error:

aln="core.aln" tree="core.newick" cpus=4 opts="" /home/qiime2/nullarbor/bin/../plugins/treebuilder/iqtree_fast.sh
ERROR: Invalid "-ntmax" option.
Makefile:128: recipe for target 'core.newick' failed
make: *** [core.newick] Error 2
make: *** Waiting for unfinished jobs....
tseemann commented 6 years ago

You need to upgrade to IQ-TREE multicore version 1.6.5, sorry.