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Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
https://ecogenomics.github.io/GTDBTk/
GNU General Public License v3.0
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FastTree is not on the system path. #16

Closed zyyalice closed 6 years ago

zyyalice commented 6 years ago

Hi When i ran "The de novo workflow" process, it showed error messages as below:

[2018-03-16 23:30:12] INFO: GTDB-Tk v0.0.4b3 [2018-03-16 23:30:12] INFO: gtdbtk de_novo_wf --genome_dir my_genome --bac120_ms --outgroup_taxon p__Acetothermia --out_dir de_novo_test [2018-03-16 23:30:12] WARNING: Results are still being validated and taxonomic assignments may be incorrect! Use at your own risk! FastTree is not on the system path. Controlled exit resulting from an unrecoverable error or warning.

Could you help me fix this problem? Thanks a lot!

Looking forward to your reply. Regards, Alice

pchaumeil commented 6 years ago

Hi Alice,

The directory to FastTree is probably not included in the PATH variable. you can fix this by running export PATH="/path/to/fasttree/binaries/:$PATH" within your terminal Make sure that both FastTree and FastreeMP are present in the binary directory

Regards, Pierre