hariszaf / darn Goto Github PK

Hi
I tried to run the pipeline, but step 2 seems to fail and I can't figure out how to solve this problem. The output files are written into the defined directory, so I think this is not the issue, but maybe DARN can't find epa-ng? Any idea on how to solve this? Thanks a lot in advance!

Here the log:

STEP 2: placement of the input reads on the reference COI phylogenetic tree of DARN,
using the EPA-ng algorithm (Barbera et al. 2018).
INFO Selected: Output dir: ./
INFO Selected: Query file: query.fasta
INFO Selected: Tree file: /home/docs/magicTree.bestTree
INFO Selected: Reference MSA: /home/docs/magic_tree_aln.fasta
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model: GTR+F+R10
INFO ______ ____ ___ _ __ ______
/ // __ \ / | / | / // /
/ __/ / // // /| | ______ / |/ // / __
/ / / // ___ |/_____// /| // // /
/_____/// // || // |/ __/ (v0.3.8)
./darn.sh: line 158: 39 Killed /home/tools/epa/bin/epa-ng -t /home/docs/magicTree.bestTree -s /home/docs/magic_tree_aln.fasta -m GTR+F+R10 -q query.fasta

<<< STEP 2 has been completed.

STEP 3: Build assignment profiles per input query,
using the examine assign of the gappa package (Czech et al. 2020).
--jplace-path: Path does not exist: epa_result.jplace
Run with --help for more information.
--jplace-path: Path does not exist: epa_result.jplace
Run with --help for more information.

After this the pipeline continues with steps 4, 5 and 6, but as DARN does not find the relevant files/data, it does not produce the right output.