epa-ng command error without any details...

[Artur Zaduryan]

Hi

I had an issue originally that reference files were not available in my installation and I was not able to pull them from the github repo, but I pulled those files instead from someone in Docker. The pipeline seem to have worked until EPA-ng:

Placing sequences onto reference tree.
hmmalign  --trim --dna --mapali /home/localadmin/bin/miniconda3/envs/newenv/lib/python3.6/site-packages/default_files/prokaryotic/reference.fna --informat FASTA -o pc_output1/intermediate/place_seqs/query_align.stockholm /home/localadmin/bin/miniconda3/envs/newenv/lib/python3.6/site-packages/default_files/prokaryotic/reference.hmm otus97.fasta
epa-ng --bfast pc_output1/intermediate/place_seqs/study_seqs_hmmalign.fasta --outdir pc_output1/intermediate/place_seqs/epa_out
INFO Converting given FASTA file to BFAST format...
INFO Resulting bfast file was written to: pc_output1/intermediate/place_seqs/epa_out/study_seqs_hmmalign.fasta.bfast
epa-ng --tree /home/localadmin/bin/miniconda3/envs/newenv/lib/python3.6/site-packages/default_files/prokaryotic/reference.tre --ref-msa pc_output1/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query pc_output1/intermediate/place_seqs/epa_out/study_seqs_hmmalign.fasta.bfast --chunk-size 5000 -T 1 -m GTR+G -w pc_output1/intermediate/place_seqs/epa_out
INFO Selected: Output dir: pc_output1/intermediate/place_seqs/epa_out/
INFO Selected: Query file: pc_output1/intermediate/place_seqs/epa_out/study_seqs_hmmalign.fasta.bfast
INFO Selected: Tree file: /home/localadmin/bin/miniconda3/envs/newenv/lib/python3.6/site-packages/default_files/prokaryotic/reference.tre
INFO Selected: Reference MSA: pc_output1/intermediate/place_seqs/ref_seqs_hmmalign.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+G
INFO Selected: Reading queries in chunks of: 5000
INFO Selected: Using threads: 1
INFO     ______ ____   ___           _   __ ______
        / ____// __ \ /   |         / | / // ____/
       / __/  / /_/ // /| | ______ /  |/ // / __
      / /___ / ____// ___ |/_____// /|  // /_/ /
     /_____//_/    /_/  |_|      /_/ |_/ \____/ (v0.3.8)
INFO Using model parameters:
INFO    Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 1 (ML),  weights&rates: (0.25,0.136954) (0.25,0.476752) (0.25,1) (0.25,2.38629)
        Base frequencies (ML): 0.25 0.25 0.25 0.25
        Substitution rates (ML): 0.5 0.5 0.5 0.5 0.5 1
INFO Output file: pc_output1/intermediate/place_seqs/epa_out/epa_result.jplace
Error running this command:
epa-ng --tree /home/localadmin/bin/miniconda3/envs/newenv/lib/python3.6/site-packages/default_files/prokaryotic/reference.tre --ref-msa pc_output1/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query pc_output1/intermediate/place_seqs/epa_out/study_seqs_hmmalign.fasta.bfast --chunk-size 5000 -T 1 -m GTR+G -w pc_output1/intermediate/place_seqs/epa_out

Here is the error output (the pipeline was terminated).

I cannot see any clues as to how to debug it, any ideas? Maybe I should also ask around at EPA forums...