I am trying run the first step (Placing reads into reference tree error) but I get the following error. I hope you can help me thanks.
Error running this command:
epa-ng --tree /home/werobon/picrust2-2.5.1/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa /tmp/tmp_ss8zm2c/ref_seqs_hmmalign.fasta --query /tmp/tmp_ss8zm2c/study_seqs_hmmalign.fasta --chunk-size 5000 -T 1 -m /home/werobon/picrust2-2.5.1/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w /tmp/tmp_ss8zm2c/epa_out --filter-acc-lwr 0.99 --filter-max 100
Standard output of the above failed command:
INFO Selected: Output dir: /tmp/tmp_ss8zm2c/epa_out/
INFO Selected: Query file: /tmp/tmp_ss8zm2c/study_seqs_hmmalign.fasta
INFO Selected: Tree file: /home/werobon/picrust2-2.5.1/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre
INFO Selected: Reference MSA: /tmp/tmp_ss8zm2c/ref_seqs_hmmalign.fasta
INFO Selected: Filtering by accumulated threshold: 0.99
INFO Selected: Maximum number of placements per query: 100
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model file: /home/werobon/picrust2-2.5.1/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model
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: 0.453141 (user), weights&rates: (0.25,0.0250674) (0.25,0.220229) (0.25,0.782933) (0.25,2.97177)
Base frequencies (user): 0.229585 0.22008 0.298596 0.251739
Substitution rates (user): 1.00319 2.79077 1.5301 0.87441 3.83966 1