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Reference.hmm missing? And other stuff

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Artur Zaduryan

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Oct 29, 2024, 11:16:11 AM10/29/24
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Hey! 
I am getting this error:

/home/localadmin/bin/miniconda3/envs/picrust2_env/lib/python3.6/site-packages/picrust2/metagenome_pipeline.py:12: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
  from pandas.util.testing import assert_frame_equal

Error: File existence/permissions problem in trying to open HMM file /home/localadmin/bin/miniconda3/envs/picrust2_env/lib/python3.6/site-packages/default_files/prokaryotic/reference.hmm.
HMM file /home/localadmin/bin/miniconda3/envs/picrust2_env/lib/python3.6/site-packages/default_files/prokaryotic/reference.hmm

Error running this command:
hmmalign --trim --dna --mapali /home/localadmin/bin/miniconda3/envs/picrust2_env/lib/python3.6/site-packages/default_files/prokaryotic/reference.fna --informat FASTA -o picrust2_out_pipeline/intermediate/place_seqs/query_align.stockholm /home/localadmin/bin/miniconda3/envs/picrust2_env/lib/python3.6/site-packages/default_files/prokaryotic/reference.hmm otus97.fasta

There seem to be two problems, the one i could identify is that a reference.hmm file seems to be missing (and actually the whole default_files folder was missing too, installed with conda), but the git repo doesn't contain such a file either (jsut some txts) 

I am pretty confused, help would be very much appreciated : )
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