Phylophlan is always running with nothing returned

Greetings!
I tried to construct a tree of life using the second example of Phylophlan (I use 15 genomes for a trial). And the output_tol folder only contains a temp fold, which was further divided by two folders: “clean_dna” and “map_dna”. The documents in the “map_dna” is all blank, and the code is still running without stopping. Please help me solve this problem.
base) winger@880729:~/examples/02_tol$ phylophlan
-i input_genomes
-d phylophlan
-f 02_tol.cfg
–diversity low
–accurate
-o output_tol
–nproc 4
–verbose 2>&1 | tee logs/phylophlan.log
tee: logs/phylophlan.log: 没有那个文件或目录
PhyloPhlAn version 3.0.60 (27 November 2020)

Command line: /home/winger/miniconda3/bin/phylophlan -i input_genomes -d phylophlan -f 02_tol.cfg --diversity low --accurate -o output_tol --nproc 4 --verbose

Automatically setting “input=input_genomes” and “input_folder=/home/winger/examples/02_tol”
[e] “/home/winger/miniconda3/lib/python3.7/site-packages/phylophlan/phylophlan_configs/” folder does not exists
Creating folder “output_tol”
Creating folder “output_tol/tmp”
“low-accurate” preset
Setting “sort=True” because “database=phylophlan”
Setting “min_num_markers=100” since no value has been specified and the “database=phylophlan”
Arguments: {‘input’: ‘input_genomes’, ‘clean’: None, ‘output’: ‘output_tol’, ‘database’: ‘phylophlan’, ‘db_type’: None, ‘config_file’: ‘02_tol.cfg’, ‘diversity’: ‘low’, ‘accurate’: True, ‘fast’: False, ‘clean_all’: False, ‘database_list’: False, ‘submat’: ‘pfasum60’, ‘submat_list’: False, ‘submod_list’: False, ‘nproc’: 4, ‘min_num_proteins’: 1, ‘min_len_protein’: 50, ‘min_num_markers’: 100, ‘trim’: ‘not_variant’, ‘gap_perc_threshold’: 0.67, ‘not_variant_threshold’: 0.99, ‘subsample’: None, ‘unknown_fraction’: 0.3, ‘scoring_function’: None, ‘sort’: True, ‘remove_fragmentary_entries’: False, ‘fragmentary_threshold’: 0.85, ‘min_num_entries’: 4, ‘maas’: None, ‘remove_only_gaps_entries’: False, ‘mutation_rates’: False, ‘force_nucleotides’: False, ‘input_folder’: ‘/home/winger/examples/02_tol/input_genomes’, ‘data_folder’: ‘output_tol/tmp’, ‘databases_folder’: ‘phylophlan_databases/’, ‘submat_folder’: ‘/home/winger/miniconda3/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_matrices/’, ‘submod_folder’: ‘/home/winger/miniconda3/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_models/’, ‘configs_folder’: None, ‘output_folder’: ‘’, ‘genome_extension’: ‘.fna’, ‘proteome_extension’: ‘.faa’, ‘update’: False, ‘verbose’: True}
Loading configuration file “02_tol.cfg”
Checking configuration file
Checking “/home/winger/miniconda3/bin/diamond”
Checking “/home/winger/miniconda3/bin/mafft”
Checking “/home/winger/miniconda3/bin/trimal”
Checking “/home/winger/miniconda3/bin/iqtree”
“db_aa” database “phylophlan_databases/phylophlan/phylophlan.dmnd” present
Loading files from “/home/winger/examples/02_tol/input_genomes”
Creating folder “output_tol/tmp/clean_dna”
Cleaning 15 inputs
Cleaning “/home/winger/examples/02_tol/input_genomes/Acetatifactor_muris.fna”
Cleaning “/home/winger/examples/02_tol/input_genomes/Acutalibacter_muris.fna”
Cleaning “/home/winger/examples/02_tol/input_genomes/Adlercreutzia_equolifaciens.fna”
Cleaning “/home/winger/examples/02_tol/input_genomes/Akkermansia_muciniphila.fna”
“output_tol/tmp/clean_dna/Akkermansia_muciniphila.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Akkermansia_muciniphila_CAG_154.fna”
“output_tol/tmp/clean_dna/Adlercreutzia_equolifaciens.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Alistipes_communis.fna”
“output_tol/tmp/clean_dna/Acutalibacter_muris.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Alistipes_putredinis.fna”
“output_tol/tmp/clean_dna/Akkermansia_muciniphila_CAG_154.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Alistipes_sp_An31A.fna”
“output_tol/tmp/clean_dna/Acetatifactor_muris.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Alistipes_sp_CAG_268.fna”
“output_tol/tmp/clean_dna/Alistipes_putredinis.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Alistipes_sp_CHKCI003.fna”
“output_tol/tmp/clean_dna/Alistipes_communis.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Alistipes_timonensis_JC136.fna”
“output_tol/tmp/clean_dna/Alistipes_sp_An31A.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Alloprevotella_rava.fna”
“output_tol/tmp/clean_dna/Alistipes_sp_CHKCI003.fna” generated in 0s
“output_tol/tmp/clean_dna/Alistipes_sp_CAG_268.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Anaerotruncus_sp_G3_2012.fna”
Cleaning “/home/winger/examples/02_tol/input_genomes/Atopobium_minutum.fna”
“output_tol/tmp/clean_dna/Alistipes_timonensis_JC136.fna” generated in 0s
Cleaning “/home/winger/examples/02_tol/input_genomes/Bacteroides_caccae.fna”
“output_tol/tmp/clean_dna/Atopobium_minutum.fna” generated in 0s
“output_tol/tmp/clean_dna/Alloprevotella_rava.fna” generated in 0s
“output_tol/tmp/clean_dna/Anaerotruncus_sp_G3_2012.fna” generated in 0s
“output_tol/tmp/clean_dna/Bacteroides_caccae.fna” generated in 0s
Loading files from “output_tol/tmp/clean_dna”
Creating folder “output_tol/tmp/map_dna”
Mapping “phylophlan” on 15 inputs (key: “map_dna”)
Mapping “output_tol/tmp/clean_dna/Acetatifactor_muris.fna”
Mapping “output_tol/tmp/clean_dna/Acutalibacter_muris.fna”
Mapping “output_tol/tmp/clean_dna/Adlercreutzia_equolifaciens.fna”
Mapping “output_tol/tmp/clean_dna/Akkermansia_muciniphila.fna”

Thank you so much.

I’m having the same problem. Anyone can help? Thanks.

Hi all, can you check you have diamond actually running? Also, can you please verify which diamond version you’ve installed?
This is likely linked to diamond version 2 which is sensibly slower than the first version due to a bug correction (read here for more). If that’s the case, most likely you just need to wait for diamond to do the mapping.

Thanks a lot,
Francesco