When I ran the program, the following error occurred.
Here is my log file：
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PhyloPhlAn version 3.0.67 (24 August 2022)
Command line: /share/home/wengenz/anaconda3/envs/phylophlan/bin/phylophlan
-i /share/home/wengenz/GIWMD/phylo/phoD_genome/
–genome_extension fa
-d phylophlan_databases/phylophlan/
-f phoD_tol_nt.cfg
–diversity high
–fast
–force_nucleotides
-o phoD_output
–nproc 20
–verbose
Automatically setting “database=phylophlan” and “databases_folder=/share/home/wengenz/GIWMD/phylo/phylophlan_databases”
Automatically setting “input=phoD_genome” and “input_folder=/share/home/wengenz/GIWMD/phylo”
[w] “/share/home/wengenz/anaconda3/envs/phylophlan/lib/python3.11/site-packages/phylophlan/phylophlan_configs/” folder does not exists
Creating folder “phoD_output”
Creating folder “phoD_output/tmp”
“high-fast” preset
Setting “sort=True” because “database=phylophlan”
Setting “min_num_markers=100” since no value has been specified and the “database=phylophlan”
Arguments: {‘input’: ‘phoD_genome’, ‘clean’: None, ‘output’: ‘phoD_output’, ‘database’: ‘phylophlan’, ‘db_type’: None, ‘config_file’: ‘phoD_tol_nt.cfg’, ‘diversity’: ‘high’, ‘accurate’: False, ‘fast’: True, ‘clean_all’: False, ‘database_list’: False, ‘submat’: ‘pfasum60’, ‘submat_list’: False, ‘submod_list’: False, ‘nproc’: 20, ‘min_num_proteins’: 1, ‘min_len_protein’: 50, ‘min_num_markers’: 100, ‘trim’: ‘greedy’, ‘gap_perc_threshold’: 0.67, ‘not_variant_threshold’: 0.9, ‘subsample’: <function phylophlan at 0x7fc0d4f2fa60>, ‘unknown_fraction’: 0.3, ‘scoring_function’: <function trident at 0x7fc0d4f30180>, ‘sort’: True, ‘remove_fragmentary_entries’: False, ‘fragmentary_threshold’: 0.67, ‘min_num_entries’: 4, ‘maas’: None, ‘remove_only_gaps_entries’: False, ‘mutation_rates’: False, ‘force_nucleotides’: True, ‘convert_N2gap’: False, ‘input_folder’: ‘/share/home/wengenz/GIWMD/phylo/phoD_genome’, ‘data_folder’: ‘phoD_output/tmp’, ‘databases_folder’: ‘/share/home/wengenz/GIWMD/phylo/phylophlan_databases’, ‘submat_folder’: ‘/share/home/wengenz/anaconda3/envs/phylophlan/lib/python3.11/site-packages/phylophlan/phylophlan_substitution_matrices/’, ‘submod_folder’: ‘/share/home/wengenz/anaconda3/envs/phylophlan/lib/python3.11/site-packages/phylophlan/phylophlan_substitution_models/’, ‘configs_folder’: None, ‘output_folder’: ‘’, ‘genome_extension’: ‘.fa’, ‘proteome_extension’: ‘.faa’, ‘update’: False, ‘verbose’: True}
Loading configuration file “phoD_tol_nt.cfg”
Checking configuration file
Checking “/share/home/wengenz/anaconda3/envs/phylophlan/bin/diamond”
Checking “/share/home/wengenz/anaconda3/envs/phylophlan/bin/muscle”
Checking “/share/home/wengenz/anaconda3/envs/phylophlan/bin/trimal”
Checking “/share/home/wengenz/anaconda3/envs/phylophlan/bin/iqtree”
Checking “/share/home/wengenz/anaconda3/envs/phylophlan/bin/raxmlHPC-PTHREADS-SSE3”
“db_aa” database “/share/home/wengenz/GIWMD/phylo/phylophlan_databases/phylophlan/phylophlan.dmnd” present
Loading files from “/share/home/wengenz/GIWMD/phylo/phoD_genome”
Creating folder “phoD_output/tmp/clean_dna”
[e] Command ‘[’/share/home/wengenz/anaconda3/envs/phylophlan/bin/muscle’, ‘-quiet’, ‘-maxiters’, ‘2’, ‘-in’, ‘phoD_output/tmp/markers/p0276.fa’, ‘-out’, ‘/share/home/wengenz/GIWMD/phylo/phoD_output/tmp/msas/p0276.aln’]’ returned non-zero
**** exit status 1.**
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This bug has been bothering me for a long time. Would someone kindly help to answer it? Thank you!