PhyloPhlAn version 3.0.67 (24 August 2022)

Command line: /home/j/jkang242/.conda/envs/myenv/bin/phylophlan -i ./spades_output/final_contigs_test --genome_extension .fasta -d phylophlan --databases_folder ./phylophlan_databases --diversity low --fast --verbose -f ./phylophlan_configs/supermatrix_aa.cfg -o ./phylophlan_output/fasta_contigs_phylophlan_test_slurm

Automatically setting "input=final_contigs_test" and "input_folder=/project3/mars_metagenomics/work_in_progress/jwkang/spades_output"
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp"
"low-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': 'final_contigs_test', 'clean': None, 'output': './phylophlan_output/fasta_contigs_phylophlan_test_slurm', 'database': 'phylophlan', 'db_type': None, 'config_file': './phylophlan_configs/supermatrix_aa.cfg', 'diversity': 'low', 'accurate': False, 'fast': True, 'clean_all': False, 'database_list': False, 'submat': 'pfasum60', 'submat_list': False, 'submod_list': False, 'nproc': 1, 'min_num_proteins': 1, 'min_len_protein': 50, 'min_num_markers': 100, 'trim': 'greedy', 'gap_perc_threshold': 0.67, 'not_variant_threshold': 0.99, 'subsample': <function fivehundred at 0x7f18ba4ae680>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x7f18ba4aeb00>, '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, 'convert_N2gap': False, 'input_folder': '/project3/mars_metagenomics/work_in_progress/jwkang/spades_output/final_contigs_test', 'data_folder': './phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp', 'databases_folder': './phylophlan_databases', 'submat_folder': '/home/j/jkang242/.conda/envs/myenv/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': '/home/j/jkang242/.conda/envs/myenv/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_models/', 'configs_folder': 'phylophlan_configs/', 'output_folder': '', 'genome_extension': '.fasta', 'proteome_extension': '.faa', 'update': False, 'verbose': True}

Loading configuration file "./phylophlan_configs/supermatrix_aa.cfg"
Checking configuration file
Checking "/home/j/jkang242/.conda/envs/myenv/bin/diamond"
Checking "/home/j/jkang242/.conda/envs/myenv/bin/mafft"
Checking "/home/j/jkang242/.conda/envs/myenv/bin/trimal"
Checking "/home/j/jkang242/.conda/envs/myenv/bin/FastTreeMP"
Checking "/home/j/jkang242/.conda/envs/myenv/bin/raxmlHPC-PTHREADS-SSE3"
Database folder "./phylophlan_databases/phylophlan" present
Database folder "./phylophlan_databases/phylophlan" present
"db_aa" database "./phylophlan_databases/phylophlan/phylophlan.dmnd" present
Loading files from "/project3/mars_metagenomics/work_in_progress/jwkang/spades_output/final_contigs_test"
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_dna"
Cleaning 3 inputs
Cleaning "/project3/mars_metagenomics/work_in_progress/jwkang/spades_output/final_contigs_test/2001.contigs.fasta"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_dna/2001.contigs.fasta" generated in 4s
Cleaning "/project3/mars_metagenomics/work_in_progress/jwkang/spades_output/final_contigs_test/2002.contigs.fasta"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_dna/2002.contigs.fasta" generated in 3s
Cleaning "/project3/mars_metagenomics/work_in_progress/jwkang/spades_output/final_contigs_test/2003.contigs.fasta"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_dna/2003.contigs.fasta" generated in 1s
Loading files from "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_dna"
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna"
Mapping "phylophlan" on 3 inputs (key: "map_dna")
Mapping "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_dna/2001.contigs.fasta"
"2001.contigs.b6o.bkp" generated in 10182s
Mapping "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_dna/2002.contigs.fasta"
"2002.contigs.b6o.bkp" generated in 6509s
Mapping "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_dna/2003.contigs.fasta"
"2003.contigs.b6o.bkp" generated in 4223s
Selecting 3 markers from "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna"
Selecting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna/2001.contigs.b6o.bkp"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna/2001.contigs.b6o.bz2" generated in 105s
Selecting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna/2002.contigs.b6o.bkp"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna/2002.contigs.b6o.bz2" generated in 53s
Selecting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna/2003.contigs.b6o.bkp"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna/2003.contigs.b6o.bz2" generated in 32s
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_dna"
Extracting markers from 3 inputs
Extracting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna/2001.contigs.b6o.bz2"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_dna/2001.contigs.fasta.bz2" generated in 16s
Extracting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna/2002.contigs.b6o.bz2"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_dna/2002.contigs.fasta.bz2" generated in 9s
Extracting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_dna/2003.contigs.b6o.bz2"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_dna/2003.contigs.fasta.bz2" generated in 6s
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/fake_proteomes"
Generate proteomes from 3 genomes
Generating "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_dna/2001.contigs.fasta.bz2"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/fake_proteomes/2001.contigs.faa.bz2" generated in 18s
Generating "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_dna/2002.contigs.fasta.bz2"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/fake_proteomes/2002.contigs.faa.bz2" generated in 11s
Generating "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_dna/2003.contigs.fasta.bz2"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/fake_proteomes/2003.contigs.faa.bz2" generated in 6s
Loading files from "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/fake_proteomes"
Decompressing input files
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/uncompressed"
Loading files from "/project3/mars_metagenomics/work_in_progress/jwkang/spades_output/final_contigs_test"
Checking 3 inputs
Checking "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/uncompressed/2001.contigs.faa"
Checking "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/uncompressed/2002.contigs.faa"
Checking "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/uncompressed/2003.contigs.faa"
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_aa"
Cleaning 3 inputs
Cleaning "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/uncompressed/2001.contigs.faa"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_aa/2001.contigs.faa" generated in 1s
Cleaning "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/uncompressed/2002.contigs.faa"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_aa/2002.contigs.faa" generated in 0s
Cleaning "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/uncompressed/2003.contigs.faa"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_aa/2003.contigs.faa" generated in 0s
Loading files from "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_aa"
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa"
Mapping "phylophlan" on 3 inputs (key: "map_aa")
Mapping "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_aa/2001.contigs.faa"
"2001.contigs.b6o.bkp" generated in 11299s
Mapping "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_aa/2002.contigs.faa"
"2002.contigs.b6o.bkp" generated in 7117s
Mapping "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/clean_aa/2003.contigs.faa"
"2003.contigs.b6o.bkp" generated in 4496s
Selecting 3 markers from "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa"
Selecting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa/2001.contigs.b6o.bkp"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa/2001.contigs.b6o.bz2" generated in 153s
Selecting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa/2002.contigs.b6o.bkp"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa/2002.contigs.b6o.bz2" generated in 88s
Selecting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa/2003.contigs.b6o.bkp"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa/2003.contigs.b6o.bz2" generated in 52s
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_aa"
Extracting markers from 3 inputs
Extracting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa/2001.contigs.b6o.bz2"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_aa/2001.contigs.faa.bz2" generated in 0s
Extracting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa/2002.contigs.b6o.bz2"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_aa/2002.contigs.faa.bz2" generated in 0s
Extracting "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/map_aa/2003.contigs.b6o.bz2"
"./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers_aa/2003.contigs.faa.bz2" generated in 0s
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/markers"
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"p0143" discarded, not enough inputs (3/4)
"p0169" discarded, not enough inputs (3/4)
"p0086" discarded, not enough inputs (3/4)
"p0148" discarded, not enough inputs (3/4)
"p0396" discarded, not enough inputs (3/4)
"p0298" discarded, not enough inputs (3/4)
"p0030" discarded, not enough inputs (3/4)
"p0162" discarded, not enough inputs (3/4)
"p0204" discarded, not enough inputs (3/4)
"p0228" discarded, not enough inputs (3/4)
"p0106" discarded, not enough inputs (3/4)
"p0236" discarded, not enough inputs (3/4)
"p0296" discarded, not enough inputs (3/4)
"p0354" discarded, not enough inputs (3/4)
"p0189" discarded, not enough inputs (3/4)
"p0315" discarded, not enough inputs (3/4)
"p0123" discarded, not enough inputs (3/4)
"p0058" discarded, not enough inputs (3/4)
"p0174" discarded, not enough inputs (3/4)
"p0386" discarded, not enough inputs (3/4)
"p0144" discarded, not enough inputs (3/4)
"p0090" discarded, not enough inputs (3/4)
"p0136" discarded, not enough inputs (3/4)
"p0067" discarded, not enough inputs (3/4)
"p0223" discarded, not enough inputs (3/4)
"p0277" discarded, not enough inputs (3/4)
"p0391" discarded, not enough inputs (3/4)
"p0045" discarded, not enough inputs (3/4)
"p0345" discarded, not enough inputs (3/4)
"p0191" discarded, not enough inputs (3/4)
"p0375" discarded, not enough inputs (3/4)
"p0111" discarded, not enough inputs (3/4)
"p0108" discarded, not enough inputs (3/4)
"p0213" discarded, not enough inputs (3/4)
"p0321" discarded, not enough inputs (3/4)
"p0334" discarded, not enough inputs (3/4)
"p0101" discarded, not enough inputs (3/4)
"p0235" discarded, not enough inputs (3/4)
"p0109" discarded, not enough inputs (3/4)
"p0260" discarded, not enough inputs (3/4)
"p0336" discarded, not enough inputs (3/4)
"p0088" discarded, not enough inputs (3/4)
"p0353" discarded, not enough inputs (3/4)
"p0271" discarded, not enough inputs (3/4)
"p0066" discarded, not enough inputs (3/4)
"p0087" discarded, not enough inputs (3/4)
"p0170" discarded, not enough inputs (3/4)
"p0113" discarded, not enough inputs (3/4)
"p0284" discarded, not enough inputs (3/4)
"p0049" discarded, not enough inputs (3/4)
"p0104" discarded, not enough inputs (3/4)
"p0091" discarded, not enough inputs (3/4)
"p0286" discarded, not enough inputs (3/4)
"p0253" discarded, not enough inputs (3/4)
"p0376" discarded, not enough inputs (3/4)
"p0025" discarded, not enough inputs (3/4)
"p0085" discarded, not enough inputs (3/4)
"p0227" discarded, not enough inputs (3/4)
"p0195" discarded, not enough inputs (3/4)
"p0133" discarded, not enough inputs (3/4)
"p0200" discarded, not enough inputs (3/4)
"p0242" discarded, not enough inputs (3/4)
"p0052" discarded, not enough inputs (3/4)
"p0256" discarded, not enough inputs (3/4)
"p0333" discarded, not enough inputs (3/4)
"p0152" discarded, not enough inputs (3/4)
"p0289" discarded, not enough inputs (3/4)
"p0084" discarded, not enough inputs (3/4)
"p0270" discarded, not enough inputs (3/4)
"p0059" discarded, not enough inputs (3/4)
"p0131" discarded, not enough inputs (3/4)
"p0107" discarded, not enough inputs (3/4)
"p0161" discarded, not enough inputs (3/4)
"p0373" discarded, not enough inputs (3/4)
"p0116" discarded, not enough inputs (3/4)
"p0114" discarded, not enough inputs (3/4)
"p0258" discarded, not enough inputs (3/4)
"p0269" discarded, not enough inputs (3/4)
"p0149" discarded, not enough inputs (3/4)
"p0383" discarded, not enough inputs (3/4)
"p0051" discarded, not enough inputs (3/4)
"p0380" discarded, not enough inputs (3/4)
"p0070" discarded, not enough inputs (3/4)
"p0361" discarded, not enough inputs (3/4)
"p0207" discarded, not enough inputs (3/4)
"p0208" discarded, not enough inputs (3/4)
"p0177" discarded, not enough inputs (3/4)
"p0062" discarded, not enough inputs (3/4)
"p0038" discarded, not enough inputs (3/4)
"p0203" discarded, not enough inputs (3/4)
"p0190" discarded, not enough inputs (3/4)
"p0026" discarded, not enough inputs (3/4)
"p0022" discarded, not enough inputs (3/4)
"p0097" discarded, not enough inputs (3/4)
"p0348" discarded, not enough inputs (3/4)
"p0221" discarded, not enough inputs (3/4)
"p0138" discarded, not enough inputs (3/4)
"p0209" discarded, not enough inputs (3/4)
"p0350" discarded, not enough inputs (3/4)
"p0371" discarded, not enough inputs (3/4)
"p0239" discarded, not enough inputs (3/4)
"p0181" discarded, not enough inputs (3/4)
"p0176" discarded, not enough inputs (3/4)
"p0359" discarded, not enough inputs (3/4)
"p0214" discarded, not enough inputs (3/4)
"p0146" discarded, not enough inputs (3/4)
"p0110" discarded, not enough inputs (3/4)
"p0134" discarded, not enough inputs (3/4)
"p0303" discarded, not enough inputs (3/4)
"p0364" discarded, not enough inputs (3/4)
"p0387" discarded, not enough inputs (3/4)
"p0050" discarded, not enough inputs (3/4)
"p0243" discarded, not enough inputs (3/4)
"p0076" discarded, not enough inputs (3/4)
"p0197" discarded, not enough inputs (3/4)
"p0367" discarded, not enough inputs (3/4)
"p0292" discarded, not enough inputs (3/4)
"p0157" discarded, not enough inputs (3/4)
"p0210" discarded, not enough inputs (3/4)
"p0372" discarded, not enough inputs (3/4)
"p0322" discarded, not enough inputs (3/4)
"p0309" discarded, not enough inputs (3/4)
"p0249" discarded, not enough inputs (3/4)
"p0331" discarded, not enough inputs (3/4)
"p0122" discarded, not enough inputs (3/4)
"p0153" discarded, not enough inputs (3/4)
"p0061" discarded, not enough inputs (3/4)
"p0034" discarded, not enough inputs (3/4)
"p0180" discarded, not enough inputs (3/4)
"p0346" discarded, not enough inputs (3/4)
"p0194" discarded, not enough inputs (3/4)
"p0259" discarded, not enough inputs (3/4)
"p0335" discarded, not enough inputs (3/4)
"p0349" discarded, not enough inputs (3/4)
"p0233" discarded, not enough inputs (3/4)
"p0389" discarded, not enough inputs (3/4)
"p0310" discarded, not enough inputs (3/4)
"p0135" discarded, not enough inputs (3/4)
"p0299" discarded, not enough inputs (3/4)
"p0275" discarded, not enough inputs (3/4)
"p0285" discarded, not enough inputs (3/4)
"p0295" discarded, not enough inputs (3/4)
"p0069" discarded, not enough inputs (3/4)
"p0156" discarded, not enough inputs (3/4)
"p0142" discarded, not enough inputs (3/4)
"p0147" discarded, not enough inputs (3/4)
"p0382" discarded, not enough inputs (3/4)
"p0178" discarded, not enough inputs (3/4)
"p0323" discarded, not enough inputs (3/4)
"p0351" discarded, not enough inputs (3/4)
"p0300" discarded, not enough inputs (3/4)
"p0255" discarded, not enough inputs (3/4)
"p0230" discarded, not enough inputs (3/4)
"p0274" discarded, not enough inputs (3/4)
"p0312" discarded, not enough inputs (1/4)
"p0384" discarded, not enough inputs (3/4)
"p0198" discarded, not enough inputs (3/4)
"p0308" discarded, not enough inputs (1/4)
"p0294" discarded, not enough inputs (3/4)
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/msas"
Markers already aligned (key: "msa")
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/trim_gap_trim"
Markers already trimmed (key: "trim")
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/trim_gap_perc"
Markers already trimmed
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/trim_not_variant"
Markers already trimmed
Substitution matrix "/home/j/jkang242/.conda/envs/myenv/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_matrices/pfasum60.pkl" loaded
Creating folder "./phylophlan_output/fasta_contigs_phylophlan_test_slurm/tmp/sub"
Markers already subsampled
Concatenating alignments

[e] No alignments found to concatenate
srun: error: slurm005: task 0: Exited with exit code 1