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': , 'unknown_fraction': 0.3, 'scoring_function': , '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" "p0027" discarded, not enough inputs (3/4) "p0021" discarded, not enough inputs (3/4) "p0077" discarded, not enough inputs (3/4) "p0220" discarded, not enough inputs (3/4) "p0055" discarded, not enough inputs (3/4) "p0222" discarded, not enough inputs (3/4) "p0262" discarded, not enough inputs (3/4) "p0273" discarded, not enough inputs (3/4) "p0201" discarded, not enough inputs (3/4) "p0357" discarded, not enough inputs (3/4) "p0393" discarded, not enough inputs (3/4) "p0326" discarded, not enough 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"p0166" discarded, not enough inputs (3/4) "p0023" discarded, not enough inputs (3/4) "p0099" discarded, not enough inputs (3/4) "p0368" discarded, not enough inputs (3/4) "p0040" discarded, not enough inputs (3/4) "p0158" discarded, not enough inputs (3/4) "p0379" discarded, not enough inputs (3/4) "p0264" discarded, not enough inputs (3/4) "p0283" discarded, not enough inputs (3/4) "p0117" discarded, not enough inputs (3/4) "p0007" discarded, not enough inputs (3/4) "p0046" discarded, not enough inputs (3/4) "p0011" discarded, not enough inputs (3/4) "p0231" discarded, not enough inputs (3/4) "p0248" discarded, not enough inputs (3/4) "p0186" discarded, not enough inputs (3/4) "p0291" discarded, not enough inputs (3/4) "p0072" discarded, not enough inputs (3/4) "p0288" discarded, not enough inputs (3/4) "p0042" discarded, not enough inputs (3/4) "p0035" discarded, not enough inputs (3/4) "p0096" discarded, not enough inputs (3/4) "p0092" discarded, not enough inputs (3/4) "p0369" discarded, not enough inputs (3/4) "p0218" discarded, not enough inputs (3/4) "p0154" discarded, not enough inputs (3/4) "p0145" discarded, not enough inputs (3/4) "p0238" discarded, not enough inputs (3/4) "p0301" discarded, not enough inputs (3/4) "p0163" discarded, not enough inputs (3/4) "p0245" discarded, not enough inputs (3/4) "p0297" discarded, not enough inputs (3/4) "p0032" discarded, not enough inputs (3/4) "p0150" discarded, not enough inputs (3/4) "p0362" discarded, not enough inputs (3/4) "p0390" discarded, not enough inputs (3/4) "p0244" discarded, not enough inputs (3/4) "p0043" discarded, not enough inputs (3/4) "p0341" discarded, not enough inputs (3/4) "p0305" discarded, not enough inputs (3/4) "p0268" discarded, not enough inputs (3/4) "p0306" discarded, not enough inputs (3/4) "p0329" discarded, not enough inputs (3/4) "p0047" discarded, not enough inputs (3/4) "p0188" discarded, not enough inputs (3/4) "p0033" discarded, not enough inputs (3/4) "p0053" discarded, not enough inputs (3/4) "p0196" discarded, not enough inputs (3/4) "p0014" discarded, not enough inputs (3/4) "p0100" discarded, not enough inputs (3/4) "p0075" discarded, not enough inputs (3/4) "p0155" discarded, not enough inputs (3/4) "p0307" discarded, not enough inputs (3/4) "p0313" discarded, not enough inputs (3/4) "p0232" discarded, not enough inputs (3/4) "p0185" discarded, not enough inputs (3/4) "p0356" discarded, not enough inputs (3/4) "p0074" discarded, not enough inputs (3/4) "p0184" discarded, not enough inputs (3/4) "p0128" discarded, not enough inputs (3/4) "p0352" discarded, not enough inputs (3/4) "p0388" discarded, not enough inputs (3/4) "p0041" discarded, not enough inputs (3/4) "p0182" discarded, not enough inputs (3/4) "p0374" discarded, not enough inputs (3/4) "p0216" discarded, not enough inputs (3/4) "p0060" discarded, not enough inputs (3/4) "p0129" discarded, not enough inputs (3/4) "p0250" discarded, not enough inputs (3/4) "p0338" discarded, not enough inputs (3/4) "p0378" discarded, not enough inputs (3/4) "p0159" discarded, not enough inputs (3/4) "p0225" discarded, not enough inputs (3/4) "p0080" discarded, not enough inputs (3/4) "p0105" discarded, not enough inputs (3/4) "p0175" discarded, not enough inputs (3/4) "p0365" discarded, not enough inputs (3/4) "p0000" discarded, not enough inputs (3/4) "p0082" discarded, not enough inputs (3/4) "p0017" discarded, not enough inputs (3/4) "p0016" discarded, not enough inputs (3/4) "p0039" discarded, not enough inputs (3/4) "p0395" discarded, not enough inputs (3/4) "p0363" discarded, not enough inputs (2/4) "p0314" discarded, not enough inputs (3/4) "p0267" discarded, not enough inputs (3/4) "p0237" discarded, not enough inputs (3/4) "p0187" discarded, not enough inputs (3/4) "p0360" discarded, not enough inputs (3/4) "p0013" discarded, not enough inputs (3/4) "p0287" discarded, not enough inputs (3/4) "p0304" discarded, not enough inputs (3/4) "p0325" discarded, not enough inputs (3/4) "p0211" discarded, not enough inputs (3/4) "p0397" discarded, not enough inputs (3/4) "p0112" discarded, not enough inputs (3/4) "p0263" discarded, not enough inputs (3/4) "p0001" discarded, not enough inputs (3/4) "p0130" discarded, not enough inputs (3/4) "p0057" discarded, not enough inputs (3/4) "p0240" discarded, not enough inputs (3/4) "p0224" discarded, not enough inputs (3/4) "p0002" discarded, not enough inputs (3/4) "p0005" discarded, not enough inputs (3/4) "p0168" discarded, not enough inputs (3/4) "p0172" discarded, not enough inputs (3/4) "p0118" discarded, not enough inputs (3/4) "p0079" discarded, not enough inputs (3/4) "p0137" discarded, not enough inputs (3/4) "p0281" discarded, not enough inputs (3/4) "p0193" discarded, not enough inputs (3/4) "p0119" discarded, not enough inputs (3/4) "p0339" discarded, not enough inputs (3/4) "p0121" discarded, not enough inputs (3/4) "p0029" discarded, not enough inputs (3/4) "p0347" discarded, not enough inputs (3/4) "p0330" discarded, not enough inputs (3/4) "p0054" discarded, not enough inputs (3/4) "p0031" discarded, not enough inputs (3/4) "p0126" discarded, not enough inputs (3/4) "p0098" discarded, not enough inputs (3/4) "p0272" discarded, not enough inputs (3/4) "p0006" discarded, not enough inputs (3/4) "p0234" discarded, not enough inputs (3/4) "p0265" discarded, not enough inputs (3/4) "p0120" discarded, not enough inputs (3/4) "p0089" discarded, not enough inputs (3/4) "p0020" discarded, not enough inputs (3/4) "p0063" discarded, not enough inputs (3/4) "p0015" discarded, not enough inputs (3/4) "p0324" discarded, not enough inputs (3/4) "p0019" discarded, not enough inputs (3/4) "p0257" discarded, not enough inputs (3/4) "p0342" discarded, not enough inputs (3/4) "p0018" discarded, not enough inputs (3/4) "p0206" discarded, not enough inputs (3/4) "p0366" discarded, not enough inputs (3/4) "p0217" discarded, not enough inputs (3/4) "p0337" discarded, not enough inputs (3/4) "p0141" discarded, not enough inputs (3/4) "p0241" discarded, not enough inputs (3/4) "p0048" discarded, not enough inputs (3/4) "p0183" discarded, not enough inputs (3/4) "p0358" discarded, not enough inputs (3/4) "p0293" discarded, not enough inputs (3/4) "p0332" discarded, not enough inputs (3/4) "p0340" discarded, not enough inputs (3/4) "p0343" discarded, not enough inputs (3/4) "p0132" discarded, not enough inputs (3/4) "p0056" discarded, not enough inputs (3/4) "p0377" discarded, not enough inputs (3/4) "p0370" discarded, not enough inputs (3/4) "p0165" discarded, not enough inputs (3/4) "p0261" discarded, not enough inputs (3/4) "p0028" discarded, not enough inputs (3/4) "p0115" discarded, not enough inputs (3/4) "p0399" discarded, not enough inputs (3/4) "p0004" discarded, not enough inputs (3/4) "p0064" discarded, not enough inputs (3/4) "p0068" discarded, not enough inputs (3/4) "p0127" discarded, not enough inputs (3/4) "p0164" discarded, not enough inputs (3/4) "p0151" discarded, not enough inputs (3/4) "p0199" discarded, not enough inputs (3/4) "p0167" discarded, not enough inputs (3/4) "p0219" discarded, not enough inputs (3/4) "p0173" discarded, not enough inputs (3/4) "p0140" discarded, not enough inputs (3/4) "p0251" discarded, not enough inputs (3/4) "p0317" discarded, not enough inputs (3/4) "p0328" discarded, not enough inputs (3/4) "p0279" discarded, not enough inputs (3/4) "p0355" discarded, not enough inputs (3/4) "p0095" discarded, not enough inputs (3/4) "p0327" discarded, not enough inputs (3/4) "p0276" discarded, not enough inputs (3/4) "p0266" discarded, not enough inputs (3/4) "p0252" discarded, not enough inputs (3/4) "p0160" discarded, not enough inputs (3/4) "p0311" discarded, not enough inputs (3/4) "p0318" discarded, not enough inputs (3/4) "p0320" discarded, not enough inputs (3/4) "p0103" discarded, not enough inputs (3/4) "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