(phylophlan) liliana@asdfghjkl:~/Documents/ASR$ phylophlan -i ~/Documents/ASR/Finals/PETases/ -d ~/Documents/ASR/BioBakery/Databases/phylophlan --diversity high -f ~/Documents/ASR/BioBakery/supermatrix_aa.cfg --output_folder ~/Documents/ASR/BioBakery/ --verbose
PhyloPhlAn version 3.0.60 (27 November 2020)

Command line: /home/liliana/miniconda3/envs/phylophlan/bin/phylophlan -i /home/liliana/Documents/ASR/Finals/PETases/ -d /home/liliana/Documents/ASR/BioBakery/Databases/phylophlan --diversity high -f /home/liliana/Documents/ASR/BioBakery/supermatrix_aa.cfg --output_folder /home/liliana/Documents/ASR/BioBakery/ --verbose

Automatically setting "database=phylophlan" and "databases_folder=/home/liliana/Documents/ASR/BioBakery/Databases"
Automatically setting "input=PETases" and "input_folder=/home/liliana/Documents/ASR/Finals"
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan"
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp"
"high-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': 'PETases', 'clean': None, 'output': '/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan', 'database': 'phylophlan', 'db_type': None, 'config_file': '/home/liliana/Documents/ASR/BioBakery/supermatrix_aa.cfg', 'diversity': 'high', 'accurate': True, 'fast': False, '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': 0.95, 'subsample': <function twentyfive at 0x7f9029d10160>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x7f9029d103a0>, 'sort': True, 'remove_fragmentary_entries': False, 'fragmentary_threshold': 0.75, 'min_num_entries': 4, 'maas': None, 'remove_only_gaps_entries': False, 'mutation_rates': False, 'force_nucleotides': False, 'input_folder': '/home/liliana/Documents/ASR/Finals/PETases', 'data_folder': '/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp', 'databases_folder': '/home/liliana/Documents/ASR/BioBakery/Databases', 'submat_folder': '/home/liliana/miniconda3/envs/phylophlan/lib/python3.10/site-packages/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': '/home/liliana/miniconda3/envs/phylophlan/lib/python3.10/site-packages/phylophlan/phylophlan_substitution_models/', 'configs_folder': '/home/liliana/miniconda3/envs/phylophlan/lib/python3.10/site-packages/phylophlan/phylophlan_configs/', 'output_folder': '/home/liliana/Documents/ASR/BioBakery/', 'genome_extension': '.fna', 'proteome_extension': '.faa', 'update': False, 'verbose': True}
Loading configuration file "/home/liliana/Documents/ASR/BioBakery/supermatrix_aa.cfg"
Checking configuration file
Checking "/home/liliana/miniconda3/envs/phylophlan/bin/diamond"
Checking "/home/liliana/miniconda3/envs/phylophlan/bin/mafft"
Checking "/home/liliana/miniconda3/envs/phylophlan/bin/trimal"
Checking "/home/liliana/miniconda3/envs/phylophlan/bin/FastTreeMP"
Checking "/home/liliana/miniconda3/envs/phylophlan/bin/raxmlHPC-PTHREADS-SSE3"
"db_aa" database "/home/liliana/Documents/ASR/BioBakery/Databases/phylophlan/phylophlan.dmnd" present
Loading files from "/home/liliana/Documents/ASR/Finals/PETases"
Loading files from "/home/liliana/Documents/ASR/Finals/PETases"
Checking 31 inputs
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETcan_202.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PmC.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETaseHom_M9.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/HiC.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/IsPETase.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PET27.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PHL1.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/HlL.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PE-H.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETaseHom_M6.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/Thc_cut2.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETcan_211.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PHL7.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETcan_405.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/FsC.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETcan_403.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETaseHom_M1.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/TtCutA.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/Sub1.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/phaZ.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/RgPETase.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PHL6.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/est119.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETcan_407.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETcan_611.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETcan_409.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETcan_204.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/BhrPETase.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/PETaseHom_M3.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/Tcur1278.faa"
Checking "/home/liliana/Documents/ASR/Finals/PETases/Tcur0390.faa"
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa"
Cleaning 31 inputs
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETcan_202.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_202.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PmC.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PmC.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETaseHom_M9.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETaseHom_M9.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/HiC.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/HiC.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/IsPETase.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/IsPETase.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PET27.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PET27.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PHL1.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PHL1.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/HlL.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/HlL.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PE-H.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PE-H.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETaseHom_M6.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETaseHom_M6.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/Thc_cut2.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/Thc_cut2.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETcan_211.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_211.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PHL7.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PHL7.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETcan_405.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_405.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/FsC.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/FsC.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETcan_403.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_403.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETaseHom_M1.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETaseHom_M1.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/TtCutA.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/TtCutA.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/Sub1.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/Sub1.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/phaZ.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/phaZ.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/RgPETase.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/RgPETase.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PHL6.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PHL6.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/est119.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/est119.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETcan_407.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_407.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETcan_611.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_611.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETcan_409.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_409.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETcan_204.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_204.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/BhrPETase.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/BhrPETase.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/PETaseHom_M3.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETaseHom_M3.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/Tcur1278.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/Tcur1278.faa" generated in 0s
Cleaning "/home/liliana/Documents/ASR/Finals/PETases/Tcur0390.faa"
"/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/Tcur0390.faa" generated in 0s
Loading files from "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa"
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa"
Mapping "phylophlan" on 31 inputs (key: "map_aa")
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_202.faa"
"PETcan_202.b6o.bkp" generated in 132s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PmC.faa"
"PmC.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETaseHom_M9.faa"
"PETaseHom_M9.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/HiC.faa"
"HiC.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/IsPETase.faa"
"IsPETase.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PET27.faa"
"PET27.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PHL1.faa"
"PHL1.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/HlL.faa"
"HlL.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PE-H.faa"
"PE-H.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETaseHom_M6.faa"
"PETaseHom_M6.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/Thc_cut2.faa"
"Thc_cut2.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_211.faa"
"PETcan_211.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PHL7.faa"
"PHL7.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_405.faa"
"PETcan_405.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/FsC.faa"
"FsC.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_403.faa"
"PETcan_403.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETaseHom_M1.faa"
"PETaseHom_M1.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/TtCutA.faa"
"TtCutA.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/Sub1.faa"
"Sub1.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/phaZ.faa"
"phaZ.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/RgPETase.faa"
"RgPETase.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PHL6.faa"
"PHL6.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/est119.faa"
"est119.b6o.bkp" generated in 130s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_407.faa"
"PETcan_407.b6o.bkp" generated in 132s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_611.faa"
"PETcan_611.b6o.bkp" generated in 133s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_409.faa"
"PETcan_409.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETcan_204.faa"
"PETcan_204.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/BhrPETase.faa"
"BhrPETase.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/PETaseHom_M3.faa"
"PETaseHom_M3.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/Tcur1278.faa"
"Tcur1278.b6o.bkp" generated in 131s
Mapping "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/clean_aa/Tcur0390.faa"
"Tcur0390.b6o.bkp" generated in 131s
Selecting 31 markers from "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PET27.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PET27.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_202.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_202.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_611.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_611.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PmC.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PmC.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/phaZ.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/phaZ.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/BhrPETase.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/BhrPETase.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/RgPETase.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/RgPETase.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/Tcur0390.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/Tcur0390.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PHL7.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PHL7.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PHL1.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PHL1.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_204.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_204.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_407.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_407.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/IsPETase.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/IsPETase.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETaseHom_M1.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETaseHom_M1.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PHL6.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PHL6.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/HiC.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/HiC.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_403.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_403.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/Thc_cut2.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/Thc_cut2.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/est119.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/est119.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_409.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_409.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETaseHom_M6.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETaseHom_M6.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/TtCutA.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/TtCutA.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_405.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_405.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETaseHom_M3.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETaseHom_M3.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PE-H.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PE-H.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/FsC.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/FsC.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/Sub1.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/Sub1.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_211.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETcan_211.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/HlL.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/HlL.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/Tcur1278.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/Tcur1278.b6o.bkp"
Selecting "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETaseHom_M9.b6o.bkp"
Not enough markers mapped (0/1) in "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/map_aa/PETaseHom_M9.b6o.bkp"
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/markers_aa"
Markers already extracted
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/markers"
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/msas"
Markers already aligned (key: "msa")
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/trim_gap_trim"
Markers already trimmed (key: "trim")
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/trim_gap_perc"
Markers already trimmed
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/trim_not_variant"
Markers already trimmed
Substitution matrix "/home/liliana/miniconda3/envs/phylophlan/lib/python3.10/site-packages/phylophlan/phylophlan_substitution_matrices/pfasum60.pkl" loaded
Creating folder "/home/liliana/Documents/ASR/BioBakery/PETases_phylophlan/tmp/sub"
Markers already subsampled
Concatenating alignments

[e] No alignments found to concatenate