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biobakery / phylophlan

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
https://huttenhower.sph.harvard.edu/phylophlan
MIT License
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gene_markers_selection crashed #27

Closed gunturus closed 4 years ago

gunturus commented 4 years ago

[e] expected str, bytes or os.PathLike object, not NoneType

[e] gene_markers_selection crashed output_tree/tmp/map_dna/JIAJIAN16_Bin_002.LargeContigs.b6o.bz2" generated in 1s

What does the following error mean? I used the following command.

phylophlan -i input_genomes -d phylophlan -f /mnt/home/gunturus/phylophlan/supermatrix_aa.cfg --diversity high --fast -o output_tree --nproc 20 --verbose

fasnicar commented 4 years ago

Hi, can you provide which version of PhyloPhlAn you've installed? If you can, please provide both

phylophlan --version

and 

conda list | grep phylophlan

Thanks

gunturus commented 4 years ago

PhyloPhlAn version 3.0.51 (11 May 2020)

and

# packages in environment at /mnt/home/gunturus/anaconda3/envs/phylophlan: phylophlan 3.0 py_5 bioconda

gunturus commented 4 years ago

Here is the log file, if it is helpful.

PhyloPhlAn version 3.0.51 (11 May 2020)

Command line: /mnt/home/gunturus/anaconda3/envs/phylophlan/bin/phylophlan -i input_genomes -d phylophlan -f /mnt/home/gunturus/phylophlan/supermatrix_aa.cfg --diversity high --fast -o output_tree --nproc 20 --verbose

Automatically setting "input=input_genomes" and "input_folder=/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all"
[e] "/mnt/home/gunturus/anaconda3/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlan_configs/" folder does not exists
"high-fast" preset
Setting "sort=True" because "database=phylophlan"
Arguments: {'input': 'input_genomes', 'clean': None, 'output': 'output_tree', 'database': 'phylophlan', 'db_type': None, 'config_file': '/mnt/home/gunturus/phylophlan/supermatrix_aa.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': 1, 'trim': 'greedy', 'gap_perc_threshold': 0.67, 'not_variant_threshold': 0.9, 'subsample': <function phylophlan at 0x2b5a9fb7fca0>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x2b5a9fb80310>, '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': False, 'input_folder': '/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes', 'data_folder': 'output_tree/tmp', 'databases_folder': 'phylophlan_databases/', 'submat_folder': '/mnt/home/gunturus/anaconda3/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': '/mnt/home/gunturus/anaconda3/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlan_substitution_models/', 'configs_folder': None, 'output_folder': '', 'genome_extension': '.fna', 'proteome_extension': '.faa', 'update': False, 'verbose': True}
Loading configuration file "/mnt/home/gunturus/phylophlan/supermatrix_aa.cfg"
Checking configuration file
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/diamond"
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/mafft"
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/trimal"
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/FastTreeMP"
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/raxmlHPC-PTHREADS-SSE3"
"db_aa" database "phylophlan_databases/phylophlan/phylophlan.dmnd" present
Loading files from "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes"
Mapping "phylophlan" on 180 inputs (key: "map_dna")
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S24_Bin_002.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B38_Bin_002.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Y16_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H34_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D10_Bin_004.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R33_Bin_002.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIAJIAN5_Bin_002.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/T10_Bin_002.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/M12_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIAJIAN11_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V3_Bin_004.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V3_Bin_003.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S26_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D10_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S5_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/W9_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P23_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S25_Bin_001.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/W9_Bin_002.LargeContigs.fna"
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Y16_Bin_004.LargeContigs.fna"
"JIAJIAN5_Bin_002.LargeContigs.b6o.bkp" generated in 655s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/O13_Bin_002.LargeContigs.fna"
"T10_Bin_002.LargeContigs.b6o.bkp" generated in 775s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIA12_Bin_002.LargeContigs.fna"
"JIAJIAN11_Bin_001.LargeContigs.b6o.bkp" generated in 1122s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R26_Bin_002.LargeContigs.fna"
"Y16_Bin_001.LargeContigs.b6o.bkp" generated in 1123s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P7_Bin_003.LargeContigs.fna"
"S25_Bin_001.LargeContigs.b6o.bkp" generated in 1178s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/M12_Bin_003.LargeContigs.fna"
"R33_Bin_002.LargeContigs.b6o.bkp" generated in 1193s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H25_Bin_003.LargeContigs.fna"
"D10_Bin_001.LargeContigs.b6o.bkp" generated in 1197s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/M12_Bin_002.LargeContigs.fna"
"Y16_Bin_004.LargeContigs.b6o.bkp" generated in 1250s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/G1_Bin_001.LargeContigs.fna"
"P23_Bin_001.LargeContigs.b6o.bkp" generated in 1276s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/A20_Bin_001.LargeContigs.fna"
"W9_Bin_002.LargeContigs.b6o.bkp" generated in 1350s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V23_Bin_001.LargeContigs.fna"
"W9_Bin_001.LargeContigs.b6o.bkp" generated in 1370s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P27_Bin_001.LargeContigs.fna"
"JIA12_Bin_002.LargeContigs.b6o.bkp" generated in 650s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Y16_Bin_003.LargeContigs.fna"
"V3_Bin_003.LargeContigs.b6o.bkp" generated in 1461s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIA12_Bin_001.LargeContigs.fna"
"D10_Bin_004.LargeContigs.b6o.bkp" generated in 1499s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V40_Bin_001.LargeContigs.fna"
"M12_Bin_001.LargeContigs.b6o.bkp" generated in 1575s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/X24_Bin_001.LargeContigs.fna"
"S5_Bin_001.LargeContigs.b6o.bkp" generated in 1592s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P15_Bin_002.LargeContigs.fna"
"H34_Bin_001.LargeContigs.b6o.bkp" generated in 1642s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/L66_Bin_001.LargeContigs.fna"
"V3_Bin_004.LargeContigs.b6o.bkp" generated in 1886s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S25_Bin_003.LargeContigs.fna"
"S24_Bin_002.LargeContigs.b6o.bkp" generated in 1942s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/A20_Bin_004.LargeContigs.fna"
"B38_Bin_002.LargeContigs.b6o.bkp" generated in 2005s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/gan14_Bin_002.LargeContigs.fna"
"S26_Bin_001.LargeContigs.b6o.bkp" generated in 2007s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V23_Bin_003.LargeContigs.fna"
"R26_Bin_002.LargeContigs.b6o.bkp" generated in 1035s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/X24_Bin_002.LargeContigs.fna"
"O13_Bin_002.LargeContigs.b6o.bkp" generated in 1538s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V3_Bin_001.LargeContigs.fna"
"P27_Bin_001.LargeContigs.b6o.bkp" generated in 1097s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/L7_Bin_002.LargeContigs.fna"
"gan14_Bin_002.LargeContigs.b6o.bkp" generated in 539s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/L40_Bin_004.LargeContigs.fna"
"V40_Bin_001.LargeContigs.b6o.bkp" generated in 1119s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R23_Bin_001.LargeContigs.fna"
"G1_Bin_001.LargeContigs.b6o.bkp" generated in 1400s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/G24_Bin_002.LargeContigs.fna"
"V23_Bin_001.LargeContigs.b6o.bkp" generated in 1337s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Y5_Bin_002.LargeContigs.fna"
"P7_Bin_003.LargeContigs.b6o.bkp" generated in 1571s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Y5_Bin_001.LargeContigs.fna"
"A20_Bin_001.LargeContigs.b6o.bkp" generated in 1601s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/I14_Bin_004.LargeContigs.fna"
"L66_Bin_001.LargeContigs.b6o.bkp" generated in 1287s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V3_Bin_002.LargeContigs.fna"
"A20_Bin_004.LargeContigs.b6o.bkp" generated in 1240s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H25_Bin_002.LargeContigs.fna"
"M12_Bin_002.LargeContigs.b6o.bkp" generated in 2006s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S25_Bin_002.LargeContigs.fna"
"P15_Bin_002.LargeContigs.b6o.bkp" generated in 1620s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/A40_Bin_002.LargeContigs.fna"
"H25_Bin_003.LargeContigs.b6o.bkp" generated in 2077s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P27_Bin_002.LargeContigs.fna"
"JIA12_Bin_001.LargeContigs.b6o.bkp" generated in 1879s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V5_Bin_002.LargeContigs.fna"
"V23_Bin_003.LargeContigs.b6o.bkp" generated in 1479s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D15_Bin_002.LargeContigs.fna"
"X24_Bin_002.LargeContigs.b6o.bkp" generated in 1362s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R24_Bin_001.LargeContigs.fna"
"X24_Bin_001.LargeContigs.b6o.bkp" generated in 1976s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Z1_Bin_001.LargeContigs.fna"
"V3_Bin_001.LargeContigs.b6o.bkp" generated in 1358s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D7_Bin_001.LargeContigs.fna"
"Y16_Bin_003.LargeContigs.b6o.bkp" generated in 2169s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S26_Bin_002.LargeContigs.fna"
"L40_Bin_004.LargeContigs.b6o.bkp" generated in 1077s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/G16_Bin_002.LargeContigs.fna"
"M12_Bin_003.LargeContigs.b6o.bkp" generated in 2536s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H7_Bin_001.LargeContigs.fna"
"S25_Bin_003.LargeContigs.b6o.bkp" generated in 1973s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S9_Bin_001.LargeContigs.fna"
"L7_Bin_002.LargeContigs.b6o.bkp" generated in 1473s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/W12_Bin_001.LargeContigs.fna"
"Y5_Bin_002.LargeContigs.b6o.bkp" generated in 1339s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H30_Bin_001.LargeContigs.fna"
"G24_Bin_002.LargeContigs.b6o.bkp" generated in 1411s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S5_Bin_004.LargeContigs.fna"
"R23_Bin_001.LargeContigs.b6o.bkp" generated in 1463s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/X3_Bin_002.LargeContigs.fna"
"A40_Bin_002.LargeContigs.b6o.bkp" generated in 1113s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V40_Bin_002.LargeContigs.fna"
"S25_Bin_002.LargeContigs.b6o.bkp" generated in 1130s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/L40_Bin_002.LargeContigs.fna"
"V3_Bin_002.LargeContigs.b6o.bkp" generated in 1468s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/A20_Bin_002.LargeContigs.fna"
"Y5_Bin_001.LargeContigs.b6o.bkp" generated in 1823s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D7_Bin_004.LargeContigs.fna"
"X3_Bin_002.LargeContigs.b6o.bkp" generated in 528s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R23_Bin_002.LargeContigs.fna"
"P27_Bin_002.LargeContigs.b6o.bkp" generated in 1379s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R9_Bin_002.LargeContigs.fna"
"V5_Bin_002.LargeContigs.b6o.bkp" generated in 1442s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R24_Bin_003.LargeContigs.fna"
"H25_Bin_002.LargeContigs.b6o.bkp" generated in 1673s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H34_Bin_002.LargeContigs.fna"
"R24_Bin_001.LargeContigs.b6o.bkp" generated in 1375s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/X8_Bin_001.LargeContigs.fna"
"G16_Bin_002.LargeContigs.b6o.bkp" generated in 1499s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P23_Bin_005.LargeContigs.fna"
"L40_Bin_002.LargeContigs.b6o.bkp" generated in 788s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/L66_Bin_003.LargeContigs.fna"
"I14_Bin_004.LargeContigs.b6o.bkp" generated in 2297s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R24_Bin_002.LargeContigs.fna"
"H30_Bin_001.LargeContigs.b6o.bkp" generated in 1156s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/T6_Bin_002.LargeContigs.fna"
"H7_Bin_001.LargeContigs.b6o.bkp" generated in 1518s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/W21_Bin_001.LargeContigs.fna"
"Z1_Bin_001.LargeContigs.b6o.bkp" generated in 1687s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/G1_Bin_002.LargeContigs.fna"
"S9_Bin_001.LargeContigs.b6o.bkp" generated in 1386s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/I14_Bin_002.LargeContigs.fna"
"D7_Bin_001.LargeContigs.b6o.bkp" generated in 1707s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R26_Bin_001.LargeContigs.fna"
"D15_Bin_002.LargeContigs.b6o.bkp" generated in 2020s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B33_Bin_002.LargeContigs.fna"
"S26_Bin_002.LargeContigs.b6o.bkp" generated in 1951s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H25_Bin_001.LargeContigs.fna"
"R24_Bin_002.LargeContigs.b6o.bkp" generated in 461s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/L7_Bin_001.LargeContigs.fna"
"D7_Bin_004.LargeContigs.b6o.bkp" generated in 1228s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R6_Bin_002.LargeContigs.fna"
"V40_Bin_002.LargeContigs.b6o.bkp" generated in 1425s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B36_Bin_001.LargeContigs.fna"
"W12_Bin_001.LargeContigs.b6o.bkp" generated in 1835s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B36_Bin_002.LargeContigs.fna"
"S5_Bin_004.LargeContigs.b6o.bkp" generated in 1797s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H7_Bin_002.LargeContigs.fna"
"H34_Bin_002.LargeContigs.b6o.bkp" generated in 1054s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/A40_Bin_003.LargeContigs.fna"
"T6_Bin_002.LargeContigs.b6o.bkp" generated in 844s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R6_Bin_001.LargeContigs.fna"
"P23_Bin_005.LargeContigs.b6o.bkp" generated in 909s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D8_Bin_002.LargeContigs.fna"
"X8_Bin_001.LargeContigs.b6o.bkp" generated in 1140s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S26_Bin_004.LargeContigs.fna"
"A20_Bin_002.LargeContigs.b6o.bkp" generated in 1700s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P21_Bin_001.LargeContigs.fna"
"R24_Bin_003.LargeContigs.b6o.bkp" generated in 1732s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S5_Bin_002.LargeContigs.fna"
"R9_Bin_002.LargeContigs.b6o.bkp" generated in 1896s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/I14_Bin_001.LargeContigs.fna"
"R23_Bin_002.LargeContigs.b6o.bkp" generated in 2081s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Y26_Bin_002.LargeContigs.fna"
"L7_Bin_001.LargeContigs.b6o.bkp" generated in 1108s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D10_Bin_002.LargeContigs.fna"
"R6_Bin_002.LargeContigs.b6o.bkp" generated in 1023s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R33_Bin_003.LargeContigs.fna"
"B33_Bin_002.LargeContigs.b6o.bkp" generated in 1287s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V23_Bin_002.LargeContigs.fna"
"B36_Bin_001.LargeContigs.b6o.bkp" generated in 1130s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P7_Bin_001.LargeContigs.fna"
"W21_Bin_001.LargeContigs.b6o.bkp" generated in 1669s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/E3_Bin_001.LargeContigs.fna"
"L66_Bin_003.LargeContigs.b6o.bkp" generated in 1787s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/1_Bin_001.LargeContigs.fna"
"H25_Bin_001.LargeContigs.b6o.bkp" generated in 1399s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H31_Bin_001.LargeContigs.fna"
"R26_Bin_001.LargeContigs.b6o.bkp" generated in 1832s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/other_Bin_001.LargeContigs.fna"
"I14_Bin_002.LargeContigs.b6o.bkp" generated in 1971s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/G51_Bin_001.LargeContigs.fna"
"G1_Bin_002.LargeContigs.b6o.bkp" generated in 1998s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H31_Bin_003.LargeContigs.fna"
"R6_Bin_001.LargeContigs.b6o.bkp" generated in 1463s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R33_Bin_004.LargeContigs.fna"
"A40_Bin_003.LargeContigs.b6o.bkp" generated in 1601s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/T7_Bin_002.LargeContigs.fna"
"E3_Bin_001.LargeContigs.b6o.bkp" generated in 634s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Y26_Bin_001.LargeContigs.fna"
"P21_Bin_001.LargeContigs.b6o.bkp" generated in 1449s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D15_Bin_001.LargeContigs.fna"
"D8_Bin_002.LargeContigs.b6o.bkp" generated in 1555s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/M42_Bin_002.LargeContigs.fna"
"H7_Bin_002.LargeContigs.b6o.bkp" generated in 1830s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/W21_Bin_002.LargeContigs.fna"
"B36_Bin_002.LargeContigs.b6o.bkp" generated in 2031s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/W22_Bin_001.LargeContigs.fna"
"other_Bin_001.LargeContigs.b6o.bkp" generated in 834s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B8_Bin_002.LargeContigs.fna"
"I14_Bin_001.LargeContigs.b6o.bkp" generated in 1417s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B38_Bin_003.LargeContigs.fna"
"V23_Bin_002.LargeContigs.b6o.bkp" generated in 1441s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/G51_Bin_002.LargeContigs.fna"
"S5_Bin_002.LargeContigs.b6o.bkp" generated in 1728s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D11_Bin_001.LargeContigs.fna"
"S26_Bin_004.LargeContigs.b6o.bkp" generated in 2222s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/W12_Bin_002.LargeContigs.fna"
"W22_Bin_001.LargeContigs.b6o.bkp" generated in 470s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/34_Bin_002.LargeContigs.fna"
"Y26_Bin_002.LargeContigs.b6o.bkp" generated in 1735s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S26_Bin_003.LargeContigs.fna"
"H31_Bin_001.LargeContigs.b6o.bkp" generated in 1522s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P21_Bin_002.LargeContigs.fna"
"D10_Bin_002.LargeContigs.b6o.bkp" generated in 1734s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D7_Bin_002.LargeContigs.fna"
"R33_Bin_003.LargeContigs.b6o.bkp" generated in 1735s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Z24_Bin_001.LargeContigs.fna"
"P7_Bin_001.LargeContigs.b6o.bkp" generated in 1675s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S24_Bin_003.LargeContigs.fna"
"G51_Bin_001.LargeContigs.b6o.bkp" generated in 1363s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P34_Bin_001.LargeContigs.fna"
"R33_Bin_004.LargeContigs.b6o.bkp" generated in 1115s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P36_Bin_001.LargeContigs.fna"
"1_Bin_001.LargeContigs.b6o.bkp" generated in 1837s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/1_Bin_002.LargeContigs.fna"
"H31_Bin_003.LargeContigs.b6o.bkp" generated in 1522s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D15_Bin_003.LargeContigs.fna"
"Y26_Bin_001.LargeContigs.b6o.bkp" generated in 1343s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Z1_Bin_002.LargeContigs.fna"
"T7_Bin_002.LargeContigs.b6o.bkp" generated in 1439s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B37_Bin_001.LargeContigs.fna"
"D15_Bin_001.LargeContigs.b6o.bkp" generated in 1441s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V5_Bin_001.LargeContigs.fna"
"Z24_Bin_001.LargeContigs.b6o.bkp" generated in 498s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H29_Bin_001.LargeContigs.fna"
"W21_Bin_002.LargeContigs.b6o.bkp" generated in 1385s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/A40_Bin_001.LargeContigs.fna"
"34_Bin_002.LargeContigs.b6o.bkp" generated in 955s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R9_Bin_001.LargeContigs.fna"
"B37_Bin_001.LargeContigs.b6o.bkp" generated in 486s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V22_Bin_001.LargeContigs.fna"
"M42_Bin_002.LargeContigs.b6o.bkp" generated in 1950s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H25_Bin_004.LargeContigs.fna"
"B38_Bin_003.LargeContigs.b6o.bkp" generated in 1691s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/X3_Bin_001.LargeContigs.fna"
"S24_Bin_003.LargeContigs.b6o.bkp" generated in 1134s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D10_Bin_003.LargeContigs.fna"
"P21_Bin_002.LargeContigs.b6o.bkp" generated in 1303s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H31_Bin_002.LargeContigs.fna"
"D11_Bin_001.LargeContigs.b6o.bkp" generated in 1540s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/L40_Bin_003.LargeContigs.fna"
"W12_Bin_002.LargeContigs.b6o.bkp" generated in 1619s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P7_Bin_002.LargeContigs.fna"
"B8_Bin_002.LargeContigs.b6o.bkp" generated in 1957s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P23_Bin_004.LargeContigs.fna"
"G51_Bin_002.LargeContigs.b6o.bkp" generated in 1673s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/L40_Bin_001.LargeContigs.fna"
"S26_Bin_003.LargeContigs.b6o.bkp" generated in 1499s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B38_Bin_001.LargeContigs.fna"
"D7_Bin_002.LargeContigs.b6o.bkp" generated in 1474s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P36_Bin_002.LargeContigs.fna"
"Z1_Bin_002.LargeContigs.b6o.bkp" generated in 1270s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIA33_Bin_002.LargeContigs.fna"
"H29_Bin_001.LargeContigs.b6o.bkp" generated in 1148s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIAJIAN5_Bin_001.LargeContigs.fna"
"X3_Bin_001.LargeContigs.b6o.bkp" generated in 522s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/V23_Bin_004.LargeContigs.fna"
"P34_Bin_001.LargeContigs.b6o.bkp" generated in 1661s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/E3_Bin_002.LargeContigs.fna"
"D15_Bin_003.LargeContigs.b6o.bkp" generated in 1482s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B33_Bin_003.LargeContigs.fna"
"P36_Bin_001.LargeContigs.b6o.bkp" generated in 1653s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R46_Bin_001.LargeContigs.fna"
"V5_Bin_001.LargeContigs.b6o.bkp" generated in 1451s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/L66_Bin_002.LargeContigs.fna"
"V22_Bin_001.LargeContigs.b6o.bkp" generated in 1076s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S24_Bin_001.LargeContigs.fna"
"A40_Bin_001.LargeContigs.b6o.bkp" generated in 1540s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIAJIAN16_Bin_001.LargeContigs.fna"
"R9_Bin_001.LargeContigs.b6o.bkp" generated in 1423s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H31_Bin_004.LargeContigs.fna"
"1_Bin_002.LargeContigs.b6o.bkp" generated in 2075s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/X8_Bin_002.LargeContigs.fna"
"H25_Bin_004.LargeContigs.b6o.bkp" generated in 1339s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/T7_Bin_001.LargeContigs.fna"
"JIA33_Bin_002.LargeContigs.b6o.bkp" generated in 830s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/G24_Bin_001.LargeContigs.fna"
"L40_Bin_003.LargeContigs.b6o.bkp" generated in 1251s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Z24_Bin_002.LargeContigs.fna"
"B38_Bin_001.LargeContigs.b6o.bkp" generated in 1171s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/B33_Bin_001.LargeContigs.fna"
"H31_Bin_002.LargeContigs.b6o.bkp" generated in 1349s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/O13_Bin_001.LargeContigs.fna"
"P36_Bin_002.LargeContigs.b6o.bkp" generated in 1253s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Y16_Bin_002.LargeContigs.fna"
"E3_Bin_002.LargeContigs.b6o.bkp" generated in 996s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIAJIAN16_Bin_002.LargeContigs.fna"
"P7_Bin_002.LargeContigs.b6o.bkp" generated in 1383s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/W2_Bin_002.LargeContigs.fna"
"P23_Bin_004.LargeContigs.b6o.bkp" generated in 1490s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/H29_Bin_002.LargeContigs.fna"
"JIAJIAN5_Bin_001.LargeContigs.b6o.bkp" generated in 1272s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/R33_Bin_001.LargeContigs.fna"
"D10_Bin_003.LargeContigs.b6o.bkp" generated in 1765s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/T10_Bin_001.LargeContigs.fna"
"G24_Bin_001.LargeContigs.b6o.bkp" generated in 486s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/S9_Bin_002.LargeContigs.fna"
"R46_Bin_001.LargeContigs.b6o.bkp" generated in 1304s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIA33_Bin_001.LargeContigs.fna"
"Z24_Bin_002.LargeContigs.b6o.bkp" generated in 544s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/JIA17_Bin_001.LargeContigs.fna"
"L40_Bin_001.LargeContigs.b6o.bkp" generated in 1690s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/A20_Bin_003.LargeContigs.fna"
"X8_Bin_002.LargeContigs.b6o.bkp" generated in 1008s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/Y16_Bin_005.LargeContigs.fna"
"JIAJIAN16_Bin_001.LargeContigs.b6o.bkp" generated in 1357s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/M42_Bin_001.LargeContigs.fna"
"T7_Bin_001.LargeContigs.b6o.bkp" generated in 1144s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/D11_Bin_002.LargeContigs.fna"
"V23_Bin_004.LargeContigs.b6o.bkp" generated in 1952s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/T4_Bin_002.LargeContigs.fna"
"L66_Bin_002.LargeContigs.b6o.bkp" generated in 1707s
Mapping "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes/P34_Bin_002.LargeContigs.fna"
"T10_Bin_001.LargeContigs.b6o.bkp" generated in 711s
"B33_Bin_003.LargeContigs.b6o.bkp" generated in 1984s
"O13_Bin_001.LargeContigs.b6o.bkp" generated in 1134s
"W2_Bin_002.LargeContigs.b6o.bkp" generated in 1216s
"S24_Bin_001.LargeContigs.b6o.bkp" generated in 1978s
"B33_Bin_001.LargeContigs.b6o.bkp" generated in 1425s
"H31_Bin_004.LargeContigs.b6o.bkp" generated in 1940s
"Y16_Bin_002.LargeContigs.b6o.bkp" generated in 1399s
"JIA33_Bin_001.LargeContigs.b6o.bkp" generated in 1134s
"H29_Bin_002.LargeContigs.b6o.bkp" generated in 1406s
"R33_Bin_001.LargeContigs.b6o.bkp" generated in 1410s
"S9_Bin_002.LargeContigs.b6o.bkp" generated in 1461s
"JIAJIAN16_Bin_002.LargeContigs.b6o.bkp" generated in 1720s
"Y16_Bin_005.LargeContigs.b6o.bkp" generated in 1452s
"JIA17_Bin_001.LargeContigs.b6o.bkp" generated in 1807s
"A20_Bin_003.LargeContigs.b6o.bkp" generated in 1954s
"M42_Bin_001.LargeContigs.b6o.bkp" generated in 1839s
"T4_Bin_002.LargeContigs.b6o.bkp" generated in 1697s
"P34_Bin_002.LargeContigs.b6o.bkp" generated in 1782s
"D11_Bin_002.LargeContigs.b6o.bkp" generated in 2052s
Selecting 199 markers from "output_tree/tmp/map_dna"
Selecting "output_tree/tmp/map_dna/M42_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/JIA33_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/R9_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/H25_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/R9_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/P7_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/S5_Bin_003.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/P27_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/Y16_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/O13_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/V40_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/A20_Bin_003.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/B36_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/B33_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/W12_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/T7_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/P36_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/D10_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/1_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/T6_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R9_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R26_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/T7_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/Y5_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/T6_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R23_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/V40_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/W2_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/D10_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/B8_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/Y16_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/G16_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P7_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/V3_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/O13_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P23_Bin_004.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/JIA33_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/H7_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P27_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/D15_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/S5_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/I14_Bin_004.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/H25_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/G51_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/B33_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/Y16_Bin_004.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P36_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/L40_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/W12_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/T10_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/A20_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/Y16_Bin_005.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/M42_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/JIAJIAN16_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/T10_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/W22_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/W22_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P21_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R23_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P23_Bin_005.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R9_Bin_002.LargeContigs.b6o.bz2" generated in 1s
Selecting "output_tree/tmp/map_dna/A40_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/G16_Bin_002.LargeContigs.b6o.bz2" generated in 0s
"output_tree/tmp/map_dna/R26_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R33_Bin_003.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/H31_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/B36_Bin_002.LargeContigs.b6o.bz2" generated in 1s
Selecting "output_tree/tmp/map_dna/W12_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/W2_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/M12_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/D15_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/D10_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/1_Bin_002.LargeContigs.b6o.bz2" generated in 1s
"output_tree/tmp/map_dna/H7_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P23_Bin_002.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/gan14_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/V3_Bin_003.LargeContigs.b6o.bz2" generated in 0s
"output_tree/tmp/map_dna/G51_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/A40_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/V3_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/Y16_Bin_004.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/G24_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/Y5_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R46_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/G24_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/X8_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/B8_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/D7_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/L40_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/S24_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P21_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/Y16_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/I14_Bin_004.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/L7_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P23_Bin_004.LargeContigs.b6o.bz2" generated in 1s
Selecting "output_tree/tmp/map_dna/V23_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/Y16_Bin_005.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/gan14_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/H31_Bin_002.LargeContigs.b6o.bz2" generated in 0s
"output_tree/tmp/map_dna/M12_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/V22_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/M12_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R33_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/X8_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R46_Bin_001.LargeContigs.b6o.bz2" generated in 0s
"output_tree/tmp/map_dna/D10_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/L66_Bin_003.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/X3_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/V3_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R26_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P23_Bin_005.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/D11_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/A40_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/34_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/W12_Bin_002.LargeContigs.b6o.bz2" generated in 0s
"output_tree/tmp/map_dna/gan14_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/G1_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/B8_Bin_001.LargeContigs.b6o.bkp"
Not enough markers mapped (0/1) in "output_tree/tmp/map_dna/B8_Bin_001.LargeContigs.b6o.bkp"
Selecting "output_tree/tmp/map_dna/G24_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/gan14_Bin_001.LargeContigs.b6o.bz2" generated in 0s
"output_tree/tmp/map_dna/A40_Bin_001.LargeContigs.b6o.bz2" generated in 0s
"output_tree/tmp/map_dna/X3_Bin_002.LargeContigs.b6o.bz2" generated in 0s

[e] expected str, bytes or os.PathLike object, not NoneType

[e] gene_markers_selection crashed
"output_tree/tmp/map_dna/JIAJIAN16_Bin_002.LargeContigs.b6o.bz2" generated in 1s
fasnicar commented 4 years ago

Hi, many thanks for the versions and the full log. I ran a test but wasn't able to reproduce your error and it is also strange because between 

[e] expected str, bytes or os.PathLike object, not NoneType

and

[e] gene_markers_selection crashed

there should other error lines.

I would suggest if you can to remove the folder output_tree/tmp/map_dna and re-run PhyloPhlAn with the same command 

phylophlan -i input_genomes -d phylophlan -f /mnt/home/gunturus/phylophlan/supermatrix_aa.cfg --diversity high --fast -o output_tree --nproc 1 --verbose

but with --nproc 1 (the steps already done will be skipped and PhyloPhlAn will process one genome at a time, so we can debug which of your input genomes is failing and maybe understand why that's happening.

Many thanks, Francesco

gunturus commented 4 years ago

If I remove map_dna, that will remove all the diamond map results. This step took approximately 20 mins per genome. If I use one processor, it will take a few days to finish all 199 genomes.

fasnicar commented 4 years ago

You can remove just the .bz2 files and keep the mappings from the map_dna folder.

gunturus commented 4 years ago 
phyloPhlAn version 3.0.51 (11 May 2020)

Command line: /mnt/home/gunturus/anaconda3/envs/phylophlan/bin/phylophlan -i input_genomes -d phylophlan -f /mnt/home/gunturus/phylophlan/supermatrix_aa.cfg --diversity high --fast -o output_tree --nproc 1 --verbose

Automatically setting "input=input_genomes" and "input_folder=/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all"
[e] "/mnt/home/gunturus/anaconda3/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlan_configs/" folder does not exists
"high-fast" preset
Setting "sort=True" because "database=phylophlan"
Arguments: {'input': 'input_genomes', 'clean': None, 'output': 'output_tree', 'database': 'phylophlan', 'db_type': None, 'config_file': '/mnt/home/gunturus/phylophlan/supermatrix_aa.cfg', 'diversity': 'high', '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': 1, 'trim': 'greedy', 'gap_perc_threshold': 0.67, 'not_variant_threshold': 0.9, 'subsample': <function phylophlan at 0x2b400bc20ca0>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x2b400bc21310>, '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': False, 'input_folder': '/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes', 'data_folder': 'output_tree/tmp', 'databases_folder': 'phylophlan_databases/', 'submat_folder': '/mnt/home/gunturus/anaconda3/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': '/mnt/home/gunturus/anaconda3/envs/phylophlan/lib/python3.8/site-packages/phylophlan/phylophlan_substitution_models/', 'configs_folder': None, 'output_folder': '', 'genome_extension': '.fna', 'proteome_extension': '.faa', 'update': False, 'verbose': True}
Loading configuration file "/mnt/home/gunturus/phylophlan/supermatrix_aa.cfg"
Checking configuration file
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/diamond"
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/mafft"
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/trimal"
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/FastTreeMP"
Checking "/mnt/home/gunturus/anaconda3/envs/phylophlan/bin/raxmlHPC-PTHREADS-SSE3"
"db_aa" database "phylophlan_databases/phylophlan/phylophlan.dmnd" present
Loading files from "/mnt/ufs18/home-131/gunturus/Jichen_genomes/PhyloPhlAn_Tree_all/input_genomes"
"phylophlan" markers already mapped (key: "map_dna")
Selecting 199 markers from "output_tree/tmp/map_dna"
Selecting "output_tree/tmp/map_dna/M42_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/M42_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/JIA33_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/JIA33_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R9_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R9_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/H25_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/H25_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R9_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R9_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P7_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P7_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/S5_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/S5_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P27_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P27_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/Y16_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/Y16_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/O13_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/O13_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/V40_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/V40_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/A20_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/A20_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/B36_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/B36_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/B33_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/B33_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/W12_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/W12_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/T7_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/T7_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P36_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P36_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/D10_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/D10_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/1_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/1_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/T6_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/T6_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R26_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R26_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/Y5_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/Y5_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R23_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R23_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/W2_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/W2_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/B8_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/B8_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/G16_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/G16_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/V3_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/V3_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P23_Bin_004.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P23_Bin_004.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/H7_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/H7_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/D15_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/D15_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/I14_Bin_004.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/I14_Bin_004.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/G51_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/G51_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/Y16_Bin_004.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/Y16_Bin_004.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/L40_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/L40_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/T10_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/T10_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/Y16_Bin_005.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/Y16_Bin_005.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/JIAJIAN16_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/JIAJIAN16_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/W22_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/W22_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P21_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P21_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P23_Bin_005.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P23_Bin_005.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/A40_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/A40_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R33_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R33_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/H31_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/H31_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/W12_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/W12_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/M12_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/M12_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/D10_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/D10_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/P23_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/P23_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/gan14_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/gan14_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/A40_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/A40_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/V3_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/V3_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/G24_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/G24_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R46_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R46_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/X8_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/X8_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/D7_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/D7_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/S24_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/S24_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/Y16_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/Y16_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/L7_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/L7_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/V23_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/V23_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/gan14_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/gan14_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/V22_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/V22_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/M12_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/M12_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/X8_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/X8_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/L66_Bin_003.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/L66_Bin_003.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/X3_Bin_002.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/X3_Bin_002.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/R26_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/R26_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/D11_Bin_001.LargeContigs.b6o.bkp"
"output_tree/tmp/map_dna/D11_Bin_001.LargeContigs.b6o.bz2" generated in 0s
Selecting "output_tree/tmp/map_dna/34_Bin_001.LargeContigs.b6o.bkp"

[e] expected str, bytes or os.PathLike object, not NoneType

[e] gene_markers_selection crashed

It didn't give any more error info.

gunturus commented 4 years ago

I attached 34_Bin_001.LargeContigs.b6o.bkp here, if that is helpful. I renamed .log since Github doesn't allow .bkp extension files. 34_Bin_001.LargeContigs.b6o.bkp.log

fasnicar commented 4 years ago

It is still strange that the extra error line is missing, in any case, it seems that it is happening with 34_Bin_001.LargeContigs. Thanks for the 34_Bin_001.LargeContigs.b6o.bkp, and at first glance seems correct, but I'll test it again the specific function to investigate more. Another thing will be that if you can put together your input genomes and send them to me (by email as well if you prefer) I'll try to run the same analysis to have a better idea.

Thanks!

gunturus commented 4 years ago

Hi I have emailed the input_genomes and my current output_tree folder with all the diamond mapping files if it is helpful. Thank you for your help!

gunturus commented 4 years ago

@fasnicar Just checking if you received my email with the genomes.

senukobla commented 4 years ago

I am having the same problem. Same error. Is there a solution?

fasnicar commented 4 years ago

Hi, can you pull the latest version from the GitHub repository, clean your output folder and run again PhyloPhlAn? It would be very useful if you can run PhyloPhlAn with the --verbose and if you can save the print info and report here if you should encounter any errors.

Many thanks, Francesco