phylophlan -i bins \
> -d phylophlan \
> -f 02_tol.cfg \
> --diversity high \
> --fast \
> -o total \
> -t a \
> --verbose
PhyloPhlAn version 3.0.51 (11 May 2020)
Command line: /home/wusu/anaconda3/envs/micro/bin/phylophlan -i bins -d phylophlan -f 02_tol.cfg --diversity high --fast -o total -t a --verbose
Automatically setting "input=bins" and "input_folder=/mnt/d/wudb"
Creating folder "total/tmp"
"high-fast" preset
Setting "sort=True" because "database=phylophlan"
Arguments: {'input': 'bins', 'clean': None, 'output': 'total', 'database': 'phylophlan', 'db_type': 'a', 'config_file': '02_tol.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 0x7f19f2da59e0>, 'unknown_fraction': 0.3, 'scoring_function': <function trident at 0x7f19f2da7050>, '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/d/wudb/bins', 'data_folder': 'total/tmp', 'databases_folder': 'phylophlan_databases/', 'submat_folder': '/home/wusu/anaconda3/envs/micro/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_matrices/', 'submod_folder': '/home/wusu/anaconda3/envs/micro/lib/python3.7/site-packages/phylophlan/phylophlan_substitution_models/', 'configs_folder': 'phylophlan_configs/', 'output_folder': '', 'genome_extension': '.fna', 'proteome_extension': '.faa', 'update': False, 'verbose': True}
Loading configuration file "02_tol.cfg"
Checking configuration file
Checking "/home/wusu/anaconda3/envs/micro/bin/diamond"
Checking "/home/wusu/anaconda3/envs/micro/bin/mafft"
Checking "/home/wusu/anaconda3/envs/micro/bin/trimal"
Checking "/home/wusu/anaconda3/envs/micro/bin/iqtree"
"db_aa" database "phylophlan_databases/phylophlan/phylophlan.dmnd" present
Loading files from "/mnt/d/wudb/bins"
Loading files from "/mnt/d/wudb/bins"
Checking 3 inputs
Checking "/mnt/d/wudb/bins/Candidatus Methanomethylophilus alvus Mx1201.faa"
Checking "/mnt/d/wudb/bins/Candidatus Methanoplasma termitum strain MpT1 chromosome.faa"
Checking "/mnt/d/wudb/bins/Candidatus_Methanomassiliicoccus_intestinalis_Issoire_Mx1.faa"
Creating folder "total/tmp/clean_aa"
Cleaning 3 inputs
Cleaning "/mnt/d/wudb/bins/Candidatus Methanomethylophilus alvus Mx1201.faa"
"total/tmp/clean_aa/Candidatus Methanomethylophilus alvus Mx1201.faa" generated in 0s
Cleaning "/mnt/d/wudb/bins/Candidatus Methanoplasma termitum strain MpT1 chromosome.faa"
"total/tmp/clean_aa/Candidatus Methanoplasma termitum strain MpT1 chromosome.faa" generated in 0s
Cleaning "/mnt/d/wudb/bins/Candidatus_Methanomassiliicoccus_intestinalis_Issoire_Mx1.faa"
"total/tmp/clean_aa/Candidatus_Methanomassiliicoccus_intestinalis_Issoire_Mx1.faa" generated in 0s
Loading files from "total/tmp/clean_aa"
Creating folder "total/tmp/map_aa"
Mapping "phylophlan" on 3 inputs (key: "map_aa")
Mapping "total/tmp/clean_aa/Candidatus Methanomethylophilus alvus Mx1201.faa"
[e] Command '['/home/wusu/anaconda3/envs/micro/bin/diamond', 'blastp', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query', 'total/tmp/clean_aa/Candidatus', 'Methanomethylophilus', 'alvus', 'Mx1201.faa', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', 'total/tmp/map_aa/Candidatus', 'Methanomethylophilus', 'alvus', 'Mx1201.b6o.bkp']' returned non-zero exit status 1.
[e] cannot execute command
command_line: /home/wusu/anaconda3/envs/micro/bin/diamond blastp --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0 --query total/tmp/clean_aa/Candidatus Methanomethylophilus alvus Mx1201.faa --db phylophlan_databases/phylophlan/phylophlan.dmnd --out total/tmp/map_aa/Candidatus Methanomethylophilus alvus Mx1201.b6o.bkp
stdin: None
stdout: None
env: {'LESSOPEN': '| /usr/bin/lesspipe %s', 'CONDA_PROMPT_MODIFIER': '(micro) ', 'USER': 'wusu', 'SHLVL': '1', 'HOME': '/home/wusu', 'CONDA_SHLVL': '2', '_CE_M': '', 'WSL_DISTRO_NAME': 'Ubuntu', 'LOGNAME': 'wusu', 'NAME': 'wusu', '_': '/home/wusu/anaconda3/envs/micro/bin/phylophlan', 'TERM': 'xterm-256color', '_CE_CONDA': '', 'PATH': '/home/wusu/anaconda3/envs/micro/bin:/home/wusu/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/d/rtools40/usr/bin:/mnt/d/bug/BugBase:/mnt/d/็งปๅจLinux่ฝฏไปถ/LxRunOffline-v3.3.3:/mnt/d/FastTree/mafft/mafft-win:/mnt/d/FastTree:/mnt/d/java/bin:/mnt/c/Users/wusu/AppData/Local/Microsoft/WindowsApps:/mnt/d/rtools40/usr/bin:/mnt/d/Rnew/R:/mnt/d/Rnew/R/bin/x64:/snap/bin', 'LANG': 'C.UTF-8', 'CONDA_PREFIX_1': '/home/wusu/anaconda3', 'LS_COLORS': 'rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:', 'CONDA_PYTHON_EXE': '/home/wusu/anaconda3/bin/python', 'SHELL': '/bin/bash', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'CONDA_DEFAULT_ENV': 'micro', 'PWD': '/mnt/d/wudb', 'CONDA_EXE': '/home/wusu/anaconda3/bin/conda', 'XDG_DATA_DIRS': '/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'CONDA_PREFIX': '/home/wusu/anaconda3/envs/micro', 'HOSTTYPE': 'x86_64', 'WSLENV': ''}
[e] Command '['/home/wusu/anaconda3/envs/micro/bin/diamond', 'blastp', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query', 'total/tmp/clean_aa/Candidatus', 'Methanomethylophilus', 'alvus', 'Mx1201.faa', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', 'total/tmp/map_aa/Candidatus', 'Methanomethylophilus', 'alvus', 'Mx1201.b6o.bkp']' returned non-zero exit status 1.
[e] error while mapping
{'program_name': '/home/wusu/anaconda3/envs/micro/bin/diamond', 'params': 'blastp --quiet --threads 1 --outfmt 6 --more-sensitive --id 50 --max-hsps 35 -k 0', 'input': '--query', 'database': '--db', 'output': '--out', 'version': 'version', 'command_line': '#program_name# #params# #input# #database# #output#'}
total/tmp/clean_aa/Candidatus Methanomethylophilus alvus Mx1201.faa
phylophlan_databases/phylophlan/phylophlan.dmnd
total/tmp/map_aa
Candidatus Methanomethylophilus alvus Mx1201.b6o.bkp
1
True
[e] Command '['/home/wusu/anaconda3/envs/micro/bin/diamond', 'blastp', '--quiet', '--threads', '1', '--outfmt', '6', '--more-sensitive', '--id', '50', '--max-hsps', '35', '-k', '0', '--query', 'total/tmp/clean_aa/Candidatus', 'Methanomethylophilus', 'alvus', 'Mx1201.faa', '--db', 'phylophlan_databases/phylophlan/phylophlan.dmnd', '--out', 'total/tmp/map_aa/Candidatus', 'Methanomethylophilus', 'alvus', 'Mx1201.b6o.bkp']' returned non-zero exit status 1.
[e] gene_markers_identification crashed
What should I do next? thanks.