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PhyloPhlAn Crash-------

Hie,
I am new to phylophan. I tried to run it, it crashed. I hope if there could be an assistance with that.
Regards
Jitesh

Mapping “output_tol/tmp/uncompressed/GCA_002883195.fna”
“GCA_002882875.b6o.bkp” generated in 1323s
Mapping “output_tol/tmp/uncompressed/GCA_002883215.fna”
“GCA_002882895.b6o.bkp” generated in 1300s
Mapping “output_tol/tmp/uncompressed/GCA_002883235.fna”
OME_TERMINAL_SCREEN’: ‘/org/gnome/Terminal/screen/1bada53f_77ec_4a5b_aa73_a42211ace110’, ‘XDG_RUNTIME_DIR’: ‘/run/user/1000’, ‘DISPLAY’: ‘:0’, ‘LANG’: ‘en_IN’, ‘CONDA_PREFIX_1’: ‘/home/jitesh/anaconda3’, ‘XDG_CURRENT_DESKTOP’: ‘ubuntu:GNOME’, ‘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:.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:’, ‘XDG_SESSION_DESKTOP’: ‘ubuntu’, ‘XMODIFIERS’: ‘@im=ibus’, ‘GNOME_TERMINAL_SERVICE’: ‘:1.891’, ‘XAUTHORITY’: ‘/run/user/1000/gdm/Xauthority’, ‘SSH_AUTH_SOCK’: ‘/run/user/1000/keyring/ssh’, ‘CONDA_PYTHON_EXE’: ‘/home/jitesh/anaconda3/bin/python’, ‘SHELL’: ‘/bin/bash’, ‘QT_ACCESSIBILITY’: ‘1’, ‘GDMSESSION’: ‘ubuntu’, ‘LESSCLOSE’: ‘/usr/bin/lesspipe %s %s’, ‘CONDA_DEFAULT_ENV’: ‘phylophlan’, ‘TEXTDOMAINDIR’: ‘/usr/share/locale/’, ‘GJS_DEBUG_OUTPUT’: ‘stderr’, ‘GPG_AGENT_INFO’: ‘/run/user/1000/gnupg/S.gpg-agent:0:1’, ‘XDG_VTNR’: ‘2’, ‘QT_IM_MODULE’: ‘ibus’, ‘PWD’: ‘/media/winshare/Jitesh_Kumar/tmp/PhyloPhlAn3.0’, ‘CLUTTER_IM_MODULE’: ‘xim’, ‘CONDA_EXE’: ‘/home/jitesh/anaconda3/bin/conda’, ‘XDG_DATA_DIRS’: ‘/usr/share/ubuntu:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop’, ‘XDG_CONFIG_DIRS’: ‘/etc/xdg/xdg-ubuntu:/etc/xdg’, ‘CONDA_PREFIX’: ‘/home/jitesh/anaconda3/envs/phylophlan’, ‘VTE_VERSION’: ‘5202’}

[e] Command ‘[’/home/jitesh/anaconda3/envs/phylophlan/bin/diamond’, ‘blastx’, ‘–quiet’, ‘–threads’, ‘1’, ‘–outfmt’, ‘6’, ‘–more-sensitive’, ‘–id’, ‘50’, ‘–max-hsps’, ‘35’, ‘-k’, ‘0’, ‘–query’, ‘output_tol/tmp/uncompressed/GCA_002882985.fna’, ‘–db’, ‘phylophlan_databases/phylophlan/phylophlan.dmnd’, ‘–out’, ‘output_tol/tmp/map_dna/GCA_002882985.b6o.bkp’]’ died with <Signals.SIGABRT: 6>.

[e] error while mapping
{‘program_name’: ‘/home/jitesh/anaconda3/envs/phylophlan/bin/diamond’, ‘params’: ‘blastx --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#’}
output_tol/tmp/uncompressed/GCA_002882985.fna
phylophlan_databases/phylophlan/phylophlan.dmnd
output_tol/tmp/map_dna
GCA_002882985.b6o.bkp
1
True

[e] Command ‘[’/home/jitesh/anaconda3/envs/phylophlan/bin/diamond’, ‘blastx’, ‘–quiet’, ‘–threads’, ‘1’, ‘–outfmt’, ‘6’, ‘–more-sensitive’, ‘–id’, ‘50’, ‘–max-hsps’, ‘35’, ‘-k’, ‘0’, ‘–query’, ‘output_tol/tmp/uncompressed/GCA_002882985.fna’, ‘–db’, ‘phylophlan_databases/phylophlan/phylophlan.dmnd’, ‘–out’, ‘output_tol/tmp/map_dna/GCA_002882985.b6o.bkp’]’ died with <Signals.SIGABRT: 6>.

[e] gene_markers_identification crashed

Hi,

Can you try running the diamond command in the error to see what the problem with diamond is? (I just removed the -quiet option)

/home/jitesh/anaconda3/envs/phylophlan/bin/diamond blastx –threads 1 –outfmt 6 –more-sensitive –id 50 –max-hsps 35 -k 0 –query output_tol/tmp/uncompressed/GCA_002882985.fna –db phylophlan_databases/phylophlan/phylophlan.dmnd –out output_tol/tmp/map_dna/GCA_002882985.b6o.bkp

Many thanks,
Francesco