Could not find "makeblastdb" executable in your PATH environment

imontero · February 14, 2022, 9:19am

I installed biobakery workflows in a python environment (Installing the workflows with pip · biobakery/biobakery_workflows Wiki · GitHub).

Kneaddata and metaphlan works, but strainfphlan fails. Humann too, but I wil work on it after I fix this.

The main problem is makeblastdb. I have reinstalled blast, phylophlan and metaphlan, but anything worked

2022-02-14 09:46:23,287 LoggerReporter log_event INFO: task 167, strainphlan_clade_0 : ready and waiting for resources
2022-02-14 09:46:23,287 LoggerReporter log_event INFO: task 167, strainphlan_clade_0 : starting to run
2022-02-14 09:46:23,296 anadama2.helpers actually_sh INFO: Executing with shell: extract_markers.py --database /home/microviable/workflows/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.pkl --clade s__Faecalibacterium_prausnitzii --output_dir /media/microviable/e/workflows_output/strainphlan
2022-02-14 09:47:11,311 anadama2.helpers actually_sh INFO: Execution complete. Stdout: b’Mon Feb 14 09:46:23 2022: Start extract markers execution\nMon Feb 14 09:46:23 2022: \tGenerating DB markers FASTA…\nMon Feb 14 09:46:59 2022: \tDone.\nMon Feb 14 09:46:59 2022: \tLoading MetaPhlan 3.0 database…\nMon Feb 14 09:47:04 2022: \tDone.\nMon Feb 14 09:47:04 2022: \tNumber of markers for the clade “s__Faecalibacterium_prausnitzii”: 41\nMon Feb 14 09:47:04 2022: \tExporting markers…\nMon Feb 14 09:47:11 2022: \tDone.\nMon Feb 14 09:47:11 2022: Finish extract markers execution (47.93 seconds): Results are stored at “/media/microviable/e/workflows_output/strainphlan/”\n’
Stderr:
2022-02-14 09:47:11,314 anadama2.helpers actually_sh INFO: Executing with shell: strainphlan --samples /media/microviable/e/workflows_output/strainphlan//.pkl --output_dir /media/microviable/e/workflows_output/strainphlan --clade s__Faecalibacterium_prausnitzii --nprocs 4 --clade_markers /media/microviable/e/workflows_output/strainphlan/s__Faecalibacterium_prausnitzii.fna > /media/microviable/e/workflows_output/strainphlan/19_clade.log && touch /media/microviable/e/workflows_output/strainphlan/19_clade.tree && if [ -f /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Faecalibacterium_prausnitzii.tree ]; then cp /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Faecalibacterium_prausnitzii.tree /media/microviable/e/workflows_output/strainphlan/19_clade.tree; fi
2022-02-14 09:47:12,058 LoggerReporter task_failed ERROR: task 167, strainphlan_clade_0 : Failed! Error message : Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/tasks/shotgun.py”, line 762, in strainphlan
args=[os.path.abspath(os.path.join(os.path.dirname(task.depends[0].name),"…")),os.path.dirname(task.targets[0].name),profile_clade,threads])
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/utilities.py”, line 1049, in run_task
return_code = sh(command)()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 1] Command `strainphlan --samples /media/microviable/e/workflows_output/strainphlan//.pkl --output_dir /media/microviable/e/workflows_output/strainphlan --clade s__Faecalibacterium_prausnitzii --nprocs 4 --clade_markers /media/microviable/e/workflows_output/strainphlan/s__Faecalibacterium_prausnitzii.fna > /media/microviable/e/workflows_output/strainphlan/19_clade.log && touch /media/microviable/e/workflows_output/strainphlan/19_clade.tree && if [ -f /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Faecalibacterium_prausnitzii.tree ]; then cp /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Faecalibacterium_prausnitzii.tree /media/microviable/e/workflows_output/strainphlan/19_clade.tree; fi’ failed.
Out: b’’
Err: b’[e] could not find “makeblastdb” (“False”) executable in your PATH environment variable\n\n[e] An error was ocurred executing a external tool, exiting…\nMon Feb 14 09:47:12 2022: Stop StrainPhlAn 3.0 execution.\n’

lauren.j.mciver · February 14, 2022, 9:47pm

Hello, The makeblastdb executable should be included in the blast install. You could try to run “makeblastdb” to see if there was an issue with the blast install. If that executable is not found, double check that the blast installed is a newer version named “blast+” that includes that executable.

Thanks!
Lauren

imontero · February 15, 2022, 9:50am

I checked if makeblastdb is installed by typing “makebla” and the type “tab”. The order was completed. I execute “makeblastdb --help” too. I think everything is installed. I checked that I have installed ncbi-blast+ 2.9.0-2. I found version 2.12.0, but it does not get installed by sudo apt get install ncbi-blast+

imontero · February 15, 2022, 3:19pm

I reinstaled ncbi-blast+ and now I received error about phyloseq_config folder. I created it and use phylophlan_write_default_configs.sh to create default config

Task 180 failed
Name: strainphlan_clade_13
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/tasks/shotgun.py”, line 762, in strainphlan
args=[os.path.abspath(os.path.join(os.path.dirname(task.depends[0].name),"…")),os.path.dirname(task.targets[0].name),profile_clade,threads])
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/utilities.py”, line 1049, in run_task
return_code = sh(command)()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 1] Command `strainphlan --samples /media/microviable/e/workflows_output/strainphlan//.pkl --output_dir /media/microviable/e/workflows_output/strainphlan --clade s__Bifidobacterium_pseudocatenulatum --nprocs 4 --clade_markers /media/microviable/e/workflows_output/strainphlan/s__Bifidobacterium_pseudocatenulatum.fna > /media/microviable/e/workflows_output/strainphlan/12_clade.log && touch /media/microviable/e/workflows_output/strainphlan/12_clade.tree && if [ -f /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Bifidobacterium_pseudocatenulatum.tree ]; then cp /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Bifidobacterium_pseudocatenulatum.tree /media/microviable/e/workflows_output/strainphlan/12_clade.tree; fi’ failed.
Out: b’’
Err: b’[e] “/home/microviable/workflows/lib/python3.7/site-packages/PhyloPhlAn-3.0.2-py3.7.egg/phylophlan/phylophlan_configs/” folder does not exists\n\n[e] Command ‘[’/home/microviable/miniconda3/bin/makeblastdb’, ‘-parse_seqids’, ‘-dbtype’, ‘nucl’, ‘-in’, ‘/media/microviable/e/workflows_output/strainphlan/tmpp30ygm_x/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum.fna’, ‘-out’, ‘/media/microviable/e/workflows_output/strainphlan/tmpp30ygm_x/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum’]’ returned non-zero exit status 1.\n\n[e] cannot execute command\n command_line: /home/microviable/miniconda3/bin/makeblastdb -parse_seqids -dbtype nucl -in /media/microviable/e/workflows_output/strainphlan/tmpp30ygm_x/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum.fna -out /media/microviable/e/workflows_output/strainphlan/tmpp30ygm_x/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum\n stdin: None\n stdout: None\n env: {‘GJS_DEBUG_TOPICS’: ‘JS ERROR;JS LOG’, ‘LESSOPEN’: ‘| /usr/bin/lesspipe %s’, ‘CONDA_PROMPT_MODIFIER’: '(base) ', ‘USER’: ‘microviable’, ‘SSH_AGENT_PID’: ‘828919’, ‘XDG_SESSION_TYPE’: ‘x11’, ‘SHLVL’: ‘1’, ‘HOME’: ‘/home/microviable’, ‘BX_DAEMON_SERVER’: ‘local:/home/microviable/.bx/rt/daemon.socket’, ‘CONDA_SHLVL’: ‘1’, ‘DESKTOP_SESSION’: ‘ubuntu’, ‘GNOME_SHELL_SESSION_MODE’: ‘ubuntu’, ‘GTK_MODULES’: ‘gail:atk-bridge’, ‘PS1’: '(workflows) (base) \\[\\e]0;\\u@\\h: \\w\\a\\]${debian_chroot:+($debian_chroot)}\\[\\033[01;32m\\]\\u@\\h\\[\\033[00m\\]:\\[\\033[01;34m\\]\\w\\[\\033[00m\\]\\$ ‘, ‘MANAGERPID’: ‘828574’, ‘DBUS_SESSION_BUS_ADDRESS’: ‘unix:path=/run/user/1000/bus’, ‘COLORTERM’: ‘truecolor’, ‘CE_M’: ‘’, ‘MANDATORY_PATH’: ‘/usr/share/gconf/ubuntu.mandatory.path’, ‘IM_CONFIG_PHASE’: ‘1’, ‘LOGNAME’: ‘microviable’, ‘JOURNAL_STREAM’: ‘8:7697253’, '’: ‘/home/microviable/workflows/bin/biobakery_workflows’, ‘XDG_SESSION_CLASS’: ‘user’, ‘DEFAULTS_PATH’: ‘/usr/share/gconf/ubuntu.default.path’, ‘USERNAME’: ‘microviable’, ‘BATCHX_ENDPOINT’: ‘api.batchx.io:8980’, ‘TERM’: ‘xterm-256color’, ‘GNOME_DESKTOP_SESSION_ID’: ‘this-is-deprecated’, ‘_CE_CONDA’: ‘’, ‘WINDOWPATH’: ‘2’, ‘PATH’: ‘/home/microviable/workflows/bin:/home/microviable/miniconda3/bin:/home/microviable/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin’, ‘SESSION_MANAGER’: ‘local/microviable:@/tmp/.ICE-unix/829008,unix/microviable:/tmp/.ICE-unix/829008’, ‘INVOCATION_ID’: ‘d2df2d7f59574fd9ab94bee18082276b’, ‘XDG_MENU_PREFIX’: ‘gnome-’, ‘GNOME_TERMINAL_SCREEN’: ‘/org/gnome/Terminal/screen/b66421c9_ed4c_4524_8a5d_8cdb37e49174’, ‘XDG_RUNTIME_DIR’: ‘/run/user/1000’, ‘DISPLAY’: ‘:1’, ‘LANG’: ‘es_ES.UTF-8’, ‘XDG_CURRENT_DESKTOP’: ‘ubuntu:GNOME’, ‘XMODIFIERS’: ‘@im=ibus’, ‘XDG_SESSION_DESKTOP’: ‘ubuntu’, ‘XAUTHORITY’: ‘/run/user/1000/gdm/Xauthority’, ‘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:’, ‘GNOME_TERMINAL_SERVICE’: ‘:1.518’, ‘SSH_AUTH_SOCK’: ‘/run/user/1000/keyring/ssh’, ‘CONDA_PYTHON_EXE’: ‘/home/microviable/miniconda3/bin/python’, ‘SHELL’: ‘/bin/bash’, ‘QT_ACCESSIBILITY’: ‘1’, ‘BATCHX_TOKEN’: ‘eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzUxMiJ9.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.pkQYQFBWVYdz8-iwbn05z-3yva0latQQQtakGrAuqrvoaODLzk1PbiVSR3KOx6XClQxJa8owpM5kdQwlyAFufA’, ‘GDMSESSION’: ‘ubuntu’, ‘LESSCLOSE’: ‘/usr/bin/lesspipe %s %s’, ‘CONDA_DEFAULT_ENV’: ‘base’, ‘GPG_AGENT_INFO’: ‘/run/user/1000/gnupg/S.gpg-agent:0:1’, ‘GJS_DEBUG_OUTPUT’: ‘stderr’, ‘VIRTUAL_ENV’: ‘/home/microviable/workflows’, ‘QT_IM_MODULE’: ‘ibus’, ‘PWD’: ‘/home/microviable’, ‘XDG_CONFIG_DIRS’: ‘/etc/xdg/xdg-ubuntu:/etc/xdg’, ‘CONDA_EXE’: ‘/home/microviable/miniconda3/bin/conda’, ‘XDG_DATA_DIRS’: ‘/usr/share/ubuntu:/home/microviable/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop’, ‘CONDA_PREFIX’: ‘/home/microviable/miniconda3’, ‘VTE_VERSION’: ‘6003’}\n\n[e] An error was ocurred executing a external tool, exiting…\nTue Feb 15 14:52:11 2022: Stop StrainPhlAn 3.0 execution.\n’

Traceback (most recent call last):
File “/home/microviable/workflows/bin/wmgx.py”, line 184, in
workflow.go()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/workflow.py”, line 801, in go
self._handle_finished()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/workflow.py”, line 833, in _handle_finished
raise RunFailed()
anadama2.workflow.RunFailed

imontero · February 15, 2022, 3:22pm

After Pyloseq_config resolution y tried again and received the error below. I tried downloading pyloseq databases and indexin with diamond but received the same error

Task 180 failed
Name: strainphlan_clade_13
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/tasks/shotgun.py”, line 762, in strainphlan
args=[os.path.abspath(os.path.join(os.path.dirname(task.depends[0].name),"…")),os.path.dirname(task.targets[0].name),profile_clade,threads])
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/utilities.py”, line 1049, in run_task
return_code = sh(command)()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 1] Command `strainphlan --samples /media/microviable/e/workflows_output/strainphlan//.pkl --output_dir /media/microviable/e/workflows_output/strainphlan --clade s__Bifidobacterium_pseudocatenulatum --nprocs 4 --clade_markers /media/microviable/e/workflows_output/strainphlan/s__Bifidobacterium_pseudocatenulatum.fna > /media/microviable/e/workflows_output/strainphlan/12_clade.log && touch /media/microviable/e/workflows_output/strainphlan/12_clade.tree && if [ -f /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Bifidobacterium_pseudocatenulatum.tree ]; then cp /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Bifidobacterium_pseudocatenulatum.tree /media/microviable/e/workflows_output/strainphlan/12_clade.tree; fi’ failed.
Out: b’’
Err: b"\n[e] Command ‘[’/home/microviable/miniconda3/bin/makeblastdb’, ‘-parse_seqids’, ‘-dbtype’, ‘nucl’, ‘-in’, ‘/media/microviable/e/workflows_output/strainphlan/tmpn6f6kksd/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum.fna’, ‘-out’, ‘/media/microviable/e/workflows_output/strainphlan/tmpn6f6kksd/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum’]’ returned non-zero exit status 1.\n\n[e] cannot execute command\n command_line: /home/microviable/miniconda3/bin/makeblastdb -parse_seqids -dbtype nucl -in /media/microviable/e/workflows_output/strainphlan/tmpn6f6kksd/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum.fna -out /media/microviable/e/workflows_output/strainphlan/tmpn6f6kksd/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum\n stdin: None\n stdout: None\n env: {‘GJS_DEBUG_TOPICS’: ‘JS ERROR;JS LOG’, ‘LESSOPEN’: ‘| /usr/bin/lesspipe %s’, ‘CONDA_PROMPT_MODIFIER’: '(base) ', ‘USER’: ‘microviable’, ‘SSH_AGENT_PID’: ‘828919’, ‘XDG_SESSION_TYPE’: ‘x11’, ‘SHLVL’: ‘1’, ‘HOME’: ‘/home/microviable’, ‘BX_DAEMON_SERVER’: ‘local:/home/microviable/.bx/rt/daemon.socket’, ‘CONDA_SHLVL’: ‘1’, ‘OLDPWD’: ‘/home/microviable/workflows/lib/python3.7/site-packages/PhyloPhlAn-3.0.2-py3.7.egg/phylophlan/phylophlan_configs’, ‘DESKTOP_SESSION’: ‘ubuntu’, ‘GNOME_SHELL_SESSION_MODE’: ‘ubuntu’, ‘GTK_MODULES’: ‘gail:atk-bridge’, ‘PS1’: '(workflows) (base) \\[\\e]0;\\u@\\h: \\w\\a\\]${debian_chroot:+($debian_chroot)}\\[\\033[01;32m\\]\\u@\\h\\[\\033[00m\\]:\\[\\033[01;34m\\]\\w\\[\\033[00m\\]\\$ ', ‘MANAGERPID’: ‘828574’, ‘DBUS_SESSION_BUS_ADDRESS’: ‘unix:path=/run/user/1000/bus’, ‘COLORTERM’: ‘truecolor’, ‘CE_M’: ‘’, ‘MANDATORY_PATH’: ‘/usr/share/gconf/ubuntu.mandatory.path’, ‘IM_CONFIG_PHASE’: ‘1’, ‘LOGNAME’: ‘microviable’, ‘JOURNAL_STREAM’: ‘8:7697253’, '’: ‘/home/microviable/workflows/bin/biobakery_workflows’, ‘XDG_SESSION_CLASS’: ‘user’, ‘DEFAULTS_PATH’: ‘/usr/share/gconf/ubuntu.default.path’, ‘USERNAME’: ‘microviable’, ‘BATCHX_ENDPOINT’: ‘api.batchx.io:8980’, ‘TERM’: ‘xterm-256color’, ‘GNOME_DESKTOP_SESSION_ID’: ‘this-is-deprecated’, ‘_CE_CONDA’: ‘’, ‘WINDOWPATH’: ‘2’, ‘PATH’: ‘/home/microviable/workflows/bin:/home/microviable/miniconda3/bin:/home/microviable/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin’, ‘SESSION_MANAGER’: ‘local/microviable:@/tmp/.ICE-unix/829008,unix/microviable:/tmp/.ICE-unix/829008’, ‘INVOCATION_ID’: ‘d2df2d7f59574fd9ab94bee18082276b’, ‘XDG_MENU_PREFIX’: ‘gnome-’, ‘GNOME_TERMINAL_SCREEN’: ‘/org/gnome/Terminal/screen/b66421c9_ed4c_4524_8a5d_8cdb37e49174’, ‘XDG_RUNTIME_DIR’: ‘/run/user/1000’, ‘DISPLAY’: ‘:1’, ‘LANG’: ‘es_ES.UTF-8’, ‘XDG_CURRENT_DESKTOP’: ‘ubuntu:GNOME’, ‘XMODIFIERS’: ‘@im=ibus’, ‘XDG_SESSION_DESKTOP’: ‘ubuntu’, ‘XAUTHORITY’: ‘/run/user/1000/gdm/Xauthority’, ‘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:’, ‘GNOME_TERMINAL_SERVICE’: ‘:1.518’, ‘SSH_AUTH_SOCK’: ‘/run/user/1000/keyring/ssh’, ‘CONDA_PYTHON_EXE’: ‘/home/microviable/miniconda3/bin/python’, ‘SHELL’: ‘/bin/bash’, ‘QT_ACCESSIBILITY’: ‘1’, ‘BATCHX_TOKEN’: ‘eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzUxMiJ9.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.pkQYQFBWVYdz8-iwbn05z-3yva0latQQQtakGrAuqrvoaODLzk1PbiVSR3KOx6XClQxJa8owpM5kdQwlyAFufA’, ‘GDMSESSION’: ‘ubuntu’, ‘LESSCLOSE’: ‘/usr/bin/lesspipe %s %s’, ‘CONDA_DEFAULT_ENV’: ‘base’, ‘GPG_AGENT_INFO’: ‘/run/user/1000/gnupg/S.gpg-agent:0:1’, ‘GJS_DEBUG_OUTPUT’: ‘stderr’, ‘VIRTUAL_ENV’: ‘/home/microviable/workflows’, ‘QT_IM_MODULE’: ‘ibus’, ‘PWD’: ‘/home/microviable’, ‘XDG_CONFIG_DIRS’: ‘/etc/xdg/xdg-ubuntu:/etc/xdg’, ‘CONDA_EXE’: ‘/home/microviable/miniconda3/bin/conda’, ‘XDG_DATA_DIRS’: ‘/usr/share/ubuntu:/home/microviable/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share/:/usr/share/:/var/lib/snapd/desktop’, ‘CONDA_PREFIX’: ‘/home/microviable/miniconda3’, ‘VTE_VERSION’: ‘6003’}\n\n[e] An error was ocurred executing a external tool, exiting…\nTue Feb 15 16:16:11 2022: Stop StrainPhlAn 3.0 execution.\n"

Traceback (most recent call last):
File “/home/microviable/workflows/bin/wmgx.py”, line 184, in
workflow.go()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/workflow.py”, line 801, in go
self._handle_finished()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/workflow.py”, line 833, in _handle_finished
raise RunFailed()
anadama2.workflow.RunFailed

imontero · September 12, 2022, 3:58pm

I received new error trying to run Strainphlan inside biobakery workflows.

2022-09-12 13:53:36,939 anadama2.helpers actually_sh INFO: Executing with shell: strainphlan --samples /media/microviable/e/ELDERLY/strainphlan//.pkl --output_dir /media/microviable/e/ELDERLY/strainphlan --clade s__Bifidobacterium_pseudocatenulatum --nprocs 7 --clade_markers /media/microviable/e/ELDERLY/strainphlan/s__Bifidobacterium_pseudocatenulatum.fna > /media/microviable/e/ELDERLY/strainphlan/5_clade.log && touch /media/microviable/e/ELDERLY/strainphlan/5_clade.tree && if [ -f /media/microviable/e/ELDERLY/strainphlan/RAxML_bestTree.s__Bifidobacterium_pseudocatenulatum.tree ]; then cp /media/microviable/e/ELDERLY/strainphlan/RAxML_bestTree.s__Bifidobacterium_pseudocatenulatum.tree /media/microviable/e/ELDERLY/strainphlan/5_clade.tree; fi
2022-09-12 13:53:38,976 LoggerReporter task_failed ERROR: task 163, strainphlan_clade_6 : Failed! Error message : Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/tasks/shotgun.py”, line 762, in strainphlan
args=[os.path.abspath(os.path.join(os.path.dirname(task.depends[0].name),“…”)),os.path.dirname(task.targets[0].name),profile_clade,threads])
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/utilities.py”, line 1049, in run_task
return_code = sh(command)()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 1] Command `strainphlan --samples /media/microviable/e/ELDERLY/strainphlan//.pkl --output_dir /media/microviable/e/ELDERLY/strainphlan --clade s__Bifidobacterium_pseudocatenulatum --nprocs 7 --clade_markers /media/microviable/e/ELDERLY/strainphlan/s__Bifidobacterium_pseudocatenulatum.fna > /media/microviable/e/ELDERLY/strainphlan/5_clade.log && touch /media/microviable/e/ELDERLY/strainphlan/5_clade.tree && if [ -f /media/microviable/e/ELDERLY/strainphlan/RAxML_bestTree.s__Bifidobacterium_pseudocatenulatum.tree ]; then cp /media/microviable/e/ELDERLY/strainphlan/RAxML_bestTree.s__Bifidobacterium_pseudocatenulatum.tree /media/microviable/e/ELDERLY/strainphlan/5_clade.tree; fi’ failed.
Out: b’’
Err: b’\n[e] Command '['/home/microviable/workflows/bin/makeblastdb', '-parse_seqids', '-dbtype', 'nucl', '-in', '/media/microviable/e/ELDERLY/strainphlan/tmp1a3n997l/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum.fna', '-out', '/media/microviable/e/ELDERLY/strainphlan/tmp1a3n997l/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum']' returned non-zero exit status 1.\n\n[e] cannot execute command\n command_line: /home/microviable/workflows/bin/makeblastdb -parse_seqids -dbtype nucl -in /media/microviable/e/ELDERLY/strainphlan/tmp1a3n997l/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum.fna -out /media/microviable/e/ELDERLY/strainphlan/tmp1a3n997l/s__Bifidobacterium_pseudocatenulatum/s__Bifidobacterium_pseudocatenulatum\n stdin: None\n stdout: None\n env: {'LESSOPEN': '| /usr/bin/lesspipe %s', 'LANGUAGE': 'es_ES', 'USER': 'microviable', 'XDG_SESSION_TYPE': 'x11', 'SHLVL': '1', 'PERL_LOCAL_LIB_ROOT': '/home/microviable/perl5', 'HOME': '/home/microviable', 'BX_DAEMON_SERVER': 'local:/home/microviable/.bx/rt/daemon.socket', 'CONDA_SHLVL': '0', 'OLDPWD': '/home/microviable/Descargas/phylophlan', 'DESKTOP_SESSION': 'ubuntu', 'GNOME_SHELL_SESSION_MODE': 'ubuntu', 'GTK_MODULES': 'gail:atk-bridge', 'XDG_SEAT_PATH': '/org/freedesktop/DisplayManager/Seat0', 'PS1': '(workflows) \\[\\e]0;\\u@\\h: \\w\\a\\]${debian_chroot:+($debian_chroot)}\\[\\033[01;32m\\]\\u@\\h\\[\\033[00m\\]:\\[\\033[01;34m\\]\\w\\[\\033[00m\\]\\$ ', 'DBUS_STARTER_BUS_TYPE': 'session', 'SYSTEMD_EXEC_PID': '12961', 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1000/bus,guid=f5c1e38c7ab5fb03b2958a4d6318739f', 'COLORTERM': 'truecolor', 'CE_M': '', 'MANDATORY_PATH': '/usr/share/gconf/ubuntu.mandatory.path', 'IM_CONFIG_PHASE': '1', 'INFOPATH': '/home/linuxbrew/.linuxbrew/share/info:', 'EGGNOG_DATA_DIR': '/media/microviable/e/biobakery_workflows_databases/eggnog_mapper:/home/microviable/miniconda3/envs/eggnog/lib/python3.7/site-packages/eggnogmapper:/home/microviable/.aspera/connect/bin:/home/microviable/Programas/megan/tools:/home/microviable/miniconda3/condabin:/home/linuxbrew/.linuxbrew/bin:/home/microviable/.local/bin:/home/microviable/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin', 'LOGNAME': 'microviable', '': '/home/microviable/workflows/bin/biobakery_workflows', 'XDG_SESSION_CLASS': 'user', 'DEFAULTS_PATH': '/usr/share/gconf/ubuntu.default.path', 'BATCHX_ENDPOINT': 'api.batchx.io:8980', 'TERM': 'xterm-256color', 'PERL_MB_OPT': '–install_base “/home/microviable/perl5”', 'GNOME_DESKTOP_SESSION_ID': 'this-is-deprecated', '_CE_CONDA': '', 'PATH': '/home/microviable/workflows/bin:/home/microviable/perl5/bin:/home/microviable/miniconda3/envs/eggnog/lib/python3.7/site-packages/eggnogmapper:/home/microviable/.aspera/connect/bin:/home/microviable/Programas/megan/tools:/home/microviable/miniconda3/condabin:/home/linuxbrew/.linuxbrew/bin:/home/microviable/.local/bin:/home/microviable/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/microviable/Programas/ncbi-blast/ncbi-blast-2.13.0+/bin', 'SESSION_MANAGER': 'local/microviable:@/tmp/.ICE-unix/12961,unix/microviable:/tmp/.ICE-unix/12961', 'GDM_LANG': 'es_ES', 'XDG_SESSION_PATH': '/org/freedesktop/DisplayManager/Session0', 'XDG_MENU_PREFIX': 'gnome-', 'GNOME_TERMINAL_SCREEN': '/org/gnome/Terminal/screen/22be90a7_7f0f_4816_b1b1_acb600741fc9', 'PERL5LIB': '/home/microviable/perl5/lib/perl5', 'XDG_RUNTIME_DIR': '/run/user/1000', 'DISPLAY': ':0', 'LANG': 'es_ES.UTF-8', 'XDG_CURRENT_DESKTOP': 'ubuntu:GNOME', 'XMODIFIERS': '@im=ibus', 'XDG_SESSION_DESKTOP': 'ubuntu', 'XAUTHORITY': '/home/microviable/.Xauthority', '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:.webp=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:', 'GNOME_TERMINAL_SERVICE': ':1.2340', 'SSH_AGENT_LAUNCHER': 'gnome-keyring', 'SSH_AUTH_SOCK': '/run/user/1000/keyring/ssh', 'XDG_GREETER_DATA_DIR': '/var/lib/lightdm-data/microviable', 'CONDA_PYTHON_EXE': '/home/microviable/miniconda3/bin/python', 'SHELL': '/bin/bash', 'INSIDE_NAUTILUS_PYTHON': '', 'QT_ACCESSIBILITY': '1', 'BATCHX_TOKEN': 'eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzUxMiJ9.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.99qlhmSVAUnlXKDBlRcXEqMZES4MponW_0zX2D0xJkxoJOr68bw32zpfEXmfix0DHcRPoKJB3hI0zVA8Ft8Y_w', 'GDMSESSION': 'ubuntu', 'LESSCLOSE': '/usr/bin/lesspipe %s %s', 'PERL_MM_OPT': 'INSTALL_BASE=/home/microviable/perl5', 'GPG_AGENT_INFO': '/run/user/1000/gnupg/S.gpg-agent:0:1', 'VIRTUAL_ENV': '/home/microviable/workflows', 'QT_IM_MODULE': 'ibus', 'JAVA_HOME': '/usr/lib/jvm/adoptopenjdk-8-hotspot-amd64', 'PWD': '/media/microviable/e/MVT-Prj-07_ELDERLY', 'XDG_CONFIG_DIRS': '/etc/xdg/xdg-ubuntu:/etc/xdg', 'CONDA_EXE': '/home/microviable/miniconda3/bin/conda', 'DBUS_STARTER_ADDRESS': 'unix:path=/run/user/1000/bus,guid=f5c1e38c7ab5fb03b2958a4d6318739f', 'XDG_DATA_DIRS': '/usr/share/ubuntu:/usr/share/gnome:/home/microviable/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share:/var/lib/snapd/desktop', 'PYTHONPATH': ':/home/microviable/miniconda3/bin/python', 'MANPATH': '/home/linuxbrew/.linuxbrew/share/man:', 'VTE_VERSION': '6800'}\n\n[e] An error was ocurred executing a external tool, exiting…\nMon Sep 12 13:53:38 2022: Stop StrainPhlAn 3.0 execution.\n’

2022-09-12 13:53:38,977 LoggerReporter finished ERROR: AnADAMA run finished with errors.