# Could not find "makeblastdb" executable in your PATH environment

**URL:** <https://forum.biobakery.org/t/could-not-find-makeblastdb-executable-in-your-path-environment/3130>\
**Category:** bioBakery workflows\
**Created:** [February 14, 2022, 9:19am UTC](https://forum.biobakery.org/t/could-not-find-makeblastdb-executable-in-your-path-environment/3130 "2022-02-14T09:19:15Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![imontero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/imontero/32/3411_2.png) [@imontero](https://forum.biobakery.org/u/imontero)\
**Post date:** [February 14, 2022, 9:19am UTC](https://forum.biobakery.org/t/could-not-find-makeblastdb-executable-in-your-path-environment/3130/1 "2022-02-14T09:19:15Z")

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I installed biobakery workflows in a python environment ([Installing the workflows with pip · biobakery/biobakery\_workflows Wiki · GitHub](https://github.com/biobakery/biobakery_workflows/wiki/Installing-the-workflows-with-pip)).

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’

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**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [February 14, 2022, 9:47pm UTC](https://forum.biobakery.org/t/could-not-find-makeblastdb-executable-in-your-path-environment/3130/2 "2022-02-14T21:47:51Z")

</div>

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

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<div class="post-metadata">

**Author:** ![imontero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/imontero/32/3411_2.png) [@imontero](https://forum.biobakery.org/u/imontero)\
**Post date:** [February 15, 2022, 9:50am UTC](https://forum.biobakery.org/t/could-not-find-makeblastdb-executable-in-your-path-environment/3130/3 "2022-02-15T09:50:46Z")

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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+

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<div class="post-metadata">

**Author:** ![imontero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/imontero/32/3411_2.png) [@imontero](https://forum.biobakery.org/u/imontero)\
**Post date:** [February 15, 2022, 3:19pm UTC](https://forum.biobakery.org/t/could-not-find-makeblastdb-executable-in-your-path-environment/3130/4 "2022-02-15T15:19:09Z")

</div>

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](http://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

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<div class="post-metadata">

**Author:** ![imontero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/imontero/32/3411_2.png) [@imontero](https://forum.biobakery.org/u/imontero)\
**Post date:** [February 15, 2022, 3:22pm UTC](https://forum.biobakery.org/t/could-not-find-makeblastdb-executable-in-your-path-environment/3130/5 "2022-02-15T15:22:16Z")

</div>

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](http://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

---

<div class="post-metadata">

**Author:** ![imontero](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/imontero/32/3411_2.png) [@imontero](https://forum.biobakery.org/u/imontero)\
**Post date:** [September 12, 2022, 3:58pm UTC](https://forum.biobakery.org/t/could-not-find-makeblastdb-executable-in-your-path-environment/3130/6 "2022-09-12T15:58:31Z")

</div>

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.