# Cannot get biobakery\_workflows vis to run

**URL:** <https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338>\
**Category:** bioBakery workflows\
**Created:** [November 3, 2022, 4:31pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338 "2022-11-03T16:31:28Z")\
**Posts on this page:** 15\
**Page:** 1

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 3, 2022, 4:31pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/1 "2022-11-03T16:31:28Z")

</div>

Hi everybody,

I cannot get to run biobakery visualisation workflow. I tried the following command in the latest Docker image  
`biobakery_workflows wmgx_vis --input /opt/biobakery_result_files/ --output /opt/vizualisation/ --project-name TEST`

Stdout :

> (Nov 03 16:15:48) [0/2 - 0.00%] \*\*Ready \*\* Task 0: document  
> (Nov 03 16:15:48) [0/2 - 0.00%] \*\*Started \*\* Task 0: document  
> Exception:  
> list index out of range  
> Error messages will be included in output document  
> Traceback (most recent call last):  
> File “/usr/local/bin/wmgx\_vis.py”, line 133, in   
> workflow.go()  
> File “/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py”, line 804, in go  
> self.\_handle\_finished()  
> File “/usr/local/lib/python3.6/dist-packages/anadama2/workflow.py”, line 836, in \_handle\_finished  
> raise RunFailed()  
> anadama2.workflow.RunFailed

And the content of anadama.log:

> 2022-11-03 16:15:51,496 LoggerReporter task\_failed ERROR: task 0, document : Failed! Error message : Error executing action 0. Original Exception:  
> Traceback (most recent call last):  
> File “/usr/local/lib/python3.6/dist-packages/anadama2/runners.py”, line 200, in \_run\_task\_locally  
> action\_func(task)  
> File “/usr/local/lib/python3.6/dist-packages/anadama2/document.py”, line 315, in create  
> doc.weave(shell=PwebProcessorSpaces)  
> File “/usr/local/lib/python3.6/dist-packages/pweave/pweb.py”, line 198, in weave  
> self.run(shell)  
> File “/usr/local/lib/python3.6/dist-packages/pweave/pweb.py”, line 149, in run  
> runner.run()  
> File “/usr/local/lib/python3.6/dist-packages/pweave/processors.py”, line 65, in run  
> self.executed = list(map(self.\_runcode, self.parsed))  
> File “/usr/local/lib/python3.6/dist-packages/pweave/processors.py”, line 131, in \_runcode  
> chunk[‘content’] = self.loadinline(chunk[‘content’])  
> File “/usr/local/lib/python3.6/dist-packages/anadama2/document.py”, line 259, in loadinline  
> result = self.loadstring(code\_str).strip()  
> File “/usr/local/lib/python3.6/dist-packages/pweave/processors.py”, line 296, in loadstring  
> exec(compiled, scope)  
> File “chunk”, line 1, in   
> **NameError: name ‘caption’ is not defined**

I then tried a different approach.  
Following the advice in [this post from Biobakery’s forum](https://forum.biobakery.org/t/biobakery-workflows-errors-with-downloading-database-unpicking-error-topological-sort-error-and-unable-to-find-trimmomatic-error/1823/7), I tried to set up biobakery through conda:  
`conda create -c biobakery -n biobakery_3.6 python=3.6 biobakery_workflows tbb=2020.2 networkx=1.11 pweave=0.25 python-leveldb`

Trying to run the vizualisation workflow failed:  
`biobakery_workflows vis --input run_test/output/ --output run_test/vis --log-level DEBUG --project-name TEST`

> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery/bin/vis.py”, line 123, in   
> args.introduction\_text = “ ![](){#id .class width=675px height=505px}\n\n”+intro\_methods  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/biobakery\_workflows/utilities.py”, line 1170, in get\_package\_file  
> found\_files=list(filter(lambda file: os.path.isfile(os.path.join(package\_install\_folder,file)),os.listdir(package\_install\_folder)))  
> FileNotFoundError: [Errno 2] No such file or directory: ‘/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/biobakery\_workflows/…/images’`

I thave been able to circumvent this problem by doing  
`ln -s /home/theoscilicium/miniconda3/envs/biobakery/images/ /home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/images`

I then ran again the vis workflow, here is the content of anadama.log:  
2022-11-03 16:35:13,339 LoggerReporter started INFO: Beginning AnADAMA run with 6 tasks.

> 2022-11-03 16:35:13,340 LoggerReporter started INFO: Workflow description = A workflow for visualization  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: Workflow version = 3.1  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: Workflow configuration options  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: input = run\_test/output/  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: project\_name = TEST  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: author\_name =  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: header\_image =  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: input\_metadata =  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: input\_file\_type =   
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: input\_picard = None  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: input\_picard\_extension = quality\_by\_cycle\_metrics  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: metadata\_categorical =   
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: metadata\_continuous =   
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: metadata\_exclude =   
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: min\_abundance = 0.01  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: min\_samples = 3  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: max\_sets\_heatmap = 25  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: max\_missing = 20.0  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: max\_sets\_barplot = 15  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: max\_groups\_barplot = 5  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: correlation\_threshold = 0.7  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: format = html  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: introduction\_text =  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: print\_template = False  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: use\_template =  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: output = run\_test/vis  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: config = None  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: jobs = 1  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid\_jobs = 0  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid = None  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid\_partition =  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid\_benchmark = off  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid\_options = None  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid\_submit\_sleep = 5  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid\_environment = None  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid\_scratch =  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid\_time\_max = None  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: grid\_mem\_max = None  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: dry\_run = False  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: skip\_nothing = False  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: quit\_early = False  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: until\_task = None  
> 2022-11-03 16:35:13,340 LoggerReporter started INFO: exclude\_task = None  
> 2022-11-03 16:35:13,341 LoggerReporter started INFO: target = None  
> 2022-11-03 16:35:13,341 LoggerReporter started INFO: exclude\_target = None  
> 2022-11-03 16:35:13,341 LoggerReporter started INFO: log\_level = DEBUG  
> 2022-11-03 16:35:13,359 anadama2.workflow go DEBUG: Sorting task\_nos by network topology  
> 2022-11-03 16:35:13,359 anadama2.workflow go DEBUG: Sorting complete  
> 2022-11-03 16:35:13,359 anadama2.tracked any\_different DEBUG: Dep ‘/home/theoscilicium/bb\_docker\_test/run\_test/vis’ of type \<class ‘anadama2.tracked.HugeTrackedFile’\> changed: wasn’t previously saved in backend  
> 2022-11-03 16:35:13,359 anadama2.workflow \_filter\_skipped\_tasks DEBUG: Can’t skip task 4 because of dep change  
> 2022-11-03 16:35:13,359 anadama2.workflow \_filter\_skipped\_tasks DEBUG: Can’t skip task 5 because of dep change  
> 2022-11-03 16:35:13,359 anadama2.tracked any\_different DEBUG: Dep ‘/home/theoscilicium/bb\_docker\_test/run\_test/vis.zip’ of type \<class ‘anadama2.tracked.HugeTrackedFile’\> changed: wasn’t previously saved in backend  
> 2022-11-03 16:35:13,359 anadama2.workflow \_filter\_skipped\_tasks DEBUG: Can’t skip task 4 because of dep change  
> 2022-11-03 16:35:13,359 anadama2.tracked any\_different DEBUG: Dep ‘/home/theoscilicium/bb\_docker\_test/run\_test/output/metaphlan/merged/metaphlan\_taxonomic\_profiles.tsv’ of type \<class ‘anadama2.tracked.HugeTrackedFile’\> changed: wasn’t previously saved in backend  
> 2022-11-03 16:35:13,359 anadama2.workflow \_filter\_skipped\_tasks DEBUG: Can’t skip task 2 because of dep change  
> 2022-11-03 16:35:13,359 anadama2.workflow \_filter\_skipped\_tasks DEBUG: Can’t skip task 3 because of dep change  
> 2022-11-03 16:35:13,360 anadama2.tracked any\_different DEBUG: Dep ‘/home/theoscilicium/bb\_docker\_test/run\_test/vis/wmgx\_report.html’ of type \<class ‘anadama2.tracked.HugeTrackedFile’\> changed: wasn’t previously saved in backend  
> 2022-11-03 16:35:13,360 anadama2.workflow \_filter\_skipped\_tasks DEBUG: Can’t skip task 2 because of dep change  
> 2022-11-03 16:35:13,360 anadama2.tracked any\_different DEBUG: Dep ‘/home/theoscilicium/bb\_docker\_test/run\_test/output/humann/merged/ecs\_relab.tsv’ of type \<class ‘anadama2.tracked.HugeTrackedFile’\> changed: wasn’t previously saved in backend  
> 2022-11-03 16:35:13,360 anadama2.workflow \_filter\_skipped\_tasks DEBUG: Can’t skip task 0 because of dep change  
> 2022-11-03 16:35:13,360 anadama2.workflow \_filter\_skipped\_tasks DEBUG: Can’t skip task 1 because of dep change  
> 2022-11-03 16:35:13,360 anadama2.tracked any\_different DEBUG: Dep ‘/home/theoscilicium/bb\_docker\_test/run\_test/vis/ecs/ecs\_relab.tsv’ of type \<class ‘anadama2.tracked.HugeTrackedFile’\> changed: wasn’t previously saved in backend  
> 2022-11-03 16:35:13,360 anadama2.workflow \_filter\_skipped\_tasks DEBUG: Can’t skip task 0 because of dep change  
> 2022-11-03 16:35:13,360 anadama2.runners run\_tasks DEBUG: Running 6 tasks locally and serially  
> 2022-11-03 16:35:13,360 LoggerReporter log\_event DEBUG: task 5, Track pre-existing dependencies : ready and waiting for resources : 0 parents: . 1 children: [4].  
> 2022-11-03 16:35:13,360 LoggerReporter log\_event DEBUG: task 5, Track pre-existing dependencies : starting to run : 0 parents: . 1 children: [4].  
> 2022-11-03 16:35:13,360 anadama2.runners \_run\_task\_locally DEBUG: Executing task 5 action 0  
> 2022-11-03 16:35:13,360 anadama2.runners \_run\_task\_locally DEBUG: Completed executing task 5 action 0  
> 2022-11-03 16:35:13,360 LoggerReporter log\_event DEBUG: task 5, Track pre-existing dependencies : completed successfully  
> 2022-11-03 16:35:13,360 LoggerReporter log\_event DEBUG: task 3, Track pre-existing dependencies : ready and waiting for resources : 0 parents: . 1 children: [2].  
> 2022-11-03 16:35:13,360 LoggerReporter log\_event DEBUG: task 3, Track pre-existing dependencies : starting to run : 0 parents: . 1 children: [2].  
> 2022-11-03 16:35:13,360 anadama2.runners \_run\_task\_locally DEBUG: Executing task 3 action 0  
> 2022-11-03 16:35:13,360 anadama2.runners \_run\_task\_locally DEBUG: Completed executing task 3 action 0  
> 2022-11-03 16:35:13,360 LoggerReporter log\_event DEBUG: task 3, Track pre-existing dependencies : completed successfully  
> 2022-11-03 16:35:13,360 LoggerReporter log\_event DEBUG: task 1, Track pre-existing dependencies : ready and waiting for resources : 0 parents: . 1 children: [0].  
> 2022-11-03 16:35:13,361 LoggerReporter log\_event DEBUG: task 1, Track pre-existing dependencies : starting to run : 0 parents: . 1 children: [0].  
> 2022-11-03 16:35:13,361 anadama2.runners \_run\_task\_locally DEBUG: Executing task 1 action 0  
> 2022-11-03 16:35:13,361 anadama2.runners \_run\_task\_locally DEBUG: Completed executing task 1 action 0  
> 2022-11-03 16:35:13,361 LoggerReporter log\_event DEBUG: task 1, Track pre-existing dependencies : completed successfully  
> 2022-11-03 16:35:13,361 LoggerReporter log\_event INFO: task 0, humann\_rename\_table\_ecs : ready and waiting for resources : 1 parents: [1]. 1 children: [2].  
> 2022-11-03 16:35:13,361 LoggerReporter log\_event INFO: task 0, humann\_rename\_table\_ecs : starting to run : 1 parents: [1]. 1 children: [2].  
> 2022-11-03 16:35:13,361 LoggerReporter task\_command INFO: Executing with shell: mkdir -p run\_test/vis/ecs && humann\_rename\_table --input /home/theoscilicium/bb\_docker\_test/run\_test/output/humann/merged/ecs\_relab.tsv --output /home/theoscilicium/bb\_docker\_test/run\_test/vis/ecs/ecs\_relab.tsv --names ec  
> 2022-11-03 16:35:13,361 anadama2.runners \_run\_task\_locally DEBUG: Executing task 0 action 0  
> 2022-11-03 16:35:13,433 anadama2.helpers actually\_sh INFO: Execution complete. Stdout:  
> Stderr: b"Loading table from: /home/theoscilicium/bb\_docker\_test/run\_test/output/humann/merged/ecs\_relab.tsv\n Treating /home/theoscilicium/bb\_docker\_test/run\_test/output/humann/merged/ecs\_relab.tsv as stratified output, e.g. [‘1.1.1.1’, ‘g\_\_Acidaminococcus.s\_\_Acidaminococcus\_intestini’]\nLoading mapping file from: /home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/humann/tools/…/data/misc/map\_level4ec\_name.txt.gz\nRenamed 224 of 232 entries (96.55%)\n"  
> 2022-11-03 16:35:13,433 anadama2.runners \_run\_task\_locally DEBUG: Completed executing task 0 action 0  
> 2022-11-03 16:35:13,433 LoggerReporter log\_event INFO: task 0, humann\_rename\_table\_ecs : completed successfully  
> 2022-11-03 16:35:13,434 LoggerReporter log\_event INFO: task 2, document : ready and waiting for resources : 2 parents: [3, 0]. 1 children: [4].  
> 2022-11-03 16:35:13,434 LoggerReporter log\_event INFO: task 2, document : starting to run : 2 parents: [3, 0]. 1 children: [4].  
> 2022-11-03 16:35:13,434 anadama2.runners \_run\_task\_locally DEBUG: Executing task 2 action 0  
> 2022-11-03 16:35:13,441 anadama2.helpers actually\_sh INFO: Executing with shell: pweave /home/theoscilicium/bb\_docker\_test/run\_test/vis/tmpy\_tmnit1/wmgx\_report.pmd -o /home/theoscilicium/bb\_docker\_test/run\_test/vis/tmpy\_tmnit1/wmgx\_report.md  
> 2022-11-03 16:35:15,080 LoggerReporter task\_failed ERROR: task 2, document : Failed! Error message : Error executing action 0. Original Exception:  
> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/anadama2/runners.py”, line 200, in \_run\_task\_locally  
> action\_func(task)  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/anadama2/document.py”, line 319, in create  
> sh(“pweave {0} -o {1}”.format(temp\_template,intermediate\_template),log\_command=True)()  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/anadama2/helpers.py”, line 107, in actually\_sh  
> ret = \_sh(s, \*\*kwargs)  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/anadama2/util/ **init**.py”, line 320, in sh  
> raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode(‘utf-8’), ret[1].decode(‘utf-8’)))  
> anadama2.util.ShellException: [Errno 1] Command ‘pweave /home/theoscilicium/bb\_docker\_test/run\_test/vis/tmpy\_tmnit1/wmgx\_report.pmd -o /home/theoscilicium/bb\_docker\_test/run\_test/vis/tmpy\_tmnit1/wmgx\_report.md’ failed.  
> Out: Error in trying to detect pandoc version  
> Your pandoc version is below 1.16, not setting figure size and id  
> Processing chunk 1 named None from line 12  
> Processing chunk 2 named read qc counts from line 27  
> Processing chunk 3 named write qc table paired from line 42  
> Processing chunk 4 named write qc table orphan from line 53  
> Processing chunk 5 named compute read ratios and show table from line 67  
> Processing chunk 6 named plot filtered read counts from line 88  
> Processing chunk 7 named read metaphlan profile and filter from line 119  
> Processing chunk 8 named compile species and genera and show table of counts from line 137  
> Processing chunk 9 named find alpha diversity plots from line 146  
> Processing chunk 10 named show alpha diversity boxplots from line 156  
> Processing chunk 11 named show alpha diversity scatterplots from line 162  
> Processing chunk 12 named show pcoa species from line 174
> 
> Err: Exception:  
> [Errno 2] No such file or directory: ‘R’: ‘R’  
> Error messages will be included in output document  
> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery/bin/pweave”, line 6, in   
> sys.exit(pweave.scripts.weave())  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/pweave/scripts.py”, line 55, in weave  
> pweave.weave(infile, \*\*opts\_dict)  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/pweave/ **init**.py”, line 73, in weave  
> doc.weave(shell)  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/pweave/pweb.py”, line 198, in weave  
> self.run(shell)  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/pweave/pweb.py”, line 149, in run  
> runner.run()  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/pweave/processors.py”, line 65, in run  
> self.executed = list(map(self.\_runcode, self.parsed))  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/pweave/processors.py”, line 131, in \_runcode  
> chunk[‘content’] = self.loadinline(chunk[‘content’])  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/pweave/processors.py”, line 331, in loadinline  
> result = self.loadstring(self.add\_echo(code\_str)).strip()  
> File “/home/theoscilicium/miniconda3/envs/biobakery/lib/python3.6/site-packages/pweave/processors.py”, line 296, in loadstring  
> exec(compiled, scope)  
> File “chunk”, line 1, in   
> **NameError: name ‘caption’ is not defined**
> 
> 2022-11-03 16:35:15,080 LoggerReporter task\_failed ERROR: task 4, archive : Failed! Error message : Task failed because parent task ‘2’ failed  
> 2022-11-03 16:35:15,080 LoggerReporter finished ERROR: AnADAMA run finished with errors.

This problem of **NameError: name ‘caption’ is not defined** has been reported [here in Aug. 2022](https://forum.biobakery.org/t/which-version-of-pweave-needed/1000/11) before, but I could not find any satisfactory workaround…  
Any help, pointers or anything would all be very appreciated :).

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 4, 2022, 9:34am UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/2 "2022-11-04T09:34:38Z")

</div>

New try with conda install and Python 3.7:  
`conda create -c biobakery -n biobakery_3.7 python=3.7 biobakery_workflows`

First try:  
`biobakery_workflows vis --input run_test/wmgx_output/ --output run_test/vis/`

> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/bin/vis.py”, line 123, in   
> args.introduction\_text = “ ![](){#id .class width=675px height=505px}\n\n”+intro\_methods  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/site-packages/biobakery\_workflows/utilities.py”, line 1170, in get\_package\_file  
> found\_files=list(filter(lambda file: os.path.isfile(os.path.join(package\_install\_folder,file)),os.listdir(package\_install\_folder)))  
> FileNotFoundError: [Errno 2] No such file or directory: ‘/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/site-packages/biobakery\_workflows/…/images’

As before, I did:  
`ln -s /home/theoscilicium/miniconda3/envs/biobakery_3.7/images /home/theoscilicium/miniconda3/envs/biobakery_3.7/lib/python3.7/site-packages/images`  
Suggestion: **fix conda install to avoid this path problem**

Second try:  
`biobakery_workflows vis --input run_test/wmgx_output/ --output run_test/vis/`

> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/site-packages/anadama2/workflow.py”, line 481, in add\_archive  
> output=subprocess.check\_output([archive\_software,“–help”])  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/subprocess.py”, line 411, in check\_output  
> \*\*kwargs).stdout  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/subprocess.py”, line 488, in run  
> with Popen(\*popenargs, \*\*kwargs) as process:  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/subprocess.py”, line 800, in **init**  
> restore\_signals, start\_new\_session)  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/subprocess.py”, line 1551, in \_execute\_child  
> raise child\_exception\_type(errno\_num, err\_msg, err\_filename)  
> FileNotFoundError: [Errno 2] No such file or directory: ‘zip’: ‘zip’
> 
> During handling of the above exception, another exception occurred:
> 
> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/bin/vis.py”, line 214, in   
> remove\_log=True)  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/site-packages/anadama2/workflow.py”, line 483, in add\_archive  
> raise EnvironmentError("Unable to archive document with software requested. Please install " +archive\_software)  
> OSError: Unable to archive document with software requested. Please install zip

Problem solved by doing `conda install zip`. **Suggestion: add zip as dependency**

Third try:  
`biobakery_workflows vis --input run_test/wmgx_output/ --output run_test/vis/`

> (Nov 04 10:15:21) [1/3 - 33.33%] \*\*Skipped \*\* Task 0: humann\_rename\_table\_ecs  
> (Nov 04 10:15:21) [1/3 - 33.33%] \*\*Ready \*\* Task 2: document  
> (Nov 04 10:15:21) [1/3 - 33.33%] \*\*Started \*\* Task 2: document  
> (Nov 04 10:15:21) [2/3 - 66.67%] \*\*Failed \*\* Task 2: document  
> (Nov 04 10:15:21) [3/3 - 100.00%] \*\*Failed \*\* Task 4: archive  
> Run Finished  
> Task 2 failed  
> Name: document  
> Original error:  
> Error executing action 0. Original Exception:  
> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/site-packages/anadama2/runners.py”, line 200, in \_run\_task\_locally  
> action\_func(task)  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/site-packages/anadama2/document.py”, line 232, in create  
> from pweave import PwebPandocFormatter, Pweb, PwebProcessor  
> ImportError: cannot import name ‘PwebProcessor’ from ‘pweave’ (/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/site-packages/pweave/ **init**.py)
> 
> Task 4 failed  
> Name: archive  
> Original error:  
> Task failed because parent task `2’ failed  
> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/bin/vis.py”, line 217, in   
> workflow.go()  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/site-packages/anadama2/workflow.py”, line 804, in go  
> self.\_handle\_finished()  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.7/lib/python3.7/site-packages/anadama2/workflow.py”, line 836, in \_handle\_finished  
> raise RunFailed()  
> anadama2.workflow.RunFailed

So, as of 04/11/2022, the problem described [in Sept. 2020](https://forum.biobakery.org/t/which-version-of-pweave-needed/1000) is still not resolved.

EDIT for more info:  
return of `conda list`

> # packages in environment at /home/theoscilicium/miniconda3/envs/biobakery\_3.7:
> 
> # 
> 
> # Name Version Build Channel
> 
> \_libgcc\_mutex 0.1 conda\_forge conda-forge  
> \_openmp\_mutex 4.5 2\_gnu conda-forge  
> alsa-lib 1.2.7.2 h166bdaf\_0 conda-forge  
> anadama2 0.10.0 pyhb8aa349\_0 biobakery  
> attrs 22.1.0 pyh71513ae\_1 conda-forge  
> backcall 0.2.0 pyh9f0ad1d\_0 conda-forge  
> backports 1.0 py\_2 conda-forge  
> backports.functools\_lru\_cache 1.6.4 pyhd8ed1ab\_0 conda-forge  
> beautifulsoup4 4.11.1 pyha770c72\_0 conda-forge  
> biobakery\_workflows 3.1 pyh0d95946\_0 biobakery  
> biom-format 2.1.12 py37hda87dfa\_1 conda-forge  
> biopython 1.79 py37h540881e\_2 conda-forge  
> blast 2.13.0 hf3cf87c\_0 bioconda  
> bleach 5.0.1 pyhd8ed1ab\_0 conda-forge  
> boost-cpp 1.74.0 h75c5d50\_8 conda-forge  
> bowtie2 2.5.0 py37hb24965f\_0 bioconda  
> brotli 1.0.9 h166bdaf\_8 conda-forge  
> brotli-bin 1.0.9 h166bdaf\_8 conda-forge  
> brotlipy 0.7.0 py37h540881e\_1004 conda-forge  
> bzip2 1.0.8 h7f98852\_4 conda-forge  
> c-ares 1.18.1 h7f98852\_0 conda-forge  
> ca-certificates 2022.9.24 ha878542\_0 conda-forge  
> cached-property 1.5.2 hd8ed1ab\_1 conda-forge  
> cached\_property 1.5.2 pyha770c72\_1 conda-forge  
> cairo 1.16.0 ha61ee94\_1014 conda-forge  
> certifi 2022.9.24 pyhd8ed1ab\_0 conda-forge  
> cffi 1.15.1 py37h43b0acd\_1 conda-forge  
> charset-normalizer 2.1.1 pyhd8ed1ab\_0 conda-forge  
> click 8.1.3 py37h89c1867\_0 conda-forge  
> cloudpickle 2.2.0 pyhd8ed1ab\_0 conda-forge  
> cryptography 38.0.2 py37h5994e8b\_1 conda-forge  
> curl 7.86.0 h2283fc2\_1 conda-forge  
> cycler 0.11.0 pyhd8ed1ab\_0 conda-forge  
> debugpy 1.6.3 py37hd23a5d3\_0 conda-forge  
> decorator 5.1.1 pyhd8ed1ab\_0 conda-forge  
> defusedxml 0.7.1 pyhd8ed1ab\_0 conda-forge  
> dendropy 4.5.2 pyh3252c3a\_0 bioconda  
> diamond 2.0.15 hb97b32f\_1 bioconda  
> entrez-direct 16.2 he881be0\_1 bioconda  
> entrypoints 0.4 pyhd8ed1ab\_0 conda-forge  
> expat 2.5.0 h27087fc\_0 conda-forge  
> fastqc 0.11.9 hdfd78af\_1 bioconda  
> font-ttf-dejavu-sans-mono 2.37 hab24e00\_0 conda-forge  
> font-ttf-inconsolata 3.000 h77eed37\_0 conda-forge  
> font-ttf-source-code-pro 2.038 h77eed37\_0 conda-forge  
> font-ttf-ubuntu 0.83 hab24e00\_0 conda-forge  
> fontconfig 2.14.1 hc2a2eb6\_0 conda-forge  
> fonts-conda-ecosystem 1 0 conda-forge  
> fonts-conda-forge 1 0 conda-forge  
> fonttools 4.38.0 py37h540881e\_0 conda-forge  
> freetype 2.12.1 hca18f0e\_0 conda-forge  
> future 0.18.2 py37h89c1867\_5 conda-forge  
> gettext 0.21.1 h27087fc\_0 conda-forge  
> giflib 5.2.1 h36c2ea0\_2 conda-forge  
> glpk 4.57 0 bioconda  
> graphite2 1.3.13 h58526e2\_1001 conda-forge  
> h5py 3.7.0 nompi\_py37hf1ce037\_101 conda-forge  
> harfbuzz 5.3.0 h418a68e\_0 conda-forge  
> hdf5 1.12.2 nompi\_h4df4325\_100 conda-forge  
> humann 3.6 pyhdf09c49\_0 biobakery  
> icu 70.1 h27087fc\_0 conda-forge  
> idna 3.4 pyhd8ed1ab\_0 conda-forge  
> importlib-metadata 4.11.4 py37h89c1867\_0 conda-forge  
> importlib\_resources 5.10.0 pyhd8ed1ab\_0 conda-forge  
> ipykernel 6.16.2 pyh210e3f2\_0 conda-forge  
> ipython 7.33.0 py37h89c1867\_0 conda-forge  
> jedi 0.18.1 py37h89c1867\_1 conda-forge  
> jinja2 3.1.2 pyhd8ed1ab\_1 conda-forge  
> jpeg 9e h166bdaf\_2 conda-forge  
> jsonschema 4.17.0 pyhd8ed1ab\_0 conda-forge  
> jupyter\_client 7.4.4 pyhd8ed1ab\_0 conda-forge  
> jupyter\_core 4.11.1 py37h89c1867\_0 conda-forge  
> jupyterlab\_pygments 0.2.2 pyhd8ed1ab\_0 conda-forge  
> keyutils 1.6.1 h166bdaf\_0 conda-forge  
> kiwisolver 1.4.4 py37h7cecad7\_0 conda-forge  
> kneaddata 0.12.0 pyhdfd78af\_0 bioconda  
> krb5 1.19.3 h08a2579\_0 conda-forge  
> lcms2 2.12 hddcbb42\_0 conda-forge  
> ld\_impl\_linux-64 2.39 hc81fddc\_0 conda-forge  
> leveldb 0.193 py37h2f20fdb\_0 biobakery  
> libblas 3.9.0 16\_linux64\_openblas conda-forge  
> libbrotlicommon 1.0.9 h166bdaf\_8 conda-forge  
> libbrotlidec 1.0.9 h166bdaf\_8 conda-forge  
> libbrotlienc 1.0.9 h166bdaf\_8 conda-forge  
> libcblas 3.9.0 16\_linux64\_openblas conda-forge  
> libcups 2.3.3 h3e49a29\_2 conda-forge  
> libcurl 7.86.0 h2283fc2\_1 conda-forge  
> libdeflate 1.6 h516909a\_0 conda-forge  
> libedit 3.1.20191231 he28a2e2\_2 conda-forge  
> libev 4.33 h516909a\_1 conda-forge  
> libffi 3.4.2 h7f98852\_5 conda-forge  
> libgcc 7.2.0 h69d50b8\_2 conda-forge  
> libgcc-ng 12.2.0 h65d4601\_19 conda-forge  
> libgfortran-ng 12.2.0 h69a702a\_19 conda-forge  
> libgfortran5 12.2.0 h337968e\_19 conda-forge  
> libglib 2.74.1 h7a41b64\_0 conda-forge  
> libgomp 12.2.0 h65d4601\_19 conda-forge  
> libiconv 1.17 h166bdaf\_0 conda-forge  
> libidn2 2.3.4 h166bdaf\_0 conda-forge  
> liblapack 3.9.0 16\_linux64\_openblas conda-forge  
> libnghttp2 1.47.0 hff17c54\_1 conda-forge  
> libnsl 2.0.0 h7f98852\_0 conda-forge  
> libopenblas 0.3.21 pthreads\_h78a6416\_3 conda-forge  
> libpng 1.6.38 h753d276\_0 conda-forge  
> libsodium 1.0.18 h36c2ea0\_1 conda-forge  
> libsqlite 3.39.4 h753d276\_0 conda-forge  
> libssh2 1.10.0 hf14f497\_3 conda-forge  
> libstdcxx-ng 12.2.0 h46fd767\_19 conda-forge  
> libtiff 4.2.0 hf544144\_3 conda-forge  
> libunistring 0.9.10 h7f98852\_0 conda-forge  
> libuuid 2.32.1 h7f98852\_1000 conda-forge  
> libwebp-base 1.2.4 h166bdaf\_0 conda-forge  
> libxcb 1.13 h7f98852\_1004 conda-forge  
> libzlib 1.2.13 h166bdaf\_4 conda-forge  
> markdown 3.4.1 pyhd8ed1ab\_0 conda-forge  
> markupsafe 2.1.1 py37h540881e\_1 conda-forge  
> matplotlib-base 3.5.3 py37hf395dca\_2 conda-forge  
> matplotlib-inline 0.1.6 pyhd8ed1ab\_0 conda-forge  
> metaphlan 3.0 pyh5ca1d4c\_1 bioconda  
> mistune 2.0.4 pyhd8ed1ab\_0 conda-forge  
> msgpack-python 1.0.4 py37h7cecad7\_0 conda-forge  
> munkres 1.0.7 py\_1 bioconda  
> muscle 5.1 h9f5acd7\_1 bioconda  
> nbclient 0.7.0 pyhd8ed1ab\_0 conda-forge  
> nbconvert 7.2.3 pyhd8ed1ab\_0 conda-forge  
> nbconvert-core 7.2.3 pyhd8ed1ab\_0 conda-forge  
> nbconvert-pandoc 7.2.3 pyhd8ed1ab\_0 conda-forge  
> nbformat 5.7.0 pyhd8ed1ab\_0 conda-forge  
> ncurses 6.3 h27087fc\_1 conda-forge  
> nest-asyncio 1.5.6 pyhd8ed1ab\_0 conda-forge  
> networkx 2.7.1 pyhd8ed1ab\_0 conda-forge  
> numpy 1.21.6 py37h976b520\_0 conda-forge  
> olefile 0.46 pyh9f0ad1d\_1 conda-forge  
> openjdk 17.0.3 hea3dc9f\_3 conda-forge  
> openjpeg 2.4.0 hb52868f\_1 conda-forge  
> openssl 3.0.7 h166bdaf\_0 conda-forge  
> packaging 21.3 pyhd8ed1ab\_0 conda-forge  
> pandas 1.3.5 py37he8f5f7f\_0 conda-forge  
> pandoc 2.19.2 h32600fe\_1 conda-forge  
> pandocfilters 1.5.0 pyhd8ed1ab\_0 conda-forge  
> parso 0.8.3 pyhd8ed1ab\_0 conda-forge  
> pcre 8.45 h9c3ff4c\_0 conda-forge  
> pcre2 10.37 hc3806b6\_1 conda-forge  
> perl 5.32.1 2\_h7f98852\_perl5 conda-forge  
> perl-archive-tar 2.40 pl5321hdfd78af\_0 bioconda  
> perl-carp 1.38 pl5321hdfd78af\_4 bioconda  
> perl-common-sense 3.75 pl5321hdfd78af\_0 bioconda  
> perl-compress-raw-bzip2 2.201 pl5321h87f3376\_1 bioconda  
> perl-compress-raw-zlib 2.105 pl5321h87f3376\_0 bioconda  
> perl-encode 3.19 pl5321hec16e2b\_1 bioconda  
> perl-exporter 5.72 pl5321hdfd78af\_2 bioconda  
> perl-exporter-tiny 1.002002 pl5321hdfd78af\_0 bioconda  
> perl-extutils-makemaker 6.66 0 bioconda  
> perl-io-compress 2.201 pl5321h87f3376\_0 bioconda  
> perl-io-zlib 1.11 pl5321hdfd78af\_0 bioconda  
> perl-json 4.10 pl5321hdfd78af\_0 bioconda  
> perl-json-xs 2.34 pl5321h9f5acd7\_5 bioconda  
> perl-list-moreutils 0.430 pl5321hdfd78af\_0 bioconda  
> perl-list-moreutils-xs 0.430 pl5321hec16e2b\_1 bioconda  
> perl-parent 0.236 pl5321hdfd78af\_2 bioconda  
> perl-pathtools 3.75 pl5321hec16e2b\_3 bioconda  
> perl-scalar-list-utils 1.62 pl5321hec16e2b\_1 bioconda  
> perl-threaded 5.32.1 hdfd78af\_1 bioconda  
> perl-types-serialiser 1.01 pl5321hdfd78af\_0 bioconda  
> pexpect 4.8.0 py37hc8dfbb8\_1 conda-forge  
> pickleshare 0.7.5 py37hc8dfbb8\_1002 conda-forge  
> pillow 8.2.0 py37h4600e1f\_1 conda-forge  
> pip 22.3 pyhd8ed1ab\_0 conda-forge  
> pixman 0.40.0 h36c2ea0\_0 conda-forge  
> pkgutil-resolve-name 1.3.10 pyhd8ed1ab\_0 conda-forge  
> prompt-toolkit 3.0.31 pyha770c72\_0 conda-forge  
> psutil 5.9.3 py37h540881e\_0 conda-forge  
> pthread-stubs 0.4 h36c2ea0\_1001 conda-forge  
> ptyprocess 0.7.0 pyhd3deb0d\_0 conda-forge  
> pweave 0.30.3 py\_1 conda-forge  
> pycparser 2.21 pyhd8ed1ab\_0 conda-forge  
> pygments 2.13.0 pyhd8ed1ab\_0 conda-forge  
> pyopenssl 22.1.0 pyhd8ed1ab\_0 conda-forge  
> pyparsing 3.0.9 pyhd8ed1ab\_0 conda-forge  
> pyrsistent 0.18.1 py37h540881e\_1 conda-forge  
> pysam 0.16.0 py37ha9a96c6\_0 bioconda  
> pysocks 1.7.1 py37h89c1867\_5 conda-forge  
> python 3.7.12 hf930737\_100\_cpython conda-forge  
> python-dateutil 2.8.2 pyhd8ed1ab\_0 conda-forge  
> python-fastjsonschema 2.16.2 pyhd8ed1ab\_0 conda-forge  
> python\_abi 3.7 2\_cp37m conda-forge  
> pytz 2022.6 pyhd8ed1ab\_0 conda-forge  
> pyzmq 24.0.1 py37h0c0c2a8\_0 conda-forge  
> raxml 8.2.12 hec16e2b\_4 bioconda  
> readline 8.1.2 h0f457ee\_0 conda-forge  
> requests 2.28.1 pyhd8ed1ab\_1 conda-forge  
> samtools 0.1.19 h20b1175\_10 bioconda  
> scipy 1.7.3 py37hf2a6cf1\_0 conda-forge  
> setuptools 59.8.0 py37h89c1867\_1 conda-forge  
> six 1.16.0 pyh6c4a22f\_0 conda-forge  
> soupsieve 2.3.2.post1 pyhd8ed1ab\_0 conda-forge  
> sqlite 3.39.4 h4ff8645\_0 conda-forge  
> tbb 2021.6.0 h924138e\_1 conda-forge  
> tinycss2 1.2.1 pyhd8ed1ab\_0 conda-forge  
> tk 8.6.12 h27826a3\_0 conda-forge  
> tornado 6.2 py37h540881e\_0 conda-forge  
> traitlets 5.5.0 pyhd8ed1ab\_0 conda-forge  
> trf 4.09.1 hec16e2b\_2 bioconda  
> trimmomatic 0.39 hdfd78af\_2 bioconda  
> typing-extensions 4.4.0 hd8ed1ab\_0 conda-forge  
> typing\_extensions 4.4.0 pyha770c72\_0 conda-forge  
> unicodedata2 14.0.0 py37h540881e\_1 conda-forge  
> urllib3 1.26.11 pyhd8ed1ab\_0 conda-forge  
> wcwidth 0.2.5 pyh9f0ad1d\_2 conda-forge  
> webencodings 0.5.1 py\_1 conda-forge  
> wget 1.20.3 ha35d2d1\_1 conda-forge  
> wheel 0.37.1 pyhd8ed1ab\_0 conda-forge  
> xorg-fixesproto 5.0 h7f98852\_1002 conda-forge  
> xorg-inputproto 2.3.2 h7f98852\_1002 conda-forge  
> xorg-kbproto 1.0.7 h7f98852\_1002 conda-forge  
> xorg-libice 1.0.10 h7f98852\_0 conda-forge  
> xorg-libsm 1.2.3 hd9c2040\_1000 conda-forge  
> xorg-libx11 1.7.2 h7f98852\_0 conda-forge  
> xorg-libxau 1.0.9 h7f98852\_0 conda-forge  
> xorg-libxdmcp 1.1.3 h7f98852\_0 conda-forge  
> xorg-libxext 1.3.4 h7f98852\_1 conda-forge  
> xorg-libxfixes 5.0.3 h7f98852\_1004 conda-forge  
> xorg-libxi 1.7.10 h7f98852\_0 conda-forge  
> xorg-libxrender 0.9.10 h7f98852\_1003 conda-forge  
> xorg-libxtst 1.2.3 h7f98852\_1002 conda-forge  
> xorg-recordproto 1.14.2 h7f98852\_1002 conda-forge  
> xorg-renderproto 0.11.1 h7f98852\_1002 conda-forge  
> xorg-xextproto 7.3.0 h7f98852\_1002 conda-forge  
> xorg-xproto 7.0.31 h7f98852\_1007 conda-forge  
> xz 5.2.6 h166bdaf\_0 conda-forge  
> zeromq 4.3.4 h9c3ff4c\_1 conda-forge  
> zip 3.0 h7f98852\_1 conda-forge  
> zipp 3.10.0 pyhd8ed1ab\_0 conda-forge  
> zlib 1.2.13 h166bdaf\_4 conda-forge  
> zstd 1.5.2 h6239696\_4 conda-forge

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 4, 2022, 11:08am UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/3 "2022-11-04T11:08:18Z")

</div>

Update:

I am trying to systematically explore biobakery\_workflow versions available through conda.  
Version `3.0.0a4 build py37hb80360e_0` results in the same error as above:  
`conda create -c biobakery -n biobakery biobakery_workflows=3.0.0a4=py37hb80360e_0`  
Once the `FileNotFoundError: [Errno 2] No such file or directory: 'zip': 'zip'` error handled by manually installing zip (`conda install zip`), I encounter:

> ImportError: cannot import name ‘PwebProcessor’ from ‘pweave’

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 4, 2022, 1:15pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/4 "2022-11-04T13:15:49Z")

</div>

With version `3.0.0a4 build pyh41f93f0_0`:  
`conda create -c biobakery -n biobakery biobakery_workflows=3.0.0a4=pyh41f93f0_0`  
and within the conda environment: `biobakery_workflows wmgx_vis --input run_test/output/ --output run_test/vis --project-name TEST`  
Returns:

> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a4/bin/wmgx\_vis.py”, line 28, in   
> from anadama2 import Workflow  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a4/lib/python3.10/site-packages/anadama2/ **init**.py”, line 83, in   
> from .workflow import Workflow  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a4/lib/python3.10/site-packages/anadama2/workflow.py”, line 24, in   
> from . import backends  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a4/lib/python3.10/site-packages/anadama2/backends.py”, line 7, in   
> import leveldb  
> ModuleNotFoundError: No module named ‘leveldb’

After fixing the dependency issue with `conda install python-leveldb`, fixing also  
the `zip` dependency, running `biobakery_workflows vis` returns:

> (Nov 04 12:24:40) [0/2 - 0.00%] \*\*Ready \*\* Task 0: document  
> (Nov 04 12:24:40) [0/2 - 0.00%] \*\*Started \*\* Task 0: document  
> (Nov 04 12:24:41) [1/2 - 50.00%] \*\*Failed \*\* Task 0: document  
> (Nov 04 12:24:41) [2/2 - 100.00%] \*\*Failed \*\* Task 6: archive  
> Run Finished  
> Task 0 failed  
> Name: document  
> Original error:  
> Error executing action 0. Original Exception:  
> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a4/lib/python3.10/site-packages/anadama2/runners.py”, line 200, in \_run\_task\_locally  
> action\_func(task)  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a4/lib/python3.10/site-packages/anadama2/document.py”, line 232, in create  
> from pweave import PwebPandocFormatter, Pweb, PwebProcessor  
> ImportError: cannot import name ‘PwebProcessor’ from ‘pweave’ (/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a4/lib/python3.10/site-packages/pweave/ **init**.py)

So same problem as with build `py37hb80360e_0`.

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 4, 2022, 1:23pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/5 "2022-11-04T13:23:23Z")

</div>

With version `3.0.0a7 build pyh0b62126_0`, exact same result as for version `3.0.0a4 build pyh41f93f0_0`: need to conda install `python-leveldb` and `zip`, and then Pweave import error:

> (Nov 04 14:20:34) [0/2 - 0.00%] \*\*Ready \*\* Task 0: document  
> (Nov 04 14:20:34) [0/2 - 0.00%] \*\*Started \*\* Task 0: document  
> (Nov 04 14:20:34) [1/2 - 50.00%] \*\*Failed \*\* Task 0: document  
> (Nov 04 14:20:34) [2/2 - 100.00%] \*\*Failed \*\* Task 6: archive  
> Run Finished  
> Task 0 failed  
> Name: document  
> Original error:  
> Error executing action 0. Original Exception:  
> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a7/lib/python3.10/site-packages/anadama2/runners.py”, line 200, in \_run\_task\_locally  
> action\_func(task)  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a7/lib/python3.10/site-packages/anadama2/document.py”, line 232, in create  
> from pweave import PwebPandocFormatter, Pweb, PwebProcessor  
> ImportError: cannot import name ‘PwebProcessor’ from ‘pweave’ (/home/theoscilicium/miniconda3/envs/biobakery\_3.0.0a7/lib/python3.10/site-packages/pweave/ **init**.py)

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 4, 2022, 1:30pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/6 "2022-11-04T13:30:33Z")

</div>

With version `0.15.1 build py27h10287d5_0`:  
Some progress? There is no unresolved dependency issue and it works directly, only to fail with the following error:

> ERROR: Unable to find file: run\_test/output/metaphlan2/merged/metaphlan2\_taxonomic\_profiles.tsv
> 
> File description:  
> A tab-delimited file with samples as columns and relative abundance as rows.  
> This file contains the merged taxonomic profiles computed by MetaPhlAn2 for all samples.

Apparently, naming of output directories and files from `biobakery_workflow wmgx` changed at some point between `biobakery_workflow` versions 0.15 and 3.0.0a4, because I have folders and files named `metaphlan` and not `metaphlan2`.

I thus manually moved my files and folders to have `metaphlan2` instead of `metaphlan` in names. Again encountering the `zip` dependency, and after fixing it:

> (Nov 04 14:33:41) [0/2 - 0.00%] \*\*Ready \*\* Task 0: document  
> (Nov 04 14:33:41) [0/2 - 0.00%] \*\*Started \*\* Task 0: document  
> Exception:  
> [Errno 2] No such file or directory  
> Error messages will be included in output document  
> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/bin/wmgx\_vis.py”, line 133, in   
> workflow.go()  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/anadama2/workflow.py”, line 804, in go  
> self.\_handle\_finished()  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/anadama2/workflow.py”, line 836, in \_handle\_finished  
> raise RunFailed()  
> anadama2.workflow.RunFailed

Content of the anadama.log file:

> 2022-11-04 14:33:41,180 LoggerReporter started INFO: Beginning AnADAMA run with 5 tasks.  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: Workflow description = A workflow for whole metagenome shotgun sequence visualization  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: Workflow version = 0.1  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: Workflow configuration options  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: metadata\_continuous =   
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: exclude\_workflow\_info = False  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: grid\_time\_max = None  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: grid\_benchmark = off  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: grid\_partition =  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: log\_level = INFO  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: dry\_run = False  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: exclude\_target = None  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: until\_task = None  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: input\_metadata = None  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: grid\_scratch =  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: input = run\_test/output/  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: config = None  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: grid\_jobs = 0  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: introduction\_text = The data was run through the standard workflow for whole metagenome shotgun sequencing.  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: grid\_submit\_sleep = 5  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: project\_name = TEST  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: jobs = 1  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: format = pdf  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: metadata\_exclude =   
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: grid = None  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: metadata\_categorical =   
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: target = None  
> 2022-11-04 14:33:41,181 LoggerReporter started INFO: grid\_environment = None  
> 2022-11-04 14:33:41,182 LoggerReporter started INFO: grid\_mem\_max = None  
> 2022-11-04 14:33:41,182 LoggerReporter started INFO: exclude\_task = None  
> 2022-11-04 14:33:41,182 LoggerReporter started INFO: quit\_early = False  
> 2022-11-04 14:33:41,182 LoggerReporter started INFO: grid\_options = None  
> 2022-11-04 14:33:41,182 LoggerReporter started INFO: output = run\_test/vis\_2.7  
> 2022-11-04 14:33:41,182 LoggerReporter started INFO: skip\_nothing = False  
> 2022-11-04 14:33:41,202 LoggerReporter log\_event INFO: task 0, document : ready and waiting for resources  
> 2022-11-04 14:33:41,202 LoggerReporter log\_event INFO: task 0, document : starting to run  
> 2022-11-04 14:33:41,989 LoggerReporter task\_failed ERROR: task 0, document : Failed! Error message : Error executing action 0. Original Exception:  
> Traceback (most recent call last):  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/anadama2/runners.py”, line 200, in \_run\_task\_locally  
> action\_func(task)  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/anadama2/document.py”, line 315, in create  
> doc.weave(shell=PwebProcessorSpaces)  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/pweave/pweb.py”, line 198, in weave  
> self.run(shell)  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/pweave/pweb.py”, line 149, in run  
> runner.run()  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/pweave/processors.py”, line 65, in run  
> self.executed = list(map(self.\_runcode, self.parsed))  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/pweave/processors.py”, line 131, in \_runcode  
> chunk[‘content’] = self.loadinline(chunk[‘content’])  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/anadama2/document.py”, line 262, in loadinline  
> result = self.loadstring(code\_str).lstrip().replace(“\n”,“”,1)  
> File “/home/theoscilicium/miniconda3/envs/biobakery\_2.7/lib/python2.7/site-packages/pweave/processors.py”, line 296, in loadstring  
> exec(compiled, scope)  
> File “chunk”, line 1, in   
> NameError: name ‘caption’ is not defined
> 
> 2022-11-04 14:33:41,989 LoggerReporter task\_failed ERROR: task 3, archive : Failed! Error message : Task failed because parent task `0’ failed  
> 2022-11-04 14:33:41,989 LoggerReporter finished ERROR: AnADAMA run finished with errors.

So, again the **caption** error

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 4, 2022, 1:57pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/7 "2022-11-04T13:57:24Z")

</div>

Summary of my trials:

- `biobakery_workflows wmgx_vis` of the latest available (to date) Docker image fails with a ‘caption’ error. `pip3 freeze` informs that biobakery\_workflow version is `3.0.0a6` in this image.

- conda versions of biobakery\_workflows fails for versions:

So, when installed with Python \>= 3.7, fails with Pweave import. According to [this post](https://forum.biobakery.org/t/which-version-of-pweave-needed/1000), it is because Pweave version needs to be \<=v0.25.

Anyway, the problem is at least 2 years old (!) as the latest Docker image is also affected.

I will try with older Docker images, but … well… not encouraging.

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 4, 2022, 2:32pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/8 "2022-11-04T14:32:48Z")

</div>

Update with tests of [Docker images](https://hub.docker.com/r/biobakery/workflows/tags):

- `3.0.0.a.7`: fails with `caption` error
- `3.0.0.a.6.metaphlanv3.0.7`: fails with `caption` error

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 4, 2022, 4:19pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/9 "2022-11-04T16:19:55Z")

</div>

To the development team:

If you have a working version, could you please provide informations about the environment, such as `pip freeze` or `conda list`?

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 7, 2022, 8:59am UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/10 "2022-11-07T08:59:18Z")

</div>

Update with tests of [Docker images](https://hub.docker.com/r/biobakery/workflows/tags):

- `3.0.0.a.7`: fails with `caption` error
- `3.0.0.a.6.metaphlanv3.0.7`: fails with `caption` error
- `3.0.0.a.6`: fails with `caption` error
- `3.0.0.alpha.5`: fails with `caption` error
- `0.15.1` fails with `caption` error
- `0.13.2` fails with `caption` error (after renaming `humann` files and directories to `humann2`)

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 7, 2022, 3:36pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/11 "2022-11-07T15:36:39Z")

</div>

**BIG NEWS!**

I finally managed to get `biobakery_workflows vis` to run!

The solution that worked for me:

1. Create conda env, but not installing biobakery\_workflows  
`mamba create -n biobakery_test python=3.7 pip zip gxx_linux-64 pandoc R `  
(If you don’t know [mamba](https://mamba.readthedocs.io/en/latest/), it is a drop-in replacement of conda that is much faster)

2. Go inside the environment:  
`conda activate biobakery_test`

3. Install biobakery\_workflows and dependencies with pip:  
`pip install numpy matplotlib humann scipy biobakery_workflows`  
_Warning:_ it is NOT recommended to mix `pip` and `conda` installs. However, installing packages with `pip` is OK as long as you do not install anything afterwards with `conda` (i.e: conda first, pip then), as per [conda documentation](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#using-pip-in-an-environment).

4. As observed previously (see first post), there is a path problem with images included for `biobakery_workflow vis`. Creating a symlink did the trick for me:  
`ln -s /home/theoscilicium/miniconda3/envs/biobakery/images /home/theoscilicium/miniconda3/envs/biobakery/lib/python3.7/site-packages/images`

5. This is probably config-dependent and may vary in your setup, and from what I read cannot be easily deported to a `conda` env, but at this step I had to install additional packages for latex:  
`sudo apt-get install texlive-latex-extra`

6. Run biobakery workflows!  
`biobakery_workflows vis --input run_test/biobakery_results/ --output run_test/vis/ --project-name TEST`

7. Exit conda env:  
`conda deactivate`

Hope this can help other people! Included bellow are further information about the setup.

Best,  
Theo

* * *

Output of `conda list`

> # packages in environment at /home/theoscilicium/miniconda3/envs/biobakery\_test:
> 
> # 
> 
> # Name Version Build Channel
> 
> \_libgcc\_mutex 0.1 conda\_forge conda-forge  
> \_openmp\_mutex 4.5 2\_gnu conda-forge  
> \_r-mutex 1.0.1 anacondar\_1 conda-forge  
> anadama2 0.10.0 pypi\_0 pypi  
> binutils\_impl\_linux-64 2.39 h6ceecb4\_0 conda-forge  
> binutils\_linux-64 2.39 h5fc0e48\_11 conda-forge  
> biobakery-workflows 3.1 pypi\_0 pypi  
> bwidget 1.9.14 ha770c72\_1 conda-forge  
> bzip2 1.0.8 h7f98852\_4 conda-forge  
> c-ares 1.18.1 h7f98852\_0 conda-forge  
> ca-certificates 2022.9.24 ha878542\_0 conda-forge  
> cairo 1.16.0 ha61ee94\_1014 conda-forge  
> cloudpickle 2.2.0 pypi\_0 pypi  
> curl 7.86.0 h2283fc2\_1 conda-forge  
> cycler 0.11.0 pypi\_0 pypi  
> expat 2.5.0 h27087fc\_0 conda-forge  
> font-ttf-dejavu-sans-mono 2.37 hab24e00\_0 conda-forge  
> font-ttf-inconsolata 3.000 h77eed37\_0 conda-forge  
> font-ttf-source-code-pro 2.038 h77eed37\_0 conda-forge  
> font-ttf-ubuntu 0.83 hab24e00\_0 conda-forge  
> fontconfig 2.14.1 hc2a2eb6\_0 conda-forge  
> fonts-conda-ecosystem 1 0 conda-forge  
> fonts-conda-forge 1 0 conda-forge  
> fonttools 4.38.0 pypi\_0 pypi  
> freetype 2.12.1 hca18f0e\_0 conda-forge  
> fribidi 1.0.10 h36c2ea0\_0 conda-forge  
> gcc\_impl\_linux-64 12.2.0 hcc96c02\_19 conda-forge  
> gcc\_linux-64 12.2.0 h4798a0e\_11 conda-forge  
> gettext 0.21.1 h27087fc\_0 conda-forge  
> gfortran\_impl\_linux-64 12.2.0 h55be85b\_19 conda-forge  
> graphite2 1.3.13 h58526e2\_1001 conda-forge  
> gsl 2.7 he838d99\_0 conda-forge  
> gxx\_impl\_linux-64 12.2.0 hcc96c02\_19 conda-forge  
> gxx\_linux-64 12.2.0 hb41e900\_11 conda-forge  
> harfbuzz 5.3.0 h418a68e\_0 conda-forge  
> humann 3.6 pypi\_0 pypi  
> icu 70.1 h27087fc\_0 conda-forge  
> importlib-metadata 5.0.0 pypi\_0 pypi  
> jpeg 9e h166bdaf\_2 conda-forge  
> kernel-headers\_linux-64 2.6.32 he073ed8\_15 conda-forge  
> keyutils 1.6.1 h166bdaf\_0 conda-forge  
> kiwisolver 1.4.4 pypi\_0 pypi  
> krb5 1.19.3 h08a2579\_0 conda-forge  
> ld\_impl\_linux-64 2.39 hc81fddc\_0 conda-forge  
> lerc 4.0.0 h27087fc\_0 conda-forge  
> leveldb 0.201 pypi\_0 pypi  
> libblas 3.9.0 16\_linux64\_openblas conda-forge  
> libcblas 3.9.0 16\_linux64\_openblas conda-forge  
> libcurl 7.86.0 h2283fc2\_1 conda-forge  
> libdeflate 1.14 h166bdaf\_0 conda-forge  
> libedit 3.1.20191231 he28a2e2\_2 conda-forge  
> libev 4.33 h516909a\_1 conda-forge  
> libffi 3.4.2 h7f98852\_5 conda-forge  
> libgcc-devel\_linux-64 12.2.0 h3b97bd3\_19 conda-forge  
> libgcc-ng 12.2.0 h65d4601\_19 conda-forge  
> libgfortran-ng 12.2.0 h69a702a\_19 conda-forge  
> libgfortran5 12.2.0 h337968e\_19 conda-forge  
> libglib 2.74.1 h606061b\_1 conda-forge  
> libgomp 12.2.0 h65d4601\_19 conda-forge  
> libiconv 1.17 h166bdaf\_0 conda-forge  
> liblapack 3.9.0 16\_linux64\_openblas conda-forge  
> libnghttp2 1.47.0 hff17c54\_1 conda-forge  
> libnsl 2.0.0 h7f98852\_0 conda-forge  
> libopenblas 0.3.21 pthreads\_h78a6416\_3 conda-forge  
> libpng 1.6.38 h753d276\_0 conda-forge  
> libsanitizer 12.2.0 h46fd767\_19 conda-forge  
> libsqlite 3.39.4 h753d276\_0 conda-forge  
> libssh2 1.10.0 hf14f497\_3 conda-forge  
> libstdcxx-devel\_linux-64 12.2.0 h3b97bd3\_19 conda-forge  
> libstdcxx-ng 12.2.0 h46fd767\_19 conda-forge  
> libtiff 4.4.0 h55922b4\_4 conda-forge  
> libuuid 2.32.1 h7f98852\_1000 conda-forge  
> libwebp-base 1.2.4 h166bdaf\_0 conda-forge  
> libxcb 1.13 h7f98852\_1004 conda-forge  
> libxml2 2.10.3 h7463322\_0 conda-forge  
> libzlib 1.2.13 h166bdaf\_4 conda-forge  
> make 4.3 hd18ef5c\_1 conda-forge  
> markdown 3.4.1 pypi\_0 pypi  
> matplotlib 3.5.3 pypi\_0 pypi  
> ncurses 6.3 h27087fc\_1 conda-forge  
> networkx 2.6.3 pypi\_0 pypi  
> numpy 1.21.6 pypi\_0 pypi  
> openssl 3.0.7 h166bdaf\_0 conda-forge  
> packaging 21.3 pypi\_0 pypi  
> pandoc 2.19.2 h32600fe\_1 conda-forge  
> pango 1.50.11 h382ae3d\_0 conda-forge  
> pcre2 10.40 hc3806b6\_0 conda-forge  
> pillow 9.3.0 pypi\_0 pypi  
> pip 22.3.1 pyhd8ed1ab\_0 conda-forge  
> pixman 0.40.0 h36c2ea0\_0 conda-forge  
> pthread-stubs 0.4 h36c2ea0\_1001 conda-forge  
> pweave 0.25 pypi\_0 pypi  
> pyparsing 3.0.9 pypi\_0 pypi  
> python 3.7.12 hf930737\_100\_cpython conda-forge  
> python-dateutil 2.8.2 pypi\_0 pypi  
> r 4.2 r42hd8ed1ab\_1006 conda-forge  
> r-base 4.2.2 hb87df5d\_1 conda-forge  
> r-boot 1.3\_28 r42hc72bb7e\_1 conda-forge  
> r-class 7.3\_20 r42h06615bd\_1 conda-forge  
> r-cluster 2.1.4 r42h8da6f51\_0 conda-forge  
> r-codetools 0.2\_18 r42hc72bb7e\_1 conda-forge  
> r-foreign 0.8\_83 r42h06615bd\_1 conda-forge  
> r-kernsmooth 2.23\_20 r42hd009a43\_1 conda-forge  
> r-lattice 0.20\_45 r42h06615bd\_1 conda-forge  
> r-mass 7.3\_58.1 r42h06615bd\_1 conda-forge  
> r-matrix 1.5\_1 r42h5f7b363\_0 conda-forge  
> r-mgcv 1.8\_41 r42h5f7b363\_0 conda-forge  
> r-nlme 3.1\_160 r42h8da6f51\_0 conda-forge  
> r-nnet 7.3\_18 r42h06615bd\_1 conda-forge  
> r-recommended 4.2 r42hd8ed1ab\_1005 conda-forge  
> r-rpart 4.1.19 r42h06615bd\_0 conda-forge  
> r-spatial 7.3\_15 r42h06615bd\_1 conda-forge  
> r-survival 3.4\_0 r42h06615bd\_1 conda-forge  
> readline 8.1.2 h0f457ee\_0 conda-forge  
> scipy 1.7.3 pypi\_0 pypi  
> sed 4.8 he412f7d\_0 conda-forge  
> setuptools 65.5.1 pyhd8ed1ab\_0 conda-forge  
> six 1.16.0 pypi\_0 pypi  
> sqlite 3.39.4 h4ff8645\_0 conda-forge  
> sysroot\_linux-64 2.12 he073ed8\_15 conda-forge  
> tk 8.6.12 h27826a3\_0 conda-forge  
> tktable 2.10 hb7b940f\_3 conda-forge  
> typing-extensions 4.4.0 pypi\_0 pypi  
> wheel 0.38.2 pyhd8ed1ab\_0 conda-forge  
> xorg-kbproto 1.0.7 h7f98852\_1002 conda-forge  
> xorg-libice 1.0.10 h7f98852\_0 conda-forge  
> xorg-libsm 1.2.3 hd9c2040\_1000 conda-forge  
> xorg-libx11 1.7.2 h7f98852\_0 conda-forge  
> xorg-libxau 1.0.9 h7f98852\_0 conda-forge  
> xorg-libxdmcp 1.1.3 h7f98852\_0 conda-forge  
> xorg-libxext 1.3.4 h7f98852\_1 conda-forge  
> xorg-libxrender 0.9.10 h7f98852\_1003 conda-forge  
> xorg-libxt 1.2.1 h7f98852\_2 conda-forge  
> xorg-renderproto 0.11.1 h7f98852\_1002 conda-forge  
> xorg-xextproto 7.3.0 h7f98852\_1002 conda-forge  
> xorg-xproto 7.0.31 h7f98852\_1007 conda-forge  
> xz 5.2.6 h166bdaf\_0 conda-forge  
> zip 3.0 h7f98852\_1 conda-forge  
> zipp 3.10.0 pypi\_0 pypi  
> zlib 1.2.13 h166bdaf\_4 conda-forge  
> zstd 1.5.2 h6239696\_4 conda-forge

* * *

Output of `pip freeze`

> anadama2==0.10.0  
> biobakery-workflows==3.1  
> cloudpickle==2.2.0  
> cycler==0.11.0  
> fonttools==4.38.0  
> humann==3.6  
> importlib-metadata==5.0.0  
> kiwisolver==1.4.4  
> leveldb==0.201  
> Markdown==3.4.1  
> matplotlib==3.5.3  
> networkx==2.6.3  
> numpy==1.21.6  
> packaging==21.3  
> Pillow==9.3.0  
> Pweave==0.25  
> pyparsing==3.0.9  
> python-dateutil==2.8.2  
> scipy==1.7.3  
> six==1.16.0  
> typing\_extensions==4.4.0  
> zipp==3.10.0

---

<div class="post-metadata">

**Author:** ![MiguelB](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/miguelb/32/1275_2.png) [@MiguelB](https://forum.biobakery.org/u/MiguelB)\
**Post date:** [November 7, 2022, 9:45pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/12 "2022-11-07T21:45:51Z")

</div>

Just had the same problem with the image directory. The `ln` approach seems to work neat.  
Thanks!

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [November 9, 2022, 3:46pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/13 "2022-11-09T15:46:22Z")

</div>

A bit of a pain not to be able to edit posts…

At step 3. above, add `hclust2` to the list of packages to install with pip if you want to have heatmaps included in the report:  
`pip install numpy matplotlib humann scipy biobakery_workflows hclust2`

---

<div class="post-metadata">

**Author:** ![Zhu\_Wenhan](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/zhu_wenhan/32/2613_2.png) [@Zhu\_Wenhan](https://forum.biobakery.org/u/Zhu_Wenhan)\
**Post date:** [December 29, 2023, 3:35pm UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/14 "2023-12-29T15:35:41Z")

</div>

Thank you! Your post is incredibly helpful! I have followed all the steps you posted but still encountered this error:

2023-12-28 13:22:26,152 LoggerReporter task\_failed ERROR: task 2, document : Failed! Error message : Error executing action 0. Original Exception:  
Traceback (most recent call last):  
File “/panfs/accrepfs.vampire/home/zhuw9/miniforge3/envs/biobakery\_vis/lib/python3.7/site-packages/anadama2/runners.py”, line 200, in \_run\_task\_locally  
action\_func(task)  
File “/panfs/accrepfs.vampire/home/zhuw9/miniforge3/envs/biobakery\_vis/lib/python3.7/site-packages/anadama2/document.py”, line 321, in create  
sh(pandoc\_command.format(intermediate\_template, temp\_report),log\_command=True)()  
File “/panfs/accrepfs.vampire/home/zhuw9/miniforge3/envs/biobakery\_vis/lib/python3.7/site-packages/anadama2/helpers.py”, line 107, in actually\_sh  
ret = \_sh(s, \*\*kwargs)  
File “/panfs/accrepfs.vampire/home/zhuw9/miniforge3/envs/biobakery\_vis/lib/python3.7/site-packages/anadama2/util/ **init**.py”, line 320, in sh  
raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode(‘utf-8’), ret[1].decode(‘utf-8’)))  
anadama2.util.ShellException: [Errno 43] Command `pandoc /panfs/accrepfs.vampire/data/zhu_group/10272023_Danyvid/Adapter_trimmed/Quality_trimmed/filter/clean_reads/Danyvid_vis1/tmpc10u64yp/wmgx_report.md -o /panfs/accrepfs.vampire/data/zhu_group/10272023_Danyvid/Adapter_trimmed/Quality_trimmed/filter/clean_reads/Danyvid_vis1/tmpc10u64yp/wmgx_report..pdf --variable=linkcolor:Blue --variable=toccolor:Blue --pdf-engine=pdflatex --standalone -V geometry:left=1in -V geometry:right=1in -V geometry:top=1in -V geometry:bottom=1in --toc' failed. Out: Err: Error producing PDF. ! LaTeX Error: File `iftex.sty’ not found.

Type X to quit or to proceed,  
or enter new name. (Default extension: sty)

Enter file name:  
! Emergency stop.  
\<read \*\>

l.10 \ifPDFTeX

2023-12-28 13:22:26,152 LoggerReporter task\_failed ERROR: task 4, archive : Failed! Error message : Task failed because parent task `2’ failed

Can you advise what is going on?

Thanks!

Best,

Wenhan

---

<div class="post-metadata">

**Author:** ![SciLiciumTheo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sciliciumtheo/32/1697_2.png) [@SciLiciumTheo](https://forum.biobakery.org/u/SciLiciumTheo)\
**Post date:** [January 9, 2024, 10:48am UTC](https://forum.biobakery.org/t/cannot-get-biobakery-workflows-vis-to-run/4338/15 "2024-01-09T10:48:30Z")

</div>

Dear Wenhan,

I am not in any way related to the team behind biobakery / biobakery workflows.

As of 2024; given the absence of answer from the development / maintenance team, the lack of official documentation and guidelines on how to solve these problems or just any feedback that these posts were helpful in any way, I would not recommend spending time trying to fix biobakery\_workflows. I would generally not recommend using this biobakery\_workflows, but instead use the individual tools that make up biobakery\_workflows, for example using a widely used workflow manager such as Snakemake.  
The time you will spend learning to use such a workflow manager and reproducing biobakery\_workflows will be on the same order as the time you will spend if you choose to go down the rabbit hole of fixing the original biobakery\_workflows, but you will have something that will be much easier to debug/use, you will have learnt how to use a new tool that is a standard in the bioinformatics community, and it will save you some headaches.

Just my opinion after 1+ year of struggling with biobakery.