# Biobakery\_workflows wmgx\_vis: Package inputenc Error, running pandoc fails

**URL:** <https://forum.biobakery.org/t/biobakery-workflows-wmgx-vis-package-inputenc-error-running-pandoc-fails/2624>\
**Category:** bioBakery workflows\
**Created:** [September 22, 2021, 12:44pm UTC](https://forum.biobakery.org/t/biobakery-workflows-wmgx-vis-package-inputenc-error-running-pandoc-fails/2624 "2021-09-22T12:44:21Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![hilasha2](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/hilasha2/32/947_2.png) [@hilasha2](https://forum.biobakery.org/u/hilasha2)\
**Post date:** [September 22, 2021, 12:44pm UTC](https://forum.biobakery.org/t/biobakery-workflows-wmgx-vis-package-inputenc-error-running-pandoc-fails/2624/1 "2021-09-22T12:44:21Z")

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So I have been trying to run the visualization workflow wmgx\_vis. However, I keep getting an error that the workflow cannot produce a pdf with the character beta.

```auto
anadama2.util.ShellException: [Errno 43] Command `pandoc $PATH_INPUT/wmgx_report.md -o $PATH_OUTPUT/wmgx_report..pdf --variable=linkcolor:Blue --variable=toccolor:Blue --pdf-engine=pdflatex --standalone --toc' failed. 
  Out: b''
  Err: b'Error producing PDF.\n
! Package inputenc Error: Unicode character \xce\xb2 (U+03B2)\n
(inputenc) not set up for use with LaTeX.\n\n
See the inputenc package documentation for explanation.\n
Type H <return> for immediate help.\n ... \n\n
l.360 dTDP-\xce\xb2-L-rhamnose biosynthesis}\n\n
Try running pandoc with --pdf-engine=xelatex.\n'

```

Basically, wmgx\_vis calls pandoc in order to create a pdf. However, the character \xce\xb2, which is beta, is not recognized. I looked up where the call for pandoc is defined, and it is defined in anadama2/document.py.

```auto
# set the pandoc command based on if a table of contents will be included
pandoc_command="pandoc {0} -o {1} --variable=linkcolor:Blue "+\
"--variable=toccolor:Blue --pdf-engine=pdflatex --standalone" 

```

I tried to call pandoc with --pdf-engine=xelatex instead of pdflatex. However, this solution didn’t work.  
Any other solutions?

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<div class="post-metadata">

**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:** [October 1, 2021, 8:24pm UTC](https://forum.biobakery.org/t/biobakery-workflows-wmgx-vis-package-inputenc-error-running-pandoc-fails/2624/2 "2021-10-01T20:24:36Z")

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Hello, Thank you for the detailed post. We have tested the workflows with the pdflatex engine but not the xelatex engine so I am not sure if it is able to compile the document.

Have you tried updating your workflows to the latest version? You also might try re-installing latex to see if this resolves the issue.

Thank you,  
Lauren

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<div class="post-metadata">

**Author:** ![hilasha2](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/hilasha2/32/947_2.png) [@hilasha2](https://forum.biobakery.org/u/hilasha2)\
**Post date:** [November 4, 2021, 3:08pm UTC](https://forum.biobakery.org/t/biobakery-workflows-wmgx-vis-package-inputenc-error-running-pandoc-fails/2624/3 "2021-11-04T15:08:44Z")

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Sorry for the late reply.  
I did update the workflow to the latest version + re-installed latex several times to no avail.  
That said, I had to run the workflow in a conda environment with python version 3.6 and not 3.7.  
The reason for that is elaborated in the following post:  
[https://forum.biobakery.org/t/which-version-of-pweave-needed/1000/4?u=hilasha2](https://forum.biobakery.org/t/which-version-of-pweave-needed/1000/4)  
(I should have most probably looked at pweave version 0.25, but didn’t for some reason -  
[https://github.com/mpastell/Pweave/compare/v0.25…v0.30.1](https://github.com/mpastell/Pweave/compare/v0.25...v0.30.1) )