# Biobakery vis workflow errors

**URL:** <https://forum.biobakery.org/t/biobakery-vis-workflow-errors/6380>\
**Category:** bioBakery workflows\
**Created:** [December 29, 2023, 3:54pm UTC](https://forum.biobakery.org/t/biobakery-vis-workflow-errors/6380 "2023-12-29T15:54:34Z")\
**Posts on this page:** 1\
**Page:** 1

<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, 3:54pm UTC](https://forum.biobakery.org/t/biobakery-vis-workflow-errors/6380/1 "2023-12-29T15:54:34Z")

</div>

Hi All,

Has anyone encountered this error when using the vis workflow of biobakery:

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