biobakery_workflows wmgx_vis error

[lk754673712]

biobakery_workflows wmgx_vis --input workflow_output/ --project-name PRJNA685168 --output PRJNA685168_vis_no_metadata
(May 15 15:57:34) [0/2 - 0.00%] **Ready ** Task 0: document
(May 15 15:57:34) [0/2 - 0.00%] **Started ** Task 0: document
Exception:
float division by zero
Error messages will be included in output document
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:588: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_under( bottom_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:594: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_over( top_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:588: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_under( bottom_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:594: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_over( top_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:588: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_under( bottom_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:594: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_over( top_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:588: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_under( bottom_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:594: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_over( top_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:588: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_under( bottom_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:594: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_over( top_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:588: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_under( bottom_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:594: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_over( top_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:588: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_under( bottom_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:594: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_over( top_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:588: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_under( bottom_col )
/home/lk/miniconda3/envs/metagenome/bin/hclust2.py:594: MatplotlibDeprecationWarning: You are modifying the state of a globally registered colormap. This has been deprecated since 3.3 and in 3.6, you will not be able to modify a registered colormap in-place. To remove this warning, you can make a copy of the colormap first. cmap = mpl.cm.get_cmap("bbcry").copy()
cm.set_over( top_col )
(May 15 15:58:43) [1/2 - 50.00%] **Failed ** Task 0: document
(May 15 15:58:43) [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/lk/.local/lib/python3.7/site-packages/anadama2/runners.py", line 201, in _run_task_locally
action_func(task)
File "/home/lk/.local/lib/python3.7/site-packages/anadama2/document.py", line 290, in create
sh(pandoc_command.format(intermediate_template, temp_report),log_command=True)()
File "/home/lk/.local/lib/python3.7/site-packages/anadama2/helpers.py", line 89, in actually_sh
ret = _sh(s, **kwargs)
File "/home/lk/.local/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 2] Command pandoc /home/lk/PRJNA685168/PRJNA685168_vis_no_metadata/tmp3g_k7qej/wmgx_report.md -o /home/lk/PRJNA685168/PRJNA685168_vis_no_metadata/tmp3g_k7qej/wmgx_report..pdf --variable=linkcolor:Blue --variable=toccolor:Blue --pdf-engine=pdflatex --standalone --toc' failed. Out: b'' Err: b"pandoc: unrecognized option --pdf-engine=pdflatex'\nTry pandoc --help for more information.\n"

Task 6 failed
Name: archive
Original error:
Task failed because parent task `0' failed
Traceback (most recent call last):
File "/home/lk/.local/bin/wmgx_vis.py", line 133, in
workflow.go()
File "/home/lk/.local/lib/python3.7/site-packages/anadama2/workflow.py", line 801, in go
self._handle_finished()
File "/home/lk/.local/lib/python3.7/site-packages/anadama2/workflow.py", line 833, in _handle_finished
raise RunFailed()
anadama2.workflow.RunFailed

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.

[pmb-piotr]

wrong:
pdf-engine=pdflatex

correct:
latex-engine=pdflatex

[github-actions]

Thank you for creating this issue.
We currently field issues through our bioBakery Discourse Support Forum.
If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.