Dear mantainers,
I’d like to use the biobakery workflow to perform my analysis on wmgx data.
However, their are some error appeared.
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
Thanks in advance
Warm regards
Kai