DEMO FAILED

[giriarteS]

OS: Ubuntu 20.04, 56 cores, ~ 132 GB RAM. Python: 3.9.12

I got the following error:
python -m charcoal run demo/demo.conf -j 4
** read 3 provided lineages
** config file checks PASSED!
** from here on out, it's all snakemake...
Building DAG of jobs...
Updating job make_index.
Using shell: /bin/bash
Provided cores: 4
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 all
2 make_html_alignment
1 make_index
2 make_notebook_alignment
6
Select jobs to execute...

[Tue May 10 13:24:43 2022]
rule make_notebook_alignment:
input: output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002685755.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002501065.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002726085.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002720975.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002726335.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002501085.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002712305.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002726655.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002724575.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002730485.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002328165.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002730555.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002725625.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002730735.mashmap.align, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.x.GCA_002731215.mashmap.align, charcoal/notebooks/report-alignment.ipynb, output.demo/stage2/TARA_PON_MAG_00084.fa.gz.matches.json, output.demo/stage2/hitlist-accessions.info.csv, output.demo/.kernel.set
output: output.demo/report/TARA_PON_MAG_00084.fa.gz.align.ipynb
jobid: 35
wildcards: g=TARA_PON_MAG_00084.fa.gz

Activating conda environment: /mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82

[Tue May 10 13:24:43 2022]
rule make_notebook_alignment:
input: output.demo/stage2/LoombaR_2017__SID1050_bax__bin.11.fa.gz.x.GCF_002159845.mashmap.align, output.demo/stage2/LoombaR_2017__SID1050_bax__bin.11.fa.gz.x.GCF_900199515.mashmap.align, output.demo/stage2/LoombaR_2017__SID1050_bax__bin.11.fa.gz.x.GCF_002160955.mashmap.align, output.demo/stage2/LoombaR_2017__SID1050_bax__bin.11.fa.gz.x.GCF_900104675.mashmap.align, output.demo/stage2/LoombaR_2017__SID1050_bax__bin.11.fa.gz.x.GCA_900066645.mashmap.align, output.demo/stage2/LoombaR_2017__SID1050_bax__bin.11.fa.gz.x.GCF_002160025.mashmap.align, output.demo/stage2/LoombaR_2017__SID1050_bax__bin.11.fa.gz.x.GCF_900142265.mashmap.align, output.demo/stage2/LoombaR_2017__SID1050_bax__bin.11.fa.gz.x.GCF_002159455.mashmap.align, charcoal/notebooks/report-alignment.ipynb, output.demo/stage2/LoombaR_2017__SID1050_bax__bin.11.fa.gz.matches.json, output.demo/stage2/hitlist-accessions.info.csv, output.demo/.kernel.set
output: output.demo/report/LoombaR_2017__SID1050_bax__bin.11.fa.gz.align.ipynb
jobid: 92
wildcards: g=LoombaR_2017__SID1050_bax__bin.11.fa.gz

Activating conda environment: /mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82
Traceback (most recent call last):
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/bin/papermill", line 10, in
sys.exit(papermill())
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/core.py", line 829, in call
Traceback (most recent call last):
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/bin/papermill", line 10, in
sys.exit(papermill())
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/core.py", line 782, in main
return self.main(*args, **kwargs)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
rv = self.invoke(ctx)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/decorators.py", line 21, in new_func
return ctx.invoke(self.callback, **ctx.params)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(*args, **kwargs)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/click/decorators.py", line 21, in new_func
return f(get_current_context(), *args, **kwargs)
return f(get_current_context(), *args, **kwargs)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/papermill/cli.py", line 267, in papermill
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/papermill/cli.py", line 267, in papermill
execution_timeout=execution_timeout,
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/papermill/execute.py", line 122, in execute_notebook
execution_timeout=execution_timeout,
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/papermill/execute.py", line 122, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
raise_for_execution_errors(nb, output_path)
File "/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/papermill/execute.py", line 234, in raise_for_execution_errors
raise error
raise error
papermill.exceptions.PapermillExecutionError:

Exception encountered at "In [3]":

ModuleNotFoundError Traceback (most recent call last)
/tmp/ipykernel_1589817/352233182.py in
----> 1 get_ipython().run_line_magic('matplotlib', 'inline')

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/IPython/core/interactiveshell.py in run_line_magic(self, magic_name, line, _stack_depth)
2415 kwargs['local_ns'] = self.get_local_scope(stack_depth)
2416 with self.builtin_trap:
-> 2417 result = fn(*args, **kwargs)
2418 return result
2419

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/decorator.py in fun(*args, **kw)
230 if not kwsyntax:
231 args, kw = fix(args, kw, sig)
--> 232 return caller(func, *(extras + args), **kw)
233 fun.name = func.name
234 fun.doc = func.doc

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/IPython/core/magic.py in (f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/IPython/core/magics/pylab.py in matplotlib(self, line)
97 print("Available matplotlib backends: %s" % backends_list)
98 else:
---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
100 self._show_matplotlib_backend(args.gui, backend)
101

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/IPython/core/interactiveshell.py in enable_matplotlib(self, gui)
3626 """
3627 from IPython.core import pylabtools as pt
-> 3628 from matplotlib_inline.backend_inline import configure_inline_support
3629 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
3630

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/matplotlib_inline/backend_inline.py in
4 # Distributed under the terms of the BSD 3-Clause License.
5
----> 6 import matplotlib
7 from matplotlib.backends.backend_agg import ( # noqa
8 new_figure_manager,

ModuleNotFoundError: No module named 'matplotlib'
papermill.exceptions.PapermillExecutionError:

Exception encountered at "In [3]":

ModuleNotFoundError Traceback (most recent call last)
/tmp/ipykernel_1589818/352233182.py in
----> 1 get_ipython().run_line_magic('matplotlib', 'inline')

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/IPython/core/interactiveshell.py in run_line_magic(self, magic_name, line, _stack_depth)
2415 kwargs['local_ns'] = self.get_local_scope(stack_depth)
2416 with self.builtin_trap:
-> 2417 result = fn(*args, **kwargs)
2418 return result
2419

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/decorator.py in fun(*args, **kw)
230 if not kwsyntax:
231 args, kw = fix(args, kw, sig)
--> 232 return caller(func, *(extras + args), **kw)
233 fun.name = func.name
234 fun.doc = func.doc

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/IPython/core/magic.py in (f, *a, **k)
185 # but it's overkill for just that one bit of state.
186 def magic_deco(arg):
--> 187 call = lambda f, *a, **k: f(*a, **k)
188
189 if callable(arg):

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/IPython/core/magics/pylab.py in matplotlib(self, line)
97 print("Available matplotlib backends: %s" % backends_list)
98 else:
---> 99 gui, backend = self.shell.enable_matplotlib(args.gui.lower() if isinstance(args.gui, str) else args.gui)
100 self._show_matplotlib_backend(args.gui, backend)
101

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/IPython/core/interactiveshell.py in enable_matplotlib(self, gui)
3626 """
3627 from IPython.core import pylabtools as pt
-> 3628 from matplotlib_inline.backend_inline import configure_inline_support
3629 gui, backend = pt.find_gui_and_backend(gui, self.pylab_gui_select)
3630

/mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82/lib/python3.7/site-packages/matplotlib_inline/backend_inline.py in
4 # Distributed under the terms of the BSD 3-Clause License.
5
----> 6 import matplotlib
7 from matplotlib.backends.backend_agg import ( # noqa
8 new_figure_manager,

ModuleNotFoundError: No module named 'matplotlib'

[Tue May 10 13:24:51 2022]
Error in rule make_notebook_alignment:
jobid: 35
[Tue May 10 13:24:51 2022]
output: output.demo/report/TARA_PON_MAG_00084.fa.gz.align.ipynb
Error in rule make_notebook_alignment:
conda-env: /mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82
jobid: 92
shell:

    papermill charcoal/notebooks/report-alignment.ipynb - -k charcoal --cwd output.demo/report               -p output_dir .. -p genome_dir ../../demo/genomes -p render ''               -p name TARA_PON_MAG_00084.fa.gz               > output.demo/report/TARA_PON_MAG_00084.fa.gz.align.ipynb

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
output: output.demo/report/LoombaR_2017__SID1050_bax__bin.11.fa.gz.align.ipynb

conda-env: /mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/conda/167a4297cb0c800d0221e17d338fae82

Removing output files of failed job make_notebook_alignment since they might be corrupted:
output.demo/report/TARA_PON_MAG_00084.fa.gz.align.ipynb
shell:

    papermill charcoal/notebooks/report-alignment.ipynb - -k charcoal --cwd output.demo/report               -p output_dir .. -p genome_dir ../../demo/genomes -p render ''               -p name LoombaR_2017__SID1050_bax__bin.11.fa.gz               > output.demo/report/LoombaR_2017__SID1050_bax__bin.11.fa.gz.align.ipynb

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job make_notebook_alignment since they might be corrupted:
output.demo/report/LoombaR_2017__SID1050_bax__bin.11.fa.gz.align.ipynb
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /mnt/DATA/git_repos/dna_qc/charcoal/.snakemake/log/2022-05-10T132439.612915.snakemake.log
Error in snakemake invocation: Command '['snakemake', '-s', '/mnt/DATA/git_repos/dna_qc/charcoal/charcoal/Snakefile', '--use-conda', '-j', '1', '-j', '4', '--configfile', '/mnt/DATA/git_repos/dna_qc/charcoal/charcoal/conf/defaults.conf', '/mnt/DATA/git_repos/dna_qc/charcoal/charcoal/conf/system.conf', 'demo/demo.conf']' returned non-zero exit status 1.

"

Gloria