Image rendering bug

[chaesee1]

Description of the bug

Hello, I'm chaehwa.
I have an issue below.

$ cat .command.err
/opt/conda/lib/python3.12/site-packages/upsetplot/data.py:303: FutureWarning: Downcasting object dtype arrays on .fillna, .ffill, . bfill is deprecated and will change in a future version. Call result.infer_objects(copy=False) instead. To opt-in to the future beh avior, set pd.set_option('future.no_silent_downcasting', True)
df.fillna(False, inplace=True)
/opt/conda/lib/python3.12/site-packages/upsetplot/plotting.py:795: FutureWarning: A value is trying to be set on a copy of a DataFr ame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[co l].method(value) instead, to perform the operation inplace on the original object.

styles["linewidth"].fillna(1, inplace=True)
/opt/conda/lib/python3.12/site-packages/upsetplot/plotting.py:796: FutureWarning: A value is trying to be set on a copy of a DataFr ame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[co l].method(value) instead, to perform the operation inplace on the original object.

styles["facecolor"].fillna(self._facecolor, inplace=True)
/opt/conda/lib/python3.12/site-packages/upsetplot/plotting.py:797: FutureWarning: A value is trying to be set on a copy of a DataFr ame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[co l].method(value) instead, to perform the operation inplace on the original object.

styles["edgecolor"].fillna(styles["facecolor"], inplace=True)
/opt/conda/lib/python3.12/site-packages/upsetplot/plotting.py:798: FutureWarning: A value is trying to be set on a copy of a DataFr ame or Series through chained assignment using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because the intermediate object on which we are setting values always behaves as a copy.

For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method({col: value}, inplace=True)' or df[col] = df[co l].method(value) instead, to perform the operation inplace on the original object.

styles["linestyle"].fillna("solid", inplace=True)
Traceback (most recent call last):
File "/ess/dlstibm/home/chseo/Analysis/circrna/work/fd/0efd5b910e88633ddf7e673fa4536b/.command.sh", line 68, in
plt.savefig(plot_file)
File "/opt/conda/lib/python3.12/site-packages/matplotlib/pyplot.py", line 1228, in savefig
res = fig.savefig(*args, **kwargs) # type: ignore[func-returns-value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/matplotlib/figure.py", line 3395, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/opt/conda/lib/python3.12/site-packages/matplotlib/backend_bases.py", line 2204, in print_figure
result = print_method(
^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/matplotlib/backend_bases.py", line 2054, in
print_method = functools.wraps(meth)(lambda *args, **kwargs: meth(
^^^^^
File "/opt/conda/lib/python3.12/site-packages/matplotlib/backends/backend_agg.py", line 496, in print_png
self._print_pil(filename_or_obj, "png", pil_kwargs, metadata)
File "/opt/conda/lib/python3.12/site-packages/matplotlib/backends/backend_agg.py", line 444, in _print_pil
FigureCanvasAgg.draw(self)
File "/opt/conda/lib/python3.12/site-packages/matplotlib/backends/backend_agg.py", line 382, in draw
self.renderer = self.get_renderer()
^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/matplotlib/backends/backend_agg.py", line 397, in get_renderer
self.renderer = RendererAgg(w, h, self.figure.dpi)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/matplotlib/backends/backend_agg.py", line 70, in init
self._renderer = _RendererAgg(int(width), int(height), dpi)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: Image size of 222400x933 pixels is too large. It must be less than 2^16 in each direction.

Command used and terminal output

nextflow run nf-core/circrna -r dev -resume run1 -params-file circrna_params.json --igenomes_ignore --genome null -profile docker

$ cat circrna_params.json
{
"input": "/ess/dlstibm/home/chseo/Analysis/circrna/samplesheet.csv",
"phenotype": "/ess/dlstibm/home/chseo/Analysis/circrna/phenotype.csv",
"outdir": "/ess/dlstibm/home/chseo/Analysis/circrna/results",
"tools": "circexplorer2,find_circ,circrna_finder,dcc,segemehl",
"min_tools": 2,
"fasta": "/ess/dlstibm/home/chseo/Analysis/circrna/genome.fa",
"fasta_fai": "/ess/dlstibm/home/chseo/Analysis/circrna/genome.fa.fai",
"gtf": "/ess/dlstibm/home/chseo/Analysis/circrna/gencode.v46.primary_assembly.annotation.gtf",
"mature": "/ess/dlstibm/home/chseo/Analysis/circrna/mature.fa",
"save_reference": true
}

Relevant files

nextflow.log.log

System information

Nextflow version : 24.04.4.5917
Hardware : HPC
Executor : Slurm
Container engine: Docker
OS : Rocky Linux release 8.6 (Green Obsidian)
Version of nf-core/circrna : dev