Data has no positive values, and therefore cannot be log-scaled.

[lculibrk]

Dear SigProfiler developers,

I'm encountering an error in SigProfilerClusters, the message is below. I noted that there was a similar issue posted previously, however there was no information on resolving it: #30

Could you please let me know how to troubleshoot this issue?

Many thanks

  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/scripts/clusters_chunked.py", line 13, in <module>
    hp.analysis(f"{args.chunk}", "GRCh37", "96", ["96"], args.dir, analysis="all", interdistance="96", sortSims=True, subClassify=True, correction=True, calculateIMD=True, max_cpu=24, variant_caller="mutect2")
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/SigProfilerClusters/SigProfilerClusters.py", line 1306, in analysis
    regions, imds = hotspot.hotSpotAnalysis(
                    ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/SigProfilerClusters/hotspot.py", line 2328, in hotSpotAnalysis
    pp.savefig()
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/backends/backend_pdf.py", line 2745, in savefig
    figure.savefig(self, format="pdf", backend="pdf", **kwargs)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/figure.py", line 3490, in savefig
    self.canvas.print_figure(fname, **kwargs)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/backend_bases.py", line 2184, in print_figure
    result = print_method(
             ^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/backend_bases.py", line 2040, in <lambda>
    print_method = functools.wraps(meth)(lambda *args, **kwargs: meth(
                                                                 ^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/backends/backend_pdf.py", line 2786, in print_pdf
    self.figure.draw(renderer)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/artist.py", line 94, in draw_wrapper
    result = draw(artist, renderer, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/artist.py", line 71, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/figure.py", line 3257, in draw
    mimage._draw_list_compositing_images(
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/image.py", line 134, in _draw_list_compositing_images
    a.draw(renderer)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/artist.py", line 71, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 3210, in draw
    mimage._draw_list_compositing_images(
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/image.py", line 134, in _draw_list_compositing_images
    a.draw(renderer)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/artist.py", line 71, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/axis.py", line 1404, in draw
    ticks_to_draw = self._update_ticks()
                    ^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/axis.py", line 1281, in _update_ticks
    major_locs = self.get_majorticklocs()
                 ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/axis.py", line 1525, in get_majorticklocs
    return self.major.locator()
           ^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/ticker.py", line 2401, in __call__
    return self.tick_values(vmin, vmax)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/ticker.py", line 2418, in tick_values
    raise ValueError(
ValueError: Data has no positive values, and therefore cannot be log-scaled.

[MousumyCSE]

Hi @lculibrk,

Thank you for sending!

Could you please share one of your input files so that I can reproduce the issue at my end? It will be great if you can share the log files(both *.err and *.out)?

Best,
Mousumy

[lculibrk]

Hi @MousumyCSE ,

Thanks for your reply. Unfortunately the data I'm using is controlled access (Hartwig medical foundation) and I don't think I can share it. If your group has access to the Hartwig Medical Foundation data, I can provide the list of samples that was used in the failing runs - the runs were chunked into batches of 100 VCFs per batches, and the VCFs are direct copies of the HMF-provided somatic.vcf files. Most succeeded, however ~10 out of 70 of these batches failed with the provided error.

Here is the *out file:

THIS FILE CONTAINS THE METADATA ABOUT SYSTEM AND RUNTIME


-------System Info-------
Operating System Name: Linux
Nodename: cn-0057
Release: 4.18.0-477.27.1.el8_8.x86_64
Version: #1 SMP Thu Aug 31 10:29:22 EDT 2023

-------Python and Package Versions-------
Python Version: 3.11.0
SigProfilerMatrixGenerator Version: 1.3.1
SigProfilerPlotting version: 1.4.1
matplotlib version: 3.10.1
scipy version: 1.15.2
numpy version: 2.2.4

-------Vital Parameters Used for the execution -------
Project: chnk10
Genome: GRCh37
Context: ['96']
interdistance: False
input_path: cluster_chunks/chnk10/
output_type: all

-------Date and Time Data-------
Date and Clock time when the execution started: 2025-03-28 11:00:40.794917


-------Runtime Checkpoints-------

Here is the *err file:

Traceback (most recent call last):
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/scripts/clusters_chunked.py", line 13, in <module>
    hp.analysis(f"{args.chunk}", "GRCh37", "96", ["96"], args.dir, analysis="all", interdistance="96", sortSims=True, subClassify=True, correction=True, calculateIMD=True, max_cpu=12, variant_caller="mutect2")
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/SigProfilerClusters/SigProfilerClusters.py", line 1306, in analysis
    regions, imds = hotspot.hotSpotAnalysis(
                    ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/SigProfilerClusters/hotspot.py", line 2328, in hotSpotAnalysis
    pp.savefig()
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/backends/backend_pdf.py", line 2745, in savefig
    figure.savefig(self, format="pdf", backend="pdf", **kwargs)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/figure.py", line 3490, in savefig
    self.canvas.print_figure(fname, **kwargs)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/backend_bases.py", line 2184, in print_figure
    result = print_method(
             ^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/backend_bases.py", line 2040, in <lambda>
    print_method = functools.wraps(meth)(lambda *args, **kwargs: meth(
                                                                 ^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/backends/backend_pdf.py", line 2786, in print_pdf
    self.figure.draw(renderer)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/artist.py", line 94, in draw_wrapper
    result = draw(artist, renderer, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/artist.py", line 71, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/figure.py", line 3257, in draw
    mimage._draw_list_compositing_images(
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/image.py", line 134, in _draw_list_compositing_images
    a.draw(renderer)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/artist.py", line 71, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 3210, in draw
    mimage._draw_list_compositing_images(
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/image.py", line 134, in _draw_list_compositing_images
    a.draw(renderer)
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/artist.py", line 71, in draw_wrapper
    return draw(artist, renderer)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/axis.py", line 1404, in draw
    ticks_to_draw = self._update_ticks()
                    ^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/axis.py", line 1281, in _update_ticks
    major_locs = self.get_majorticklocs()
                 ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/axis.py", line 1525, in get_majorticklocs
    return self.major.locator()
           ^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/ticker.py", line 2401, in __call__
    return self.tick_values(vmin, vmax)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs/data/petljaklab/lculibrk_prj/misc/hmf_x_tx/conda_spc/lib/python3.11/site-packages/matplotlib/ticker.py", line 2418, in tick_values
    raise ValueError(
ValueError: Data has no positive values, and therefore cannot be log-scaled

[MousumyCSE]

Hi @lculibrk,

Thank you for sending and apologies for the late response.
We are currently working on the changes and will include them in our next release. We will keep you updated once the tool has been updated.

Best,
Mousumy

[MousumyCSE]

Hi @lculibrk,

We’ve implemented the necessary changes to resolve the issue. Please update your SigProfilerClusters tool to version v1.2.2.
Let us know if you encounter any further issues or need assistance.

Best,
Mousumy