Re: Error in generating UMI count plot

[Yiming Yang]

Hi Laura,

This error usually indicates that the generated count matrix does not capture any valid feature UMI, and thus is an empty matrix. You may want to check if the feature barcode sequences you provided is correct.

Sincerely,

Yiming

On Thu, Mar 13, 2025 at 12:59 AM 'Laura Drepanos' via Cumulus Support <cumulus...@googlegroups.com> wrote:

Updated: issue resolved!

On Tue, Mar 11, 2025 at 11:11 AM Laura Drepanos <ldre...@broadinstitute.org> wrote:

Hello,

When running cellranger_workflow to apply count to feature barcode data, the pipeline seemed to run nearly to completion then failed with the following error:

Traceback (most recent call last): File "/software/cumulus_feature_barcoding-1.0.0/filter_chimeric_reads", line 57, in <module> generate_umi_count_plot(count_vec, count_threshold, argv[5] + '.umi_count.pdf') File "/software/cumulus_feature_barcoding-1.0.0/filter_chimeric_reads", line 36, in generate_umi_count_plot plt.xlim(0, min(count_vec.index.max() + 1, 50)) File "/software/python/lib/python3.11/site-packages/matplotlib/pyplot.py", line 2117, in xlim ret = ax.set_xlim(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/software/python/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 3812, in set_xlim return self.xaxis._set_lim(left, right, emit=emit, auto=auto) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/software/python/lib/python3.11/site-packages/matplotlib/axis.py", line 1217, in _set_lim v1 = self.axes._validate_converted_limits(v1, self.convert_units) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/software/python/lib/python3.11/site-packages/matplotlib/axes/_base.py", line 3733, in _validate_converted_limits raise ValueError("Axis limits cannot be NaN or Inf") ValueError: Axis limits cannot be NaN or Inf

I am not sure how to handle input on my end to ameliorate this issue (especially I have now done multiple runs with essentially the same settings that have completed successfully), so I was wondering if this issue has happened before.

Best,

Laura Drepanos

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Laura Drepanos

Computational Associate II 

Genetic Perturbation Platform R&D

Broad Institute of MIT and Harvard

300 Binney St, Office 3143-H

Cambridge, MA 02142

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