PNG files created but blank

[safrye]

Hi,
Using the latest version 1.44.1 of NanoPlot, installed with Conda, I get a perfect HTML output of the Ploty graphs but the PNG files are blank, meaning that they are without any data. No dots shown on the LengthvsQualityScatterPlot_kde.png and only a N50 line in the other plots.
My command looks like this:

❯ NanoPlot --verbose --outdir "./test" \ --N50 --maxlength 2000 --color black --colormap Greys \ --plot kde -t "8" --format png \ --fastq ./*.fastq.gz

There are no error messages from NanoPlot.
May it be that there was a change in some supporting software?

Cheers,
Stephan

[wdecoster]

Hi Stephan,

That's odd. Note that you can still save the plotly HTML images to PNG from a web browser.
Could you share the log file?

Best,
Wouter

[safrye]

Hi Wouter,
First, sorry that I posted this under nanocomp and not under NanoPlot. Maybe you can move this thread.
Yes, I know that I can use the export from the HTML file but I use the PNG file with quality vs. length in my script that produces an HTML summary of several analyses. I could use pauvre for that plot/PNG but that program only works with single FASTQ files and the graph i not as nice and easy to look at due to the use of shaded hexagons.
Here is the output of NanoPlot with the --verbose option.

`
❯ NanoPlot --verbose --outdir "./test"
--N50 --maxlength 2000 --color black --colormap Greys
--plot kde -t "8" --format png
--fastq ./*.fastq.gz

2025-04-25 11:35:35,486 NanoPlot 1.44.1 started with arguments Namespace(threads=8, verbose=True, store=False, raw=False, huge=False, outdir='./test', no_static=False, prefix='', tsv_stats=False, only_report=False, info_in_report=False, maxlength=2000, minlength=None, drop_outliers=False, downsample=None, loglength=False, percentqual=False, alength=False, minqual=None, runtime_until=None, readtype='1D', barcoded=False, no_supplementary=False, color='black', colormap='Greys', format=['png'], plots=['kde'], legacy=None, listcolors=False, listcolormaps=False, no_N50=False, N50=True, title=None, font_scale=1, dpi=100, hide_stats=False, fastq=['./FAX37770_pass_barcode01_a207a923_a87e6f5d_5.fastq.gz'], fasta=None, fastq_rich=None, fastq_minimal=None, summary=None, bam=None, ubam=None, cram=None, pickle=None, feather=None, path='./test/')
2025-04-25 11:35:35,486 Python version is: 3.12.10 | packaged by conda-forge | (main, Apr 10 2025, 22:21:13) [GCC 13.3.0]
2025-04-25 11:35:35,492 Nanoget: Starting to collect statistics from plain fastq file.
2025-04-25 11:35:35,492 Nanoget: Decompressing gzipped fastq ./FAX37770_pass_barcode01_a207a923_a87e6f5d_5.fastq.gz
2025-04-25 11:35:35,506 Reduced DataFrame memory usage from 0.000293731689453125Mb to 0.000293731689453125Mb
2025-04-25 11:35:35,510 Nanoget: Gathered all metrics of 11 reads
2025-04-25 11:35:35,515 Calculated statistics
2025-04-25 11:35:35,515 Using sequenced read lengths for plotting.
2025-04-25 11:35:35,516 Hidding 0 reads longer than 2000bp in length plots.
2025-04-25 11:35:35,516 NanoPlot: Valid color black.
2025-04-25 11:35:35,516 NanoPlot: Valid colormap Greys.
2025-04-25 11:35:35,517 NanoPlot: Creating length plots for Read length.
2025-04-25 11:35:35,517 NanoPlot: Using 11 reads with read length N50 of 312bp and maximum of 540bp.
2025-04-25 11:35:35,905 Saved ./test/WeightedHistogramReadlength as png (or png for --legacy)
2025-04-25 11:35:36,246 Saved ./test/WeightedLogTransformed_HistogramReadlength as png (or png for --legacy)
2025-04-25 11:35:36,588 Saved ./test/Non_weightedHistogramReadlength as png (or png for --legacy)
2025-04-25 11:35:36,922 Saved ./test/Non_weightedLogTransformed_HistogramReadlength as png (or png for --legacy)
2025-04-25 11:35:36,922 NanoPlot: Creating yield by minimal length plot for Read length.
2025-04-25 11:35:37,355 Saved ./test/Yield_By_Length as png (or png for --legacy)
2025-04-25 11:35:37,355 Created length plots
2025-04-25 11:35:37,355 NanoPlot: Creating Read lengths vs Average read quality plots using 11 reads.
2025-04-25 11:35:37,702 Saved ./test/LengthvsQualityScatterPlot_kde as png (or png for --legacy)
2025-04-25 11:35:37,702 Created LengthvsQual plot
2025-04-25 11:35:37,702 Writing html report.
2025-04-25 11:35:37,706 Finished!

`
I' ll also attach the PNG files, the one from NanoPlot and the one exported from the HTML.
Cheers,
Stephan

[wdecoster]

I don't see an obvious problem in the logs, but creating static images has been a headache and often results in issues that I cannot control. If you need static images, I would suggest you open the HTML file in a browser and save the images from there.

[safrye]

Hi,
That's what I thought, too. :(
Unfortunately I would like to have the PNG files automatically produced through my script. I tested NanoPlot on another machine, newly updated with mamba, and it had the same problem. For the time being I may have to switch to pauvre.
Anyway, many thanks for your help. :)

[TimD1]

I'm encountering the same issue with blank PNG files, using bioconda::nanoplot version 1.44.1 on MacOS (running Rosetta 32-bit Intel emulation).

[safrye]

Hei,
The problem seems to be solved. I ran my script again today and NanoPlot v1.46.1 works as it used to. Unfortunately I cannot say which package update made it work as I didn't run NanoPlot in a while.

[wdecoster]

That's good to hear! Unable to explain but at least it's solved. Thanks for letting me know

[safrye]

I can send you the output of "mamba list" if you want to have a look at the version of the other installed packages.