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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
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ValueError: Transform failed with error code in NanoPlot #237

Closed hwlim closed 3 years ago

hwlim commented 3 years ago

Hi

I see that this error has been reported before, but I am seeing this in my recent installation. I get the same error in running for fastq files. I also updated plotly to v4.14, and nanoplot is 1.34.1. Any suggestion to correct it?

Also, as a walkaround, is there an option to skip plotly and generate static image directly?

Thank you.

2021-03-15 19:00:06,255 Python version is: 3.6.3 (default, Dec 18 2019, 14:21:37) [GCC 4.8.5 20150623 (Red Hat 4.8.5-39)] 2021-03-15 19:00:06,257 NanoPlot: valid output format png 2021-03-15 19:00:06,290 Nanoget: Starting to collect statistics from bam file ../Minimap/align.bam. 2021-03-15 19:00:06,328 Nanoget: Bam file ../Minimap/align.bam contains 1756525 mapped and 55450 unmapped reads. 2021-03-15 19:02:57,189 Nanoget: bam ../Minimap/align.bam contains 974280 primary alignments. 2021-03-15 19:02:58,510 Reduced DataFrame memory usage from 138.44309616088867Mb to 113.35615921020508Mb 2021-03-15 19:02:59,516 Nanoget: Gathered all metrics of 974280 reads 2021-03-15 19:03:00,392 Calculated statistics 2021-03-15 19:03:00,394 Using sequenced read lengths for plotting. 2021-03-15 19:03:00,430 Using log10 scaled read lengths. 2021-03-15 19:03:00,544 NanoPlot: Valid color #4CB391. 2021-03-15 19:03:00,545 NanoPlot: Valid colormap Greens. 2021-03-15 19:03:00,600 NanoPlot: Creating length plots for Read length. 2021-03-15 19:03:00,601 NanoPlot: Using 974280 reads maximum of 107656bp. 2021-03-15 19:03:15,725 Transform failed with error code 1: Failed to serialize document: Uncaught Traceback (most recent call last): File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 105, in main plots = make_plots(datadf, settings) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 159, in make_plots title=settings["title"]) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/nanoplotter_main.py", line 328, in length_plots plots.append(dynamic_histogram(array=array, name=name, path=path, title=title, color=color)) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/nanoplotter_main.py", line 351, in dynamic_histogram dynhist.save() File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/plot.py", line 42, in save self.save_static() File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/plot.py", line 60, in save_static f.write(scope.transform(self.fig, format="png")) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/kaleido/scopes/plotly.py", line 163, in transform code=code, message=message ValueError: Transform failed with error code 1: Failed to serialize document: Uncaught

wdecoster commented 3 years ago

Are you sure this is from a recent NanoPlot version? In the log file, the first line should mention the version identifier and arguments... or did you delete that?

hwlim commented 3 years ago

Sorry for the confusion. Here is the full log and python module version list. Thank you.

2021-03-16 11:29:50,474 NanoPlot 1.34.1 started with arguments Namespace(N50=False, alength=False, bam=['../Minimap/align.bam'], barcoded=False, color='#4CB391', colormap='Greens', cram=None, downsample=None, dpi=100, drop_outliers=False, fasta=None, fastq=None, fastq_minimal=None, fastq_rich=None, feather=None, font_scale=1, format='png', hide_stats=False, huge=False, info_in_report=False, listcolormaps=False, listcolors=False, loglength=True, maxlength=None, minlength=None, minqual=None, no_N50=False, no_supplementary=False, outdir='.', path='./bam', percentqual=False, pickle=None, plots=['kde', 'dot'], prefix='bam', raw=False, readtype='1D', runtime_until=None, store=False, summary=None, threads=4, title='bam_nano_plot', tsv_stats=False, ubam=None, verbose=False) 2021-03-16 11:29:50,474 Python version is: 3.6.3 (default, Dec 18 2019, 14:21:37) [GCC 4.8.5 20150623 (Red Hat 4.8.5-39)] 2021-03-16 11:29:50,475 NanoPlot: valid output format png 2021-03-16 11:29:50,500 Nanoget: Starting to collect statistics from bam file ../Minimap/align.bam. 2021-03-16 11:29:50,582 Nanoget: Bam file ../Minimap/align.bam contains 1756525 mapped and 55450 unmapped reads. 2021-03-16 11:33:48,293 Nanoget: bam ../Minimap/align.bam contains 974280 primary alignments. 2021-03-16 11:33:50,236 Reduced DataFrame memory usage from 138.44309616088867Mb to 113.35615921020508Mb 2021-03-16 11:33:51,193 Nanoget: Gathered all metrics of 974280 reads 2021-03-16 11:33:51,918 Calculated statistics 2021-03-16 11:33:51,920 Using sequenced read lengths for plotting. 2021-03-16 11:33:51,964 Using log10 scaled read lengths. 2021-03-16 11:33:52,079 NanoPlot: Valid color #4CB391. 2021-03-16 11:33:52,079 NanoPlot: Valid colormap Greens. 2021-03-16 11:33:52,148 NanoPlot: Creating length plots for Read length. 2021-03-16 11:33:52,149 NanoPlot: Using 974280 reads maximum of 107656bp. 2021-03-16 11:34:39,581 Transform failed with error code 1: Failed to serialize document: Uncaught Traceback (most recent call last): File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 105, in main plots = make_plots(datadf, settings) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 159, in make_plots title=settings["title"]) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/nanoplotter_main.py", line 328, in length_plots plots.append(dynamic_histogram(array=array, name=name, path=path, title=title, color=color)) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/nanoplotter_main.py", line 351, in dynamic_histogram dynhist.save() File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/plot.py", line 42, in save self.save_static() File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/plot.py", line 60, in save_static f.write(scope.transform(self.fig, format="png")) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/kaleido/scopes/plotly.py", line 163, in transform code=code, message=message ValueError: Transform failed with error code 1: Failed to serialize document: Uncaught

wdecoster commented 3 years ago

Could you try again using NanoPlot v1.35.0? It's now available through pip. If you still get the same error we can fix it quite easily I think. (@iliasbukraa maybe we need another except in the save_static() method...)

hwlim commented 3 years ago

Thanks a lot. I'll try and keep you posted!

hwlim commented 3 years ago

Hi

I think I get the same error:

===================== /usr/local/python/3.6.3/lib/python3.6/site-packages/ipykernel/kernelbase.py:16: VisibleDeprecationWarning: zmq.eventloop.minitornado is deprecated in pyzmq 14.0 and will be removed. Install tornado itself to use zmq with the tornado IOLoop.

from jupyter_client.session import utcnow as now

If you read this then NanoPlot 1.35.1 has crashed :-( Please try updating NanoPlot and see if that helps...

If not, please report this issue at https://github.com/wdecoster/NanoPlot/issues If you could include the log file that would be really helpful. Thanks!

Traceback (most recent call last): File "/usr/local/python/3.6.3/bin/NanoPlot", line 11, in sys.exit(main()) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 106, in main plots = make_plots(datadf, settings) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplot/NanoPlot.py", line 163, in make_plots title=settings["title"]) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/nanoplotter_main.py", line 417, in length_plots histogram.save() File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/plot.py", line 44, in save self.save_static() File "/usr/local/python/3.6.3/lib/python3.6/site-packages/nanoplotter/plot.py", line 65, in save_static f.write(scope.transform(self.fig, format="png")) File "/usr/local/python/3.6.3/lib/python3.6/site-packages/kaleido/scopes/plotly.py", line 163, in transform code=code, message=message ValueError: Transform failed with error code 1: Failed to serialize document: Uncaught

wdecoster commented 3 years ago

Thanks for letting us know, we will look into this matter and make sure to fix it in the following days.

wdecoster commented 3 years ago

Thanks for your patience, the error should be fixed in NanoPlot v1.35.3, which is now available through pip. I cannot reproduce your error, so I can't test if it actually helps. Please let us know if you have further issues.