No static plots are saved due to some kaleido problem

[felixlee0608]

Hi, NanoPlot 1.38.0 encounter new error! how to solve it ?

running logs as below：

2021-06-15 18:51:24,384 NanoPlot 1.38.0 started with arguments Namespace(N50=True, alength=False, bam=None, barcoded=False, color='#4CB391', colormap='Greens', cram=None, downsample=None, dpi=100, drop_outliers=False, fasta=None, fastq=['/nfs1/public2/Data/Project/CC/Nanopore/fastq20200102/20191227-NPL1707-P5-PAE39885-barcode.pass.fastq.gz', '/nfs1/public2/Data/Project/CC/Nanopore/fastq20191220/20191212-NPL1536-P5-PAE20000.pass.fastq.gz'], fastq_minimal=None, fastq_rich=None, feather=None, font_scale=1, format='pdf', hide_stats=False, huge=False, info_in_report=False, legacy=None, listcolormaps=False, listcolors=False, loglength=False, maxlength=None, minlength=None, minqual=None, no_N50=False, no_supplementary=False, outdir='summary-plots-log-transformed-pass', path='summary-plots-log-transformed-pass/', percentqual=False, pickle=None, plots=['kde', 'hex', 'dot'], prefix='', raw=False, readtype='1D', runtime_until=None, store=False, summary=None, threads=40, title='Ailanthus_altissima Genome Nanopore sequencing pass data statistics', tsv_stats=False, ubam=None, verbose=False)
2021-06-15 18:51:24,385 Python version is: 3.7.10 (default, Jun 4 2021, 14:48:32) [GCC 7.5.0]
2021-06-15 18:51:24,592 Nanoget: Starting to collect statistics from plain fastq file.
2021-06-15 18:51:24,592 Nanoget: Starting to collect statistics from plain fastq file.
2021-06-15 18:51:24,597 Nanoget: Decompressing gzipped fastq /nfs1/public2/Data/Project/CC/Nanopore/fastq20191220/20191212-NPL1536-P5-PAE20000.pass.fastq.gz
2021-06-15 18:51:24,597 Nanoget: Decompressing gzipped fastq /nfs1/public2/Data/Project/CC/Nanopore/fastq20200102/20191227-NPL1707-P5-PAE39885-barcode.pass.fastq.gz
2021-06-15 19:08:07,369 Reduced DataFrame memory usage from 14.87786865234375Mb to 9.9185791015625Mb
2021-06-15 20:47:31,403 Reduced DataFrame memory usage from 100.87776947021484Mb to 67.25184631347656Mb
2021-06-15 20:47:31,987 Nanoget: Gathered all metrics of 5057441 reads
2021-06-15 20:47:36,044 Calculated statistics
2021-06-15 20:47:36,117 Using sequenced read lengths for plotting.
2021-06-15 20:47:36,449 NanoPlot: Valid color #4CB391.
2021-06-15 20:47:36,450 NanoPlot: Valid colormap Greens.
2021-06-15 20:47:37,390 NanoPlot: Creating length plots for Read length.
2021-06-15 20:47:37,398 NanoPlot: Using 5057441 reads with read length N50 of 17951bp and maximum of 229740bp.
2021-06-15 20:48:15,657 No static plots are saved due to some kaleido problem:
2021-06-15 20:48:15,660 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-15 20:48:48,769 No static plots are saved due to some kaleido problem:
2021-06-15 20:48:48,771 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-15 20:49:21,074 No static plots are saved due to some kaleido problem:
2021-06-15 20:49:21,077 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-15 20:49:53,872 No static plots are saved due to some kaleido problem:
2021-06-15 20:49:53,874 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-15 20:50:31,133 No static plots are saved due to some kaleido problem:
2021-06-15 20:50:31,136 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-15 20:50:31,176 Created length plots
2021-06-15 20:50:31,612 NanoPlot: Creating Read lengths vs Average read quality plots using statistics from 5057441 reads.
2021-06-15 20:51:08,003 No static plots are saved due to some kaleido problem:
2021-06-15 20:51:08,006 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-15 20:51:41,107 No static plots are saved due to some kaleido problem:
2021-06-15 20:51:41,110 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-15 20:51:41,173 Created LengthvsQual plot
2021-06-15 20:51:41,173 Writing html report.
2021-06-15 20:51:41,724 Finished!

Thanks！！

[felixlee0608]

kaleido-core 0.2.1 h3644ca4_0 conda-forge
python-kaleido 0.2.1 pyhd8ed1ab_0 conda-forge

[felixlee0608]

2021/06/15 20:50:34 LengthvsQualityScatterPlot_dot.pdf
2021/06/15 20:51:08 LengthvsQualityScatterPlot_kde.pdf
2021/06/15 20:48:48 Non_weightedHistogramReadlength.pdf
2021/06/15 20:49:21 Non_weightedLogTransformed_HistogramReadlength.pdf
2021/06/15 20:47:38 WeightedHistogramReadlength.pdf
2021/06/15 20:48:16 WeightedLogTransformed_HistogramReadlength.pdf
2021/06/15 20:49:59 Yield_By_Length.pdf

all pdf files are empty！

[wdecoster]

Do you have an internet connection where NanoPlot was running (on the cluster?)?

[felixlee0608]

Do you have an internet connection where NanoPlot was running (on the cluster?)?

yes,have an internet connection.
-f option set as "svg" or "png" can work!

[wdecoster]

You mean svg and png does work but pdf does not? Hmmm, that's interesting.

[felixlee0608]

You mean svg and png does work but pdf does not? Hmmm, that's interesting.

yes!

[wdecoster]

I have opened an issue in the kaleido repository to ask for help.

[hirari6319]

Dear wdecoster,

My NanoPlot job with -f png also had problems with kaleido.
I had only .html file as result.

I generated conda env. with Python3.6 and installed NanoPlot via pip.
And also installed python-kaleido via conda.

Do you have any idea fot solve this problem?

Best,

2021-06-18 13:08:23,451 NanoPlot 1.38.0 started with arguments Namespace(N50=False, alength=False, bam=None, barcoded=False, color='#4CB391', co
lormap='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, legacy=None, listcolormaps=False, listcolors=False, loglen
gth=True, maxlength=None, minlength=None, minqual=None, no_N50=False, no_supplementary=False, outdir='Ty-0_plot', path='Ty-0_plot/', percentqual
=False, pickle=None, plots=['kde', 'dot'], prefix='', raw=False, readtype='1D', runtime_until=None, store=False, summary=['sequencing_summary.tx
t'], threads=4, title=None, tsv_stats=False, ubam=None, verbose=False)
2021-06-18 13:08:23,451 Python version is: 3.6.13 | packaged by conda-forge | (default, Feb 19 2021, 05:36:01) [GCC 9.3.0]
2021-06-18 13:08:23,476 Nanoget: Collecting metrics from summary file sequencing_summary.txt for 1D sequencing
2021-06-18 13:08:23,888 Nanoget: Finished collecting statistics from summary file sequencing_summary.txt
2021-06-18 13:08:23,969 Reduced DataFrame memory usage from 10.924530029296875Mb to 5.917453765869141Mb
2021-06-18 13:08:24,034 Nanoget: Gathered all metrics of 238650 reads
2021-06-18 13:08:24,179 Calculated statistics
2021-06-18 13:08:24,180 Using sequenced read lengths for plotting.
2021-06-18 13:08:24,192 Using log10 scaled read lengths.
2021-06-18 13:08:24,207 NanoPlot: Valid color #4CB391.
2021-06-18 13:08:24,207 NanoPlot: Valid colormap Greens.
2021-06-18 13:08:24,226 NanoPlot: Creating length plots for Read length.
2021-06-18 13:08:24,226 NanoPlot: Using 238650 reads maximum of 214366bp.
2021-06-18 13:09:05,671 No static plots are saved due to some kaleido problem:
2021-06-18 13:09:05,671 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-18 13:09:45,980 No static plots are saved due to some kaleido problem:
2021-06-18 13:09:45,980 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-18 13:10:26,281 No static plots are saved due to some kaleido problem:
2021-06-18 13:10:26,281 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-18 13:11:06,601 No static plots are saved due to some kaleido problem:
2021-06-18 13:11:06,601 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-18 13:11:50,567 No static plots are saved due to some kaleido problem:
2021-06-18 13:11:50,567 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-18 13:11:50,567 Created length plots
2021-06-18 13:11:50,590 NanoPlot: Creating Read lengths vs Average read quality plots using statistics from 238650 reads.
2021-06-18 13:12:31,150 No static plots are saved due to some kaleido problem:
2021-06-18 13:12:31,150 Transform failed with error code 1: Failed to serialize document: Uncaught

///////

2021-06-18 13:23:57,979 No static plots are saved due to some kaleido problem:
2021-06-18 13:23:57,979 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-18 13:24:38,340 No static plots are saved due to some kaleido problem:
2021-06-18 13:24:38,340 Transform failed with error code 1: Failed to serialize document: Uncaught
2021-06-18 13:24:38,340 Created timeplots.
2021-06-18 13:24:38,341 Writing html report.
2021-06-18 13:24:38,378 Finished!

[wdecoster]

Do you have an internet connection where NanoPlot was running (on the cluster?)?

[hirari6319]

yes, I ran NanoPlot on analysis server of our organization with internet connection.

[hirari6319]

Dear wdecoster,

I got .png output, the problem was resolved!
In my case, I did run NanoPlot on analysis server using qsub command and shell script. This case, the internet connection while running the job seemed to be unstable.
I ran it on a managed node and it worked.
Thank you for your response.

Best,

[pclavell]

Why does Nanoplot need internet access for? I need to run it from a cluster without internet connection and I am getting this in the log

No static plots are saved due to some kaleido problem: Transform failed with error code 1: Failed to serialize document: Uncaught

[wdecoster]

That is kaleido, which converts HTML plots to static (PNG) images. You can turn that off with --no_static. I don't know what kaleido exactly does :)