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No static plots are saved due to some kaleido problem #266
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kaleido-core 0.2.1 h3644ca4_0 conda-forge |
2021/06/15 20:50:34 LengthvsQualityScatterPlot_dot.pdf all pdf files are empty! |
Do you have an internet connection where NanoPlot was running (on the cluster?)? |
yes,have an internet connection. |
You mean svg and png does work but pdf does not? Hmmm, that's interesting. |
yes! |
I have opened an issue in the kaleido repository to ask for help. |
Dear wdecoster, My NanoPlot job with -f png also had problems with kaleido. I generated conda env. with Python3.6 and installed NanoPlot via pip. 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 /////// 2021-06-18 13:23:57,979 No static plots are saved due to some kaleido problem: |
Do you have an internet connection where NanoPlot was running (on the cluster?)? |
yes, I ran NanoPlot on analysis server of our organization with internet connection. |
Dear wdecoster, I got .png output, the problem was resolved! Best, |
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
|
That is kaleido, which converts HTML plots to static (PNG) images. You can turn that off with |
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!!
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