Closed felixlee0608 closed 2 weeks ago
kaleido-core 0.2.1 h3644ca4_0 conda-forge python-kaleido 0.2.1 pyhd8ed1ab_0 conda-forge
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!
Do you have an internet connection where NanoPlot was running (on the cluster?)?
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!
You mean svg and png does work but pdf does not? Hmmm, that's interesting.
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 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
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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!
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! 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,
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
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 :)
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!!