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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
407 stars 48 forks source link

Transform failed with error code 1: Failed to serialize document: Uncaught #313

Closed genkiguan closed 1 year ago

genkiguan commented 1 year ago

Hello! I used NanoPlot 1.40. 2 to obtain the QC plot, and it worked perfectly, but two hours later, I reran the command in the same environment, and NanoPlot encountered an error, and the process just stuck in the shell, no crash or stop. Here's the log:

2022-10-11 17:08:47,317 NanoPlot 1.40.2 started with arguments Namespace(N50=False, alength=False, bam=None, barcoded=False, color='#4CB391', colormap='Greens', cram=None, downsample=None, dpi=100, drop_outliers=False, fasta=None, fastq=['barcode15.fastq'], 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, loglength=False, maxlength=None, minlength=None, minqual=None, no_N50=False, no_static=False, no_supplementary=False, outdir='nanoplot', path='nanoplot/', percentqual=False, pickle=None, plots=['kde', 'dot'], prefix='', raw=False, readtype='1D', runtime_until=None, store=False, summary=None, threads=4, title=None, tsv_stats=False, ubam=None, verbose=False) 2022-10-11 17:08:47,318 Python version is: 3.8.10 (default, Jun 22 2022, 20:18:18) [GCC 9.4.0] 2022-10-11 17:08:47,394 Nanoget: Starting to collect statistics from plain fastq file. 2022-10-11 17:09:10,598 Reduced DataFrame memory usage from 2.8521881103515625Mb to 1.0696468353271484Mb 2022-10-11 17:09:10,622 Nanoget: Gathered all metrics of 186913 reads 2022-10-11 17:09:10,761 Calculated statistics 2022-10-11 17:09:10,762 Using sequenced read lengths for plotting. 2022-10-11 17:09:10,776 NanoPlot: Valid color #4CB391. 2022-10-11 17:09:10,776 NanoPlot: Valid colormap Greens. 2022-10-11 17:09:10,791 NanoPlot: Creating length plots for Read length. 2022-10-11 17:09:10,792 NanoPlot: Using 186913 reads maximum of 1199bp. 2022-10-11 17:09:12,346 No static plots are saved due to some kaleido problem: 2022-10-11 17:09:12,347 Transform failed with error code 1: Failed to serialize document: Uncaught

Could you tell me how to solve this problem?

wdecoster commented 1 year ago

Hi,

Similar issues have been reported before, these come from the kaleido module to convert HTML to static (e.g. PNG) files. It could be due to no internet access, a proxy or a firewall. Regardless, NanoPlot should not stop on this error, but just proceed without creating static images.

If errors persist you can try with the --no_static argument to avoid executing kaleido entirely.

genkiguan commented 1 year ago

Great! I tried with --no_static, and it worked! Thanks for your reply!