Closed hsatosd closed 1 year ago
wdecoster
commented
2 years ago Hi,
That's odd! Can you show me the log file?
FYI, you also have a typo in the code for the first example in example usage. "Nanoplot" is missing a capital P.
Fixed, thanks!
Wouter
hsatosd
commented
2 years ago (base) ubuntu@ip-172-31-5-240:~/ont6/guppy$ NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed --verbose 2021-09-22 18:57:31,907 NanoPlot 1.38.1 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=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, loglength=True, maxlength=None, minlength=None, minqual=None, no_N50=False, no_supplementary=False, outdir='summary-plots-log-transformed', path='summary-plots-log-transformed/', percentqual=False, pickle=None, plots=['kde', 'dot'], prefix='', raw=False, readtype='1D', runtime_until=None, store=False, summary=['sequencing_summary.txt'], threads=4, title=None, tsv_stats=False, ubam=None, verbose=True) 2021-09-22 18:57:31,907 Python version is: 3.8.8 (default, Apr 13 2021, 19:58:26) [GCC 7.3.0] 2021-09-22 18:57:31,916 Nanoget: Collecting metrics from summary file sequencing_summary.txt for 1D sequencing 2021-09-22 18:57:36,934 Nanoget: Finished collecting statistics from summary file sequencing_summary.txt 2021-09-22 18:57:36,939 NumExpr defaulting to 4 threads. 2021-09-22 18:57:37,334 Reduced DataFrame memory usage from 103.43540954589844Mb to 56.02751350402832Mb 2021-09-22 18:57:37,789 Nanoget: Gathered all metrics of 2259581 reads 2021-09-22 18:57:38,913 NumExpr defaulting to 4 threads. 2021-09-22 18:57:39,021 Calculated statistics 2021-09-22 18:57:39,022 Using sequenced read lengths for plotting. 2021-09-22 18:57:39,053 Using log10 scaled read lengths. 2021-09-22 18:57:39,185 NanoPlot: Valid color #4CB391. 2021-09-22 18:57:39,186 NanoPlot: Valid colormap Greens. 2021-09-22 18:57:39,315 NanoPlot: Creating length plots for Read length. 2021-09-22 18:57:39,318 NanoPlot: Using 2259581 reads maximum of 473692bp. 2021-09-22 18:57:40,430 Saved summary-plots-log-transformed/WeightedHistogramReadlength as png (or png for --legacy) 2021-09-22 18:57:41,310 Saved summary-plots-log-transformed/WeightedLogTransformed_HistogramReadlength as png (or png for --legacy) 2021-09-22 18:57:42,202 Saved summary-plots-log-transformed/Non_weightedHistogramReadlength as png (or png for --legacy) 2021-09-22 18:57:43,042 Saved summary-plots-log-transformed/Non_weightedLogTransformed_HistogramReadlength as png (or png for --legacy) 2021-09-22 18:57:44,367 Saved summary-plots-log-transformed/Yield_By_Length as png (or png for --legacy) 2021-09-22 18:57:44,368 Created length plots 2021-09-22 18:57:44,527 NanoPlot: Creating Read lengths vs Average read quality plots using statistics from 2259581 reads. 2021-09-22 18:57:46,232 Saved summary-plots-log-transformed/LengthvsQualityScatterPlot_dot as png (or png for --legacy) 2021-09-22 18:57:48,223 Saved summary-plots-log-transformed/LengthvsQualityScatterPlot_kde as png (or png for --legacy) 2021-09-22 18:57:48,388 NanoPlot: Creating Read lengths vs Average read quality plots using statistics from 2259581 reads. 2021-09-22 18:57:50,179 Saved summary-plots-log-transformed/LengthvsQualityScatterPlot_loglength_dot as png (or png for --legacy) 2021-09-22 18:57:52,811 Saved summary-plots-log-transformed/LengthvsQualityScatterPlot_loglength_kde as png (or png for --legacy) 2021-09-22 18:57:52,815 Created LengthvsQual plot 2021-09-22 18:57:52,816 Nanoplotter: Creating heatmap of reads per channel using 2259581 reads. 2021-09-22 18:57:53,522 Saved summary-plots-log-transformed/ActivityMap_ReadsPerChannel as png (or png for --legacy) 2021-09-22 18:57:53,523 Created spatialheatmap for succesfull basecalls. 2021-09-22 18:57:53,523 Nanoplotter: Creating timeplots using 2259581 (full) or 10000 (subsampled dataset) reads. 2021-09-22 18:57:54,861 Saved summary-plots-log-transformed/CumulativeYieldPlot_Gigabases as png (or png for --legacy) 2021-09-22 18:57:55,651 Saved summary-plots-log-transformed/CumulativeYieldPlot_NumberOfReads as png (or png for --legacy) 2021-09-22 18:57:56,498 Saved summary-plots-log-transformed/NumberOfReads_Over_Time as png (or png for --legacy) 2021-09-22 18:57:57,615 Saved summary-plots-log-transformed/ActivePores_Over_Time as png (or png for --legacy) 2021-09-22 18:57:58,597 Saved summary-plots-log-transformed/TimeLengthViolinPlot as png (or png for --legacy) 2021-09-22 18:57:59,404 Saved summary-plots-log-transformed/TimeQualityViolinPlot as png (or png for --legacy) 2021-09-22 18:58:00,202 Saved summary-plots-log-transformed/TimeSequencingSpeed_ViolinPlot as png (or png for --legacy) 2021-09-22 18:58:00,204 Nanoplotter: Creating timeplots using 2259581 (full) or 10000 (subsampled dataset) reads. 2021-09-22 18:58:01,371 Saved summary-plots-log-transformed/CumulativeYieldPlot_Gigabases as png (or png for --legacy) 2021-09-22 18:58:02,160 Saved summary-plots-log-transformed/CumulativeYieldPlot_NumberOfReads as png (or png for --legacy) 2021-09-22 18:58:03,226 Saved summary-plots-log-transformed/NumberOfReads_Over_Time as png (or png for --legacy) 2021-09-22 18:58:04,377 Saved summary-plots-log-transformed/ActivePores_Over_Time as png (or png for --legacy) 2021-09-22 18:58:05,224 Saved summary-plots-log-transformed/TimeLogLengthViolinPlot as png (or png for --legacy) 2021-09-22 18:58:06,042 Saved summary-plots-log-transformed/TimeQualityViolinPlot as png (or png for --legacy) 2021-09-22 18:58:06,844 Saved summary-plots-log-transformed/TimeSequencingSpeed_ViolinPlot as png (or png for --legacy) 2021-09-22 18:58:06,846 Created timeplots. 2021-09-22 18:58:06,847 Writing html report. 2021-09-22 18:58:06,869 Finished!
Hi,
My input was the sequencing_summary.txt file from guppy. I was able to generate all of the plots except for the cumulative yield plots and the active pores plot. Any suggestions on how to fix this?
I used the code below:
NanoPlot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformedFYI, you also have a typo in the code for the first example in example usage. "Nanoplot" is missing a capital P.
Thanks!