2020-09-14 08:49:48,971 NanoPlot 1.32.1 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=None, fastq_minimal=None, fastq_rich=None, feather=None, font_scale=1, format='png', hide_stats=False, huge=False, listcolormaps=False, listcolors=False, loglength=False, maxlength=None, minlength=None, minqual=None, no_N50=False, no_supplementary=False, outdir='/gscratch/scrubbed/samwhite/outputs/20200914_cbai_nanoplot_nanopore-data/ont_FAL58500_94244ffd_20102558-2729', path='/gscratch/scrubbed/samwhite/outputs/20200914_cbai_nanoplot_nanopore-data/ont_FAL58500_94244ffd_20102558-2729/', percentqual=False, pickle=None, plots=['kde', 'dot'], prefix='', raw=False, readtype='1D', runtime_until=None, store=False, summary=['/gscratch/srlab/sam/data/C_bairdi/DNAseq/ont_FAL58500_94244ffd_20102558-2729/sequencing_summary.txt'], threads=28, title=None, tsv_stats=False, ubam=None, verbose=False)
2020-09-14 08:49:48,971 Python version is: 3.7.9 (default, Aug 31 2020, 12:42:55)  [GCC 7.3.0]
2020-09-14 08:49:48,972 NanoPlot:  valid output format png
2020-09-14 08:49:48,988 Nanoget: Collecting metrics from summary file /gscratch/srlab/sam/data/C_bairdi/DNAseq/ont_FAL58500_94244ffd_20102558-2729/sequencing_summary.txt for 1D sequencing
2020-09-14 08:49:49,280 Nanoget: Finished collecting statistics from summary file /gscratch/srlab/sam/data/C_bairdi/DNAseq/ont_FAL58500_94244ffd_20102558-2729/sequencing_summary.txt
2020-09-14 08:49:49,317 Reduced DataFrame memory usage from 3.603515625Mb to 1.951904296875Mb
2020-09-14 08:49:49,368 Nanoget: Gathered all metrics of 78720 reads
2020-09-14 08:49:49,429 Calculated statistics
2020-09-14 08:49:49,430 Using sequenced read lengths for plotting.
2020-09-14 08:49:49,436 NanoPlot:  Valid color #4CB391.
2020-09-14 08:49:49,436 NanoPlot:  Valid colormap Greens.
2020-09-14 08:49:49,447 NanoPlot:  Creating length plots for Read length.
2020-09-14 08:49:49,447 NanoPlot:  Using 78720 reads with read length N50 of 1254bp and maximum of 62629bp.
2020-09-14 08:49:51,933 Nanoplotter: orca not found, not creating static image of html. See https://github.com/plotly/orca
2020-09-14 08:49:51,933 Image generation requires the psutil package.

Install using pip:
    $ pip install psutil

Install using conda:
    $ conda install psutil
Traceback (most recent call last):
  File "/gscratch/srlab/programs/anaconda3/envs/nanoplot_env/lib/python3.7/site-packages/nanoplotter/plot.py", line 60, in save_static
    pio.write_image(self.fig, self.path.replace('html', 'png'))
  File "/gscratch/srlab/programs/anaconda3/envs/nanoplot_env/lib/python3.7/site-packages/plotly/io/_kaleido.py", line 252, in write_image
    engine=engine,
  File "/gscratch/srlab/programs/anaconda3/envs/nanoplot_env/lib/python3.7/site-packages/plotly/io/_kaleido.py", line 109, in to_image
    validate=validate,
  File "/gscratch/srlab/programs/anaconda3/envs/nanoplot_env/lib/python3.7/site-packages/plotly/io/_orca.py", line 1535, in to_image
    ensure_server()
  File "/gscratch/srlab/programs/anaconda3/envs/nanoplot_env/lib/python3.7/site-packages/plotly/io/_orca.py", line 1370, in ensure_server
    """
ValueError: Image generation requires the psutil package.

Install using pip:
    $ pip install psutil

Install using conda:
    $ conda install psutil

2020-09-14 08:49:52,273 Created length plots
2020-09-14 08:49:52,280 NanoPlot:  Creating Read lengths vs Average read quality plots using statistics from 78720 reads.
2020-09-14 08:49:54,079 Created LengthvsQual plot
2020-09-14 08:49:54,079 Nanoplotter: Creating heatmap of reads per channel using 78720 reads.
2020-09-14 08:49:54,641 Created spatialheatmap for succesfull basecalls.
2020-09-14 08:49:54,662 Nanoplotter: Creating timeplots using 78720 reads.
2020-09-14 08:49:56,791 Created timeplots.
2020-09-14 08:49:56,792 Writing html report.
2020-09-14 08:50:00,184 Finished!