2020-03-23 13:31:57,454 NanoPlot 1.26.3 started with arguments Namespace(N50=False, alength=False, bam=['Guppy3.1.5_Minimap2Default.minimap2.sorted.bam'], 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, font_scale=1, format='png', listcolormaps=False, listcolors=False, loglength=False, maxlength=5000, minlength=None, minqual=None, no_N50=False, outdir='Guppy3.1.5_Minimap2Default_plot', path='Guppy3.1.5_Minimap2Default_plot/', percentqual=False, pickle=None, plots=['kde', 'dot'], prefix='', raw=False, readtype='1D', runtime_until=None, store=False, summary=None, threads=8, title=None, ubam=None, verbose=False)
2020-03-23 13:31:57,454 Python version is: 3.6.3 (default, Sep 19 2019, 00:30:43)  [GCC 4.8.5 20150623 (Red Hat 4.8.5-39)]
2020-03-23 13:31:57,456 NanoPlot:  valid output format png
2020-03-23 13:31:57,468 Nanoget: Starting to collect statistics from bam file Guppy3.1.5_Minimap2Default.minimap2.sorted.bam.
2020-03-23 13:32:04,926 Nanoget: No index for bam file could be found, created index.
2020-03-23 13:32:04,927 Nanoget: Bam file Guppy3.1.5_Minimap2Default.minimap2.sorted.bam contains 874896 mapped and 0 unmapped reads.
2020-03-23 13:32:04,927 Nanoget: lots of contigs (>100), not running in separate processes
2020-03-23 13:33:36,323 Nanoget: bam Guppy3.1.5_Minimap2Default.minimap2.sorted.bam contains 423944 primary alignments.
2020-03-23 13:33:41,381 Reduced DataFrame memory usage from 60.241371154785156Mb to 47.70793151855469Mb
2020-03-23 13:33:41,713 Nanoget: Gathered all metrics of 423944 reads
2020-03-23 13:33:41,980 Calculated statistics
2020-03-23 13:33:41,982 Using sequenced read lengths for plotting.
2020-03-23 13:33:42,042 Hidding 2094 reads longer than 5000bp in length plots.
2020-03-23 13:33:42,137 NanoPlot:  Valid color #4CB391.
2020-03-23 13:33:42,138 NanoPlot:  Valid colormap Greens.
2020-03-23 13:33:42,178 NanoPlot:  Creating length plots for Read length.
2020-03-23 13:33:42,179 NanoPlot:  Using 421850 reads maximum of 5000bp.
2020-03-23 13:33:45,528 Nanoplotter: orca not found, not creating static image of html. See https://github.com/plotly/orca
2020-03-23 13:33:45,529 Image generation requires the psutil package.

Install using pip:
    $ pip install psutil

Install using conda:
    $ conda install psutil
Traceback (most recent call last):
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/nanoplotter/plot.py", line 60, in save_static
    pio.write_image(self.fig, self.path.replace('html', 'png'))
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/plotly/io/_orca.py", line 1767, in write_image
    fig, format=format, scale=scale, width=width, height=height, validate=validate
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/plotly/io/_orca.py", line 1532, in to_image
    ensure_server()
  File "/usr/local/python/versions/3.6.3/lib/python3.6/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

2020-03-23 13:33:49,460 Created length plots
2020-03-23 13:33:49,518 NanoPlot:  Creating Read lengths vs Average read quality plots using statistics from 421850 reads.
2020-03-23 13:33:58,352 Created LengthvsQual plot
2020-03-23 13:33:58,410 NanoPlot:  Creating Aligned read lengths vs Sequenced read length plots using statistics from 421850 reads.
2020-03-23 13:34:07,175 Created AlignedLength vs Length plot.
2020-03-23 13:34:07,176 NanoPlot:  Creating Read mapping quality vs Average basecall quality plots using statistics from 423944 reads.
2020-03-23 13:34:16,089 Created MapQvsBaseQ plot.
2020-03-23 13:34:16,144 NanoPlot:  Creating Read length vs Read mapping quality plots using statistics from 421850 reads.
2020-03-23 13:34:24,766 Created Mapping quality vs read length plot.
2020-03-23 13:34:24,769 NanoPlot:  Creating Percent identity vs Average Base Quality plots using statistics from 423944 reads.
2020-03-23 13:34:37,237 Created Percent ID vs Base quality plot.
2020-03-23 13:34:37,290 NanoPlot:  Creating Aligned read length vs Percent identity plots using statistics from 421850 reads.
2020-03-23 13:34:49,241 Nanoplotter: orca not found, not creating static image of html. See https://github.com/plotly/orca
2020-03-23 13:34:49,241 Image generation requires the psutil package.

Install using pip:
    $ pip install psutil

Install using conda:
    $ conda install psutil
Traceback (most recent call last):
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/nanoplotter/plot.py", line 60, in save_static
    pio.write_image(self.fig, self.path.replace('html', 'png'))
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/plotly/io/_orca.py", line 1767, in write_image
    fig, format=format, scale=scale, width=width, height=height, validate=validate
  File "/usr/local/python/versions/3.6.3/lib/python3.6/site-packages/plotly/io/_orca.py", line 1532, in to_image
    ensure_server()
  File "/usr/local/python/versions/3.6.3/lib/python3.6/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

2020-03-23 13:34:49,242 Created Percent ID vs Length plot
2020-03-23 13:34:49,242 Writing html report.
2020-03-23 13:35:22,774 Finished!