2020-03-23 12:51:48,871 NanoPlot 1.26.3 started with arguments Namespace(N50=False, alength=False, bam=['Vero_Infected.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='Vero_Infected_plot', path='Vero_Infected_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 12:51:48,871 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 12:51:48,873 NanoPlot:  valid output format png
2020-03-23 12:51:48,882 Nanoget: Starting to collect statistics from bam file Vero_Infected.minimap2.sorted.bam.
2020-03-23 12:51:52,179 Nanoget: No index for bam file could be found, created index.
2020-03-23 12:51:52,181 Nanoget: Bam file Vero_Infected.minimap2.sorted.bam contains 368221 mapped and 0 unmapped reads.
2020-03-23 12:51:52,181 Nanoget: lots of contigs (>100), not running in separate processes
2020-03-23 12:52:31,742 Nanoget: bam Vero_Infected.minimap2.sorted.bam contains 179874 primary alignments.
2020-03-23 12:52:33,808 Reduced DataFrame memory usage from 25.559640884399414Mb to 20.584945678710938Mb
2020-03-23 12:52:33,947 Nanoget: Gathered all metrics of 179874 reads
2020-03-23 12:52:34,058 Calculated statistics
2020-03-23 12:52:34,059 Using sequenced read lengths for plotting.
2020-03-23 12:52:34,087 Hidding 1417 reads longer than 5000bp in length plots.
2020-03-23 12:52:34,105 NanoPlot:  Valid color #4CB391.
2020-03-23 12:52:34,106 NanoPlot:  Valid colormap Greens.
2020-03-23 12:52:34,117 NanoPlot:  Creating length plots for Read length.
2020-03-23 12:52:34,118 NanoPlot:  Using 178457 reads maximum of 5000bp.
2020-03-23 12:52:37,029 Nanoplotter: orca not found, not creating static image of html. See https://github.com/plotly/orca
2020-03-23 12:52:37,029 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 12:52:38,857 Created length plots
2020-03-23 12:52:38,883 NanoPlot:  Creating Read lengths vs Average read quality plots using statistics from 178457 reads.
2020-03-23 12:52:45,327 Created LengthvsQual plot
2020-03-23 12:52:45,356 NanoPlot:  Creating Aligned read lengths vs Sequenced read length plots using statistics from 178457 reads.
2020-03-23 12:52:51,696 Created AlignedLength vs Length plot.
2020-03-23 12:52:51,696 NanoPlot:  Creating Read mapping quality vs Average basecall quality plots using statistics from 179874 reads.
2020-03-23 12:52:58,261 Created MapQvsBaseQ plot.
2020-03-23 12:52:58,289 NanoPlot:  Creating Read length vs Read mapping quality plots using statistics from 178457 reads.
2020-03-23 12:53:04,682 Created Mapping quality vs read length plot.
2020-03-23 12:53:04,685 NanoPlot:  Creating Percent identity vs Average Base Quality plots using statistics from 179874 reads.
2020-03-23 12:53:12,918 Created Percent ID vs Base quality plot.
2020-03-23 12:53:12,945 NanoPlot:  Creating Aligned read length vs Percent identity plots using statistics from 178457 reads.
2020-03-23 12:53:25,976 Nanoplotter: orca not found, not creating static image of html. See https://github.com/plotly/orca
2020-03-23 12:53:25,977 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 12:53:25,977 Created Percent ID vs Length plot
2020-03-23 12:53:25,977 Writing html report.
2020-03-23 12:53:51,809 Finished!