acceptance test failure in eel-pond/plot-expression.py

[mr-c]

Writing differentially expressed genes list to 0-vs-6-hour.changed.csv
Got sample spec: 5 from condition 1, 5 from condition 2
Loading differentially expressed gene names from 0-vs-6-hour.changed.csv
Loading gene matrix from 0-vs-6-hour.matrix
plotting...
Output figure to: 0-vs-6-hour.matrix.png
Traceback (most recent call last):
  File "/usr/local/share/eel-pond/plot-expression.py", line 89, in <module>
    main()
  File "/usr/local/share/eel-pond/plot-expression.py", line 86, in main
    savefig(filename)
  File "/usr/lib/pymodules/python2.7/matplotlib/pyplot.py", line 561, in savefig
    return fig.savefig(*args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 1421, in savefig
    self.canvas.print_figure(*args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 2220, in print_figure
    **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 505, in print_png
    FigureCanvasAgg.draw(self)
  File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 451, in draw
    self.figure.draw(self.renderer)
  File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 1034, in draw
    func(*args)
  File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 2086, in draw
    a.draw(renderer)
  File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/lines.py", line 530, in draw
    gc.set_foreground(ln_color_rgba)
  File "/usr/lib/pymodules/python2.7/matplotlib/backend_bases.py", line 921, in set_foreground
    self._rgb = colors.colorConverter.to_rgba(fg)
  File "/usr/lib/pymodules/python2.7/matplotlib/colors.py", line 365, in to_rgba
    'to_rgba: Invalid rgba arg "%s"\n%s' % (str(arg), exc))
ValueError: to_rgba: Invalid rgba arg "(0.0, 0.0, 1.0, '0.1')"
number in rbga sequence outside 0-1 range

root@ip-10-180-216-14:/usr/local/share/eel-pond# git status
HEAD detached at protocols-v0.8.3
root@ip-10-180-216-14:~/khmer-protocols# git status
On branch acceptance
Your branch is up-to-date with 'origin/acceptance'.
root@ip-10-180-216-14:/usr/local/share/khmer# git branch -v
* master 792a62a Merge pull request #572 from ged-lab/fix/no-asserts

[mr-c]

Same with khmer v1.1

[mr-c]

@ctb @luizirber Any ideas? I'm running it using the ancient 'beacon' AMI right now.

[ctb]

On Tue, Aug 05, 2014 at 12:16:39PM -0700, Michael R. Crusoe wrote:

@ctb @luizirber Any ideas? I'm running it using the ancient 'beacon' AMI right now.

Well, it's irrelevant to khmer itself, since it happens well after any khmer scripts. I'll fix it later.

--t

https://github.com/ged-lab/khmer-protocols/issues/129#issuecomment-51245527

C. Titus Brown, ctb@msu.edu

[mr-c]

The command

for i in [1-8]-*.txt.sh
do
   bash $i
done

Completes successfully using the ancient ami-c17ec8a8 AMI with one twist: I had to run sed -i 's/archive/old-releases/g' /etc/apt/sources.list first.

The output from assemstats3 is a bit off:

root@ip-10-231-135-216:~/khmer-protocols/mrnaseq#  /usr/local/share/khmer/sandbox/assemstats3.py 500 /mnt/work/trinity_out_dir/Trinity.fasta
** cutoff: 500
N       sum     max     filename
35      61061   4449    /mnt/work/trinity_out_dir/Trinity.fasta

Should be

** cutoff: 500
N       sum     max     filename
76      134259  4452    /mnt/work/trinity_out_dir/Trinity.fasta

according to https://github.com/ged-lab/literate-resting/tree/master/kp

The command grep "zinc transporter" /mnt/blast/trinity.x.mouse | wc -l returns 24.

[mr-c]

This is still an issue.