RuntimeWarning: invalid value encountered in log10

[johnsolk]

Pipeline completes (.dammit.fasta is generated), but there's no gff because of error below. Looks like dependency issue in shmlast? Is there something I can do?

• gff3-merge:F_rathbuni.trinity_out.Trinity.fasta.dammit.gff3:
  • Cmd: echo "##gff-version 3.2.1" > /home/ljcohen/osmotic_damit/F_rathbuni.dammit_out/F_rathbuni.trinity_out.Trinity.fasta.dammit.gff3; cat /home/ljcohen/osmotic_damit/F_rathbuni.dammit_out/F_rathbuni.trinity_out.Trinity.fasta.transdecoder.gff3 /home/ljcohen/osmotic_damit/F_rathbuni.dammit_out/F_rathbuni.trinity_out.Trinity.fasta.x.pfam-A.gff3 /home/ljcohen/osmotic_damit/F_rathbuni.dammit_out/F_rathbuni.trinity_out.Trinity.fasta.x.OrthoDB.best.gff3 /home/ljcohen/osmotic_damit/F_rathbuni.dammit_out/F_rathbuni.trinity_out.Trinity.fasta.x.protein.fa.crbl.gff3 /home/ljcohen/osmotic_damit/F_rathbuni.dammit_out/F_rathbuni.trinity_out.Trinity.fasta.x.rfam.gff3 | sed '/^#/ d' | sort | sed '/^$/d' >> /home/ljcohen/osmotic_damit/F_rathbuni.dammit_out/F_rathbuni.trinity_out.Trinity.fasta.dammit.gff3
    /home/ljcohen/anaconda2/envs/py3.dammit/lib/python3.5/site-packages/IPython/html.py:14: ShimWarning: The IPython.html package has been deprecated. You should import from notebook instead. IPython.html.widgets has moved to ipywidgets.
    "IPython.html.widgets has moved to ipywidgets.", ShimWarning)
    /home/ljcohen/anaconda2/envs/py3.dammit/lib/python3.5/site-packages/shmlast-1.0-py3.5.egg/shmlast/crbl.py:61: RuntimeWarning: invalid value encountered in log10
    df[scaled_col_name] = -np.log10(df[scaled_col_name])

[johnsolk]

(py3.dammit) ljcohen@farm:~$ conda list
# packages in environment at /home/ljcohen/anaconda2/envs/py3.dammit:
#
alabaster                 0.7.9                     <pip>
Babel                     2.3.4                     <pip>
click                     6.7                       <pip>
cycler                    0.10.0                   py35_0  
dammit                    1.0.dev0                  <pip>
dbus                      1.10.10                       0  
decorator                 4.0.10                   py35_0  
decorator                 4.0.11                    <pip>
docutils                  0.12                      <pip>
doit                      0.29.0                    <pip>
expat                     2.1.0                         0  
ficus                     0.3.3                     <pip>
fontconfig                2.11.1                        6  
freetype                  2.5.5                         1  
glib                      2.43.0                        1  
gst-plugins-base          1.8.0                         0  
gstreamer                 1.8.0                         0  
icu                       54.1                          0  
imagesize                 0.7.1                     <pip>
ipython                   5.1.0                    py35_0  
ipython_genutils          0.1.0                    py35_0  
Jinja2                    2.8                       <pip>
jpeg                      8d                            2  
khmer                     2.0                       <pip>
libffi                    3.2.1                         0  
libgcc                    5.2.0                         0  
libgfortran               3.0.0                         1  
libpng                    1.6.22                        0  
libxcb                    1.12                          1  
libxml2                   2.9.2                         0  
MarkupSafe                0.23                      <pip>
matplotlib                1.5.1                     <pip>
matplotlib                1.5.3               np111py35_1  
mkl                       11.3.3                        0  
networkx                  1.11                      <pip>
nose                      1.3.7                     <pip>
numexpr                   2.6.1                     <pip>
numpy                     1.12.0                    <pip>
numpy                     1.11.2                   py35_0  
openssl                   1.0.2j                        0  
pandas                    0.19.2                    <pip>
pandas                    0.19.1              np111py35_0  
path.py                   8.2.1                    py35_0  
pexpect                   4.0.1                    py35_0  
pickleshare               0.7.4                    py35_0  
pip                       8.1.2                    py35_0  
pip                       9.0.1                     <pip>
prompt_toolkit            1.0.8                    py35_0  
ptyprocess                0.5.1                    py35_0  
py                        1.4.31                    <pip>
pygments                  2.1.3                    py35_0  
Pygments                  2.1.3                     <pip>
pyparsing                 2.1.10                    <pip>
pyparsing                 2.1.4                    py35_0  
pyqt                      5.6.0                    py35_0  
pytest                    3.0.3                     <pip>
python                    3.5.2                         0  
python-dateutil           2.5.3                    py35_0  
python-dateutil           2.6.0                     <pip>
pytz                      2016.10                   <pip>
pytz                      2016.7                   py35_0  
PyYAML                    3.12                      <pip>
qt                        5.6.0                         1  
rapclust                  0.1.1                     <pip>
readline                  6.2                           2  
scipy                     0.18.1              np111py35_0  
screed                    0.9                       <pip>
seaborn                   0.7.1                     <pip>
setuptools                27.2.0                   py35_0  
shmlast                   1.0                       <pip>
simplegeneric             0.8.1                    py35_1  
sip                       4.18                     py35_0  
six                       1.10.0                   py35_0  
snowballstemmer           1.2.1                     <pip>
Sphinx                    1.4.8                     <pip>
sphinx-rtd-theme          0.1.9                     <pip>
sqlite                    3.13.0                        0  
tk                        8.5.18                        0  
traitlets                 4.3.1                    py35_0  
wcwidth                   0.1.7                    py35_0  
wheel                     0.29.0                   py35_0  
xz                        5.2.2                         0  
zlib                      1.2.8                         3