RuntimeWarning: divide by zero encountered in log10 self.df["log10-p-value"] = -np.log10(self.df["p-value"])

[Michael Apostolides]

[TB]

We encountered the same problem when running vispr server results/*ymal. Any idea?

This is our packages installed.

aioeasywebdav==2.2.0
aiohttp==3.4.4
appdirs==1.4.3
asn1crypto==0.24.0
async-timeout==3.0.0
attrs==18.2.0
backcall==0.1.0
bcrypt==3.1.4
bz2file==0.98
certifi==2018.10.15
cffi==1.11.5
chardet==3.0.4
Click==7.0
cryptography==2.3.1
cryptography-vectors==2.3.1
cutadapt==1.18
Cython==0.29
decorator==4.3.0
docutils==0.14
dropbox==5.2.1
filechunkio==1.6
Flask==1.0.2
ftputil==3.2
idna==2.7
idna-ssl==1.0.0
ipython==7.0.1
ipython-genutils==0.2.0
itsdangerous==0.24
jedi==0.13.1
Jinja2==2.10
mageck==0.5.7
mageck-vispr==0.5.3
MarkupSafe==1.0
mkl-fft==1.0.6
mkl-random==1.0.1
multidict==4.4.2
numpy==1.15.0
pandas==0.23.4
paramiko==2.4.1
parso==0.3.1
pexpect==4.6.0
pickleshare==0.7.5
prompt-toolkit==2.0.6
psutil==5.4.7
ptyprocess==0.6.0
pyasn1==0.4.4
pycparser==2.19
Pygments==2.2.0
PyNaCl==1.3.0
pysftp==0.2.9
python-dateutil==2.7.3
pytz==2018.5
PyYAML==3.13
requests==2.13.0
rpy2==2.9.4
scikit-learn==0.19.1
scipy==1.1.0
simplegeneric==0.8.1
six==1.11.0
snakemake==4.0.0
traitlets==4.3.2
tzlocal==1.5.1
urllib3==1.12
vispr==0.4.14
wcwidth==0.1.7
Werkzeug==0.14.1
wrapt==1.10.11
xopen==0.3.2
yarl==1.2.6

We used source activate mageck-vispr. We also tried different versions of numpy 1.140, 1.151. Not working. Could you please help us about this? Thanks in advance.

[Michael Apostolides]

Hi TB,

I manage to successfully run the mageck-vispr pipeline, even though this error was appearing. It doesn't seem to affect the core functionality. I don't think you need to worry about it.

Michael

[Former user]

Hi all,

just to say that I am experiencing this issue and it does affect the core functionality as the server doesn't start like in OP's case.

/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/server.py:23: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  CAPTIONS = yaml.load(f)
Loading data.
/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/cli.py:40: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
  config = yaml.load(f)
/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py:124: FutureWarning: read_table is deprecated, use read_csv instead, passing sep='\t'.
  results = pd.read_table(path, na_filter=False, low_memory=False)
/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/target.py:32: RuntimeWarning: divide by zero encountered in log10
  self.df["log10-p-value"] = -np.log10(self.df["p-value"])
Traceback (most recent call last):
  File "/home/jamie/miniconda3/envs/mageck-vispr/bin/vispr", line 6, in <module>
    sys.exit(vispr.cli.main())
  File "/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/cli.py", line 207, in main
    init_server(*args.config, host=args.host, port=args.port)
  File "/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/cli.py", line 42, in init_server
    app.screens.add(config, parentdir=os.path.dirname(path))
  File "/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 29, in add
    self.screens[screen] = Screen(config, parentdir=parentdir)
  File "/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 76, in __init__
    get_path(config["targets"]["results"]))
  File "/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 147, in parse_target_results
    for condition in conditions
  File "/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 147, in <dictcomp>
    for condition in conditions
  File "/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 145, in <dictcomp>
    for selection in selections
  File "/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 139, in get_results
    return target.Results(res.copy(), table_filter=table_filter)
  File "/home/jamie/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/target.py", line 46, in __init__
    pval_cdf.index = np.maximum(0, pval_cdf.index)
  File "pandas/_libs/interval.pyx", line 301, in pandas._libs.interval.Interval.__richcmp__
TypeError: unorderable types: Interval() <= int()

[briana prager]

Downgrading to pandas version 0.19.2 allowed me to run despite this warning. The server didn’t start with recent versions of pandas.

[YANG QIYUAN]

Hi, all,

I have same problem, even downgrading to pandas version 0.19.2 can not solve, does any one finally find a way? @briana prager @Michael Apostolides @{5a32641d1171c83e46983da0}

---

Successfully installed numpy-1.17.0 pandas-0.19.2 python-dateutil-2.8.0 pytz-2019.2

(base) QIYUANs-MBP:~ qiyuanyang$ source activate mageck-vispr

(mageck-vispr) QIYUANs-MBP:~ qiyuanyang$ cd /Users/qiyuanyang/Document/190509\ Yang-crisper

(mageck-vispr) QIYUANs-MBP:190509 Yang-crisper qiyuanyang$ vispr server results/*.vispr.yaml

/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/server.py:23: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.

CAPTIONS = yaml.load(f)

Loading data.

/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/cli.py:40: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.

config = yaml.load(f)

/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/pandas/core/series.py:853: RuntimeWarning: divide by zero encountered in log10

result = getattr(ufunc, method)(*inputs, **kwargs)

Traceback (most recent call last):

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/bin/vispr", line 6, in <module>

sys.exit(vispr.cli.main())

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/cli.py", line 207, in main

init_server(*args.config, host=args.host, port=args.port)

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/cli.py", line 42, in init_server

app.screens.add(config, parentdir=os.path.dirname(path))

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 29, in add

self.screens[screen] = Screen(config, parentdir=parentdir)

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 76, in __init__

get_path(config["targets"]["results"]))

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 147, in parse_target_results

for condition in conditions

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 147, in <dictcomp>

for condition in conditions

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 145, in <dictcomp>

for selection in selections

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/__init__.py", line 139, in get_results

return target.Results(res.copy(), table_filter=table_filter)

File "/Users/qiyuanyang/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/results/target.py", line 46, in __init__

pval_cdf.index = np.maximum(0, pval_cdf.index)

File "pandas/_libs/interval.pyx", line 358, in pandas._libs.interval.Interval.__richcmp__

TypeError: unorderable types: Interval() <= int()

[briana prager]

Odd - it looks like it’s still a pandas error. Maybe double check the version of pandas that is being used in your mageck-vispr environment? It looks like you updated outside of if in base.

[YANG QIYUAN]

Hi, Briana prager, appreciate your reply. I only checked the version of pandas in my computer is 0.19.2, but don’t know how to check specifically in my mageck-vispr environment. I tried but seems doesn’t work. I may try to test other pandas versions. @briana prager

[Jian Song]

Thank you guys for your reply so quickly! Apparently I resolved the problem by reinstall it - ‘conda install --channel bioconda vispr’