vispr server results error when running on test data

[Former user]

I got the following error when running MAGeCK-vispr on the test data, during the vispr server results/*.vispr.yaml step. I get the following error:

Loading data. /Users/nadia/miniconda3/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 "/Users/nadia/miniconda3/bin/vispr", line 6, in <module> sys.exit(vispr.cli.main()) File "/Users/nadia/miniconda3/lib/python3.6/site-packages/vispr/cli.py", line 207, in main init_server(*args.config, host=args.host, port=args.port) File "/Users/nadia/miniconda3/lib/python3.6/site-packages/vispr/cli.py", line 42, in init_server app.screens.add(config, parentdir=os.path.dirname(path)) File "/Users/nadia/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 29, in add self.screens[screen] = Screen(config, parentdir=parentdir) File "/Users/nadia/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 76, in init get_path(config["targets"]["results"])) File "/Users/nadia/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 147, in parse_target_results for condition in conditions File "/Users/nadia/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 147, in <dictcomp> for condition in conditions File "/Users/nadia/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 145, in <dictcomp> for selection in selections File "/Users/nadia/miniconda3/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/nadia/miniconda3/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 104, in pandas._libs.interval.Interval.richcmp TypeError: unorderable types: Interval() <= int()

[natallah]

the newer pandas is not compatible with vispr at this time. So if you run python -m pip install pandas==0.19.2

before you run vispr server results/*.vispr.yaml

it fixes the issue

[simarjot singh]

I am getting a similar error despite reverting to panda 0.19.2

Loading data. /home/simarjot/miniconda3/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/simarjot/miniconda3/bin/vispr", line 6, in <module> sys.exit(vispr.cli.main()) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/cli.py", line 207, in main init_server(*args.config, host=args.host, port=args.port) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/cli.py", line 42, in init_server app.screens.add(config, parentdir=os.path.dirname(path)) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 29, in add self.screens[screen] = Screen(config, parentdir=parentdir) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 76, in init get_path(config["targets"]["results"])) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 147, in parse_target_results for condition in conditions File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 147, in <dictcomp> for condition in conditions File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 145, in <dictcomp> for selection in selections File "/home/simarjot/miniconda3/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/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/target.py", line 45, in init pval_cdf = pval_cdf.value_counts(normalize=True, sort=False, bins=1000).cumsum() File "/home/simarjot/miniconda3/lib/python3.6/site-packages/pandas/core/base.py", line 951, in value_counts normalize=normalize, bins=bins, dropna=dropna) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/pandas/core/algorithms.py", line 365, in value_counts cat, bins = cut(values, bins, retbins=True) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/pandas/tools/tile.py", line 119, in cut include_lowest=include_lowest) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/pandas/tools/tile.py", line 194, in _bins_to_cuts raise ValueError('Bin edges must be unique: %s' % repr(bins)) ValueError: Bin edges must be unique: array([0., 0., 0., ..., 0., 0., 0.])

[qzhu2018]

I have the same issue. I reverted pandas to the old version and still get the following error: anaconda/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"]) Starting server.

Open: go to 127.0.0.1:5000 in your browser. Note: Safari and Internet Explorer are currently unsupported.

Can anyone help me with this?

[mweijer]

Same here qzhu2018. Reverted back to panda 0.19.2, still getting an error. It would be great if this issue could be resolved. Much appreciated!

[Former user]

I'm also stuck in the same place as qzhu2018!

[pierremkt]

Same here :

vispr test Loading data. /home/pierre/miniconda3/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/pierre/miniconda3/bin/vispr", line 6, in <module> sys.exit(vispr.cli.main()) File "/home/pierre/miniconda3/lib/python3.6/site-packages/vispr/cli.py", line 209, in main test_server(port=args.port, host=args.host, update=args.update) File "/home/pierre/miniconda3/lib/python3.6/site-packages/vispr/cli.py", line 80, in test_server port=port) File "/home/pierre/miniconda3/lib/python3.6/site-packages/vispr/cli.py", line 42, in init_server app.screens.add(config, parentdir=os.path.dirname(path)) File "/home/pierre/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 29, in add self.screens[screen] = Screen(config, parentdir=parentdir) File "/home/pierre/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 76, in init get_path(config["targets"]["results"])) File "/home/pierre/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 147, in parse_target_results for condition in conditions File "/home/pierre/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 147, in <dictcomp> for condition in conditions File "/home/pierre/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 145, in <dictcomp> for selection in selections File "/home/pierre/miniconda3/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/pierre/miniconda3/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 125, in pandas._libs.interval.Interval.richcmp TypeError: unorderable types: Interval() <= int()