vispr server results/*.vispr.yaml running fail

[Lai Wei]

Hi Wei,

Thank you for developing such a wonderful tool to analyze CRISPR screening results. However, I've encountered a problem when running the final visualization step using vispr server code

(mageck-vispr) Larrys-MacBook-Pro:MAGeCK_VISPR weilai$ vispr server /Users/weilai/Desktop/Hypoxia_Norm_Matrix/vispr.yaml 
Loading data.
/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/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/weilai/miniconda3/envs/mageck-vispr/bin/vispr", line 6, in <module>
    sys.exit(vispr.cli.main())
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/vispr/cli.py", line 207, in main
    init_server(*args.config, host=args.host, port=args.port)
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/vispr/cli.py", line 42, in init_server
    app.screens.add(config, parentdir=os.path.dirname(path))
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/vispr/results/__init__.py", line 29, in add
    self.screens[screen] = Screen(config, parentdir=parentdir)
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/vispr/results/__init__.py", line 76, in __init__
    get_path(config["targets"]["results"]))
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/vispr/results/__init__.py", line 147, in parse_target_results
    for condition in conditions
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/vispr/results/__init__.py", line 147, in <dictcomp>
    for condition in conditions
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/vispr/results/__init__.py", line 145, in <dictcomp>
    for selection in selections
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/vispr/results/__init__.py", line 139, in get_results
    return target.Results(res.copy(), table_filter=table_filter)
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/vispr/results/target.py", line 45, in __init__
    pval_cdf = pval_cdf.value_counts(normalize=True, sort=False, bins=1000).cumsum()
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/pandas/core/base.py", line 951, in value_counts
    normalize=normalize, bins=bins, dropna=dropna)
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/pandas/core/algorithms.py", line 365, in value_counts
    cat, bins = cut(values, bins, retbins=True)
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/site-packages/pandas/tools/tile.py", line 119, in cut
    include_lowest=include_lowest)
  File "/Users/weilai/miniconda3/envs/mageck-vispr/lib/python3.5/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.])

I tried many times but it still come out the same error. However, the vispr test works well. That means my settings are okay.

It will really appriciated if you can have look at the problem. Thank you very much.

Best, Larry

[Lai Wei]

I've figured out the problem. Don't bother to solve this. Thank you.

[Lai Wei]

Modified the config.yaml file

[Wei Li]

Thanks Larry. Do you know what causes this error?

[Lai Wei]

• In the config.yaml file cannot use

~/Desktop/data/...

as the pathway. It can only use

/home/skllr-a/Desktop/data/..

• I forgot to delet a "#" before the MAGECK MLE
• If I import the FASTQ file which uses *.fq.gz as the file type. It will report that the program can only import files with fastq.gz as extension. But actually they are the same type of files, and you can just ignore the warning and add files manually in the config.yaml file.