Error messages while running drugz

[ADvorkinGheva]

Greetings,

I am trying to run Drugz by using the example provided here (I have copied and pasted the example into a tab-delimited txt file); however, I am getting an error:

python drugz.py -i drugz_trial_unix.txt -o drugz-output.txt -c T15_A_control,T15_B_control -x T15_A_olaparib,T15_B_olaparib

INFO:main:Initiating analysis
INFO:main:Loading the read count matrix
INFO:main:Normalizing read counts
INFO:main:Calculating raw fold change for replicate 1
Traceback (most recent call last):
File "drugz.py", line 478, in
main()
File "drugz.py", line 475, in main
drugZ_analysis(args)
File "drugz.py", line 450, in drugZ_analysis
fc_zscore_id='zscore_fc_{replicate}'.format(replicate=i))
File "drugz.py", line 187, in empirical_bayes
results = fold_change.iloc[no_of_guides - (half_window_size + 1)][empirical_bayes_id]
File "/home/annadv/.local/lib/python3.6/site-packages/pandas/core/indexing.py", line 879, in getitem
return self._getitem_axis(maybe_callable, axis=axis)
File "/home/annadv/.local/lib/python3.6/site-packages/pandas/core/indexing.py", line 1496, in _getitem_axis
self._validate_integer(key, axis)
File "/home/annadv/.local/lib/python3.6/site-packages/pandas/core/indexing.py", line 1437, in _validate_integer
raise IndexError("single positional indexer is out-of-bounds")
IndexError: single positional indexer is out-of-bounds

I am attaching the input file I tried to use. I have tried both Unix(LF) and Windows(CR LF) formatting, but both led to the same errors.

I will greatly appreciate any help or advice.

Thank you very much.

Regards,
Anna
drugz_trial_unix.txt

[mcolic]

Hi Anna,

The error you are receiving is due to the --half_window_size parameter, which as default is 500. Given that in the example input file are only 9 rows (i.e. guides), the calculation of smoothed empirical Bayes estimate of std can't be calculated using that default half_window_size. Try setting the parameter to 2 or anything smaller than the number of guides in your input, and you will be able to successfully run it.

Apologies for a delay in response.
Best,
Medina