Test Mode ValueError

[JP971]

• spladder version: 3.0.3
• Python version: 3.7.8
• Operating System: Ubuntu 20

I am trying to run Spladder on test mode with 6 sorted bam files divided into two conditions. I already ran Spladder on build mode with no significant problems, but it returns "ValueError: zero-size array to reduction operation maximum which has no identity" on test mode.

Here is my input for the build mode:
spladder build --annotation Naegleria_fowleri.gtf --filter-overlap-genes --bams files.txt --outdir spladder

Here is my input for the test mode:
spladder test --conditionA SRR12265722.sorted.bam,SRR12265723.sorted.bam,SRR12265724.sorted.bam --conditionB SRR12265725.sorted.bam,SRR12265726.sorted.bam,SRR12265727.sorted.bam --labelA Livre --labelB Parasita --outdir spladder --out-tag Round1 --parallel 4

And here is the Traceback:
Capped 1935/83124 outlier expression counts (2.33 percent)
Found dispersion fit
Found dispersion fit
Found dispersion fit
Found dispersion fit
Traceback (most recent call last):
File "/home/lenovo/miniconda3/bin/spladder", line 8, in
sys.exit(main())
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/spladder/spladder.py", line 229, in main
options.func(options)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/spladder/spladder_test.py", line 716, in spladder_test
(pvals, cov_used, disp_raw_used, disp_adj_used) = run_testing(cov, dmatrix0, dmatrix1, sf, options, event_type, test_idx)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/spladder/spladder_test.py", line 460, in run_testing
(disp_fitted, Lambda, disp_idx) = fit_dispersion(cov, disp_raw, disp_raw_conv[:, 0][:, np.newaxis], sf, options, dmatrix1, event_type)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/spladder/spladder_test.py", line 178, in fit_dispersion
modGamma = sm.GLM(disp_raw[idx], matrix, family=sm.families.Gamma(sm.families.links.identity()))
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/statsmodels/genmod/generalized_linear_model.py", line 314, in init
var_weights=var_weights, **kwargs)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/statsmodels/base/model.py", line 237, in init
super(LikelihoodModel, self).init(endog, exog, **kwargs)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/statsmodels/base/model.py", line 78, in init
**kwargs)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/statsmodels/base/model.py", line 101, in _handle_data
data = handle_data(endog, exog, missing, hasconst, **kwargs)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/statsmodels/base/data.py", line 673, in handle_data
**kwargs)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/statsmodels/base/data.py", line 87, in init
self._handle_constant(hasconst)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/statsmodels/base/data.py", line 131, in _handle_constant
exog_max = np.max(self.exog, axis=0)
File "<array_function internals>", line 6, in amax
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 2734, in amax
keepdims=keepdims, initial=initial, where=where)
File "/home/lenovo/miniconda3/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 87, in _wrapreduction
return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
ValueError: zero-size array to reduction operation maximum which has no identity

Does anyone know any solutions? I am going to upload the directory containing the output of the build mode
spladder.zip

[akahles]

Dear @JP971 ,

Thank you very much for reporting and for sharing the SplAdder output data. I will have a look and get back to you.

Best,
Andre