Error at step 8 of the PROCEDURE

[hoichman]

Hi,

I was trying to run locally the procedure (mouse example). I encountered the following error at step 8:

> cnRes1<-cn_apply(expList[['normalized']], stQuery, cnProc)
119 21  
1715 21  
94 21  
141 21  
451 21  
273 21  
236 21  
2122 21  
221 21  
705 21  
985 21  
165 21  
189 21  
272 21  
955 21  
1113 21  
Error in predict.randomForest(classList[[ctt]], t(expDat[xgenes, ]), type = "prob") :  
  missing values in newdata

I noticed that expList[['normalized']] is empty. Also at step 6 the following warning had been issued multiple times:

[2021-04-06 11:57:18.354] [jointLog] [warning] Only 0 fragments were mapped, but the number of burn-in fragments was set to 5000000.  
The effective lengths have been computed using the observed mappings.

I am using conda with the following packages installed:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
boost                     1.60.0                   py35_3    conda-forge
bz2file                   0.98                       py_0    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2020.12.5            ha878542_0    conda-forge
certifi                   2018.8.24             py35_1001    conda-forge
cutadapt                  1.18                     py35_0    bioconda
icu                       56.1                          4    conda-forge
libffi                    3.2.1             he1b5a44_1007    conda-forge
libgcc                    7.2.0                h69d50b8_2    conda-forge
libgcc-ng                 9.3.0               h2828fa1_18    conda-forge
libgomp                   9.3.0               h2828fa1_18    conda-forge
libstdcxx-ng              9.3.0               h6de172a_18    conda-forge
ncurses                   6.2                  h58526e2_4    conda-forge
openssl                   1.0.2u               h516909a_0    conda-forge
parallel                  20170422             pl5.22.0_0    bioconda
perl                      5.22.0.1                      0    conda-forge
pigz                      2.6                  h27826a3_0    conda-forge
pip                       20.3.4             pyhd8ed1ab_0    conda-forge
python                    3.5.5                h5001a0f_2    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
salmon                    0.7.2               boost1.60_3    bioconda
setuptools                40.4.3                   py35_0    conda-forge
sqlite                    3.28.0               h8b20d00_0    conda-forge
tbb                       2020.2               h4bd325d_4    conda-forge
tk                        8.6.10               h21135ba_1    conda-forge
wheel                     0.36.2             pyhd3deb0d_0    conda-forge
xopen                     0.7.3                      py_0    bioconda
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h516909a_1010    conda-forge

Any help is greatly appreciated!