Error in load("data/2020plus_10k.Rdata") : error reading from connection

[HengqiLiu]

Hi KarchinLab:
This error occurred when 2020plus was about to run to completion.
2020plus_10k.Rdata has already located in the /data directory. ../../2020plus/2020plus-1.2.3/data/2020plus_10k.Rdata

`[Sat Dec 11 05:30:02 2021]
rule predict_test:
input: data/2020plus_10k.Rdata, 2021.12.10_2020plus_1/features.txt, 2021.12.10_2020plus_1/simulated_summary/simulated_features.txt
output: 2021.12.10_2020plus_1/pretrained_output/results/r_random_forest_prediction.txt
jobid: 1
resources: tmpdir=/tmp

    python `which 2020plus.py` --log-level=INFO classify --trained-classifier data/2020plus_10k.Rdata --null-distribution 2021.12.10_2020plus_1/simulated_null_dist.txt --fe>
    python `which 2020plus.py` --out-dir 2021.12.10_2020plus_1/pretrained_output --log-level=INFO classify -n 200 --trained-classifier data/2020plus_10k.Rdata -d .7 -o 1.0 >

Version: 1.2.3
Command: /home/data/vip13t22/wes_cancer/biosoft/2020plus/2020plus-1.2.3//2020plus.py --log-level=INFO classify --trained-classifier data/2020plus_10k.Rdata --null-distribution >
Running Random forest . . .
Type: <class 'rpy2.rinterface.RRuntimeError'>
Exception: Error in load("data/2020plus_10k.Rdata") : error reading from connection

Traceback:
File "/home/data/vip13t22/wes_cancer/biosoft/2020plus/2020plus-1.2.3//2020plus.py", line 275, in
args.func() # run function corresponding to user's command
File "/home/data/vip13t22/wes_cancer/biosoft/2020plus/2020plus-1.2.3//2020plus.py", line 37, in _classify
src.classify.python.classifier.main(opts) # run code
File "/home/data/vip13t22/wes_cancer/biosoft/2020plus/2020plus-1.2.3/src/classify/python/classifier.py", line 184, in main
rrclf.clf.load_cv(cli_opts['trained_classifier'])
File "/home/data/vip13t22/wes_cancer/biosoft/2020plus/2020plus-1.2.3/src/classify/python/r_random_forest_clf.py", line 164, in load_cv
ro.r('load("{0}")'.format(path))
File "/home/data/vip13t22/miniconda3/envs/snakemake/lib/python3.6/site-packages/rpy2/robjects/init.py", line 321, in call
res = self.eval(p)
File "/home/data/vip13t22/miniconda3/envs/snakemake/lib/python3.6/site-packages/rpy2/robjects/functions.py", line 178, in call
return super(SignatureTranslatedFunction, self).call(*args, **kwargs)
File "/home/data/vip13t22/miniconda3/envs/snakemake/lib/python3.6/site-packages/rpy2/robjects/functions.py", line 106, in call
res = super(Function, self).call(*new_args, **new_kwargs)

---

AN ERROR HAS OCCURRED: check the log file

---

[Sat Dec 11 05:30:05 2021]
Error in rule predict_test:
jobid: 1
output: 2021.12.10_2020plus_1/pretrained_output/results/r_random_forest_prediction.txt
shell:

    python `which 2020plus.py` --log-level=INFO classify --trained-classifier data/2020plus_10k.Rdata --null-distribution 2021.12.10_2020plus_1/simulated_null_dist.txt --fe>
    python `which 2020plus.py` --out-dir 2021.12.10_2020plus_1/pretrained_output --log-level=INFO classify -n 200 --trained-classifier data/2020plus_10k.Rdata -d .7 -o 1.0 >
    
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/data/vip13t22/wes_cancer/biosoft/2020plus/2020plus-1.2.3/.snakemake/log/2021-12-10T142639.085265.snakemake.log`

[ctokheim]

This seems like it may be a path error to where the 2020plus_10k.Rdata is located, and therefore R throws an error. I suspect if you put the full path to the data directory in the config file it likely will fix your problem. Specifically, change the following line "data_dir: data/" to "data_dir: /your/full/path/data/" in "config.yaml". If you used ".." in the path for the config file, it is possible that python is reading that path correctly but R may be throwing an error (as suggested by your above error message).