Error in job simMAf : Called processor error : about 2020plus HOT 7 OPEN

Can you try the latest version of probabilistic2020 (v1.2.3)? I just uploaded and you should be able to install it via pip. I think it should fix the issue.

from 2020plus.

By uninstalling and reinstalling probabilistic2020 I found an error building wheel for probabilistic2020

from 2020plus.

Can you paste what the problem is? I do not get any installation problems on a clean python version.

from 2020plus.

Okay, after going back and installing a new instance of 2020plus with all its requirements we have tried to run the prediction again. Still an error is thrown and it seems similar to the one before:

Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 features
1 finishSim
1 og
1 predict_test
1 pretrained_predict
10 simFeatures
10 simMaf
10 simOg
10 simSummary
10 simTsg
1 summary
1 tsg
57

rule simMaf:
input: data_/test.hg19_2.txt
output: output_test/simulated_summary/chasm_sim_maf7.txt
jobid: 53
wildcards: iter=7

mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data_/test.hg19_2.txt -p 0 -n 1 --maf --seed=$((742)) -r 3 --unique -o output_test/simulated_summary/chasm_sim_maf7.txt
Traceback (most recent call last):
File "/anaconda3/envs/2020plus/bin/mut_annotate", line 6, in
from prob2020.console.annotate import cli_main
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/console/annotate.py", line 12, in
import prob2020.cython.cutils as cutils
File "prob2020/cython/cutils.pyx", line 8, in init prob2020.cython.cutils
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/scores.py", line 4, in
import prob2020.python.mymath as mymath
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/mymath.py", line 2, in
from scipy.misc import logsumexp
ImportError: cannot import name 'logsumexp'
Error in job simMaf while creating output file output_test/simulated_summary/chasm_sim_maf7.txt.
RuleException:
CalledProcessError in line 135 of /Users/josephnovak/Desktop/2020plus-master/Snakefile:
Command 'mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data_/test.hg19_2.txt -p 0 -n 1 --maf --seed=$((742)) -r 3 --unique -o output_test/simulated_summary/chasm_sim_maf7.txt' returned non-zero exit status 1.
File "/Users/josephnovak/Desktop/2020plus-master/Snakefile", line 135, in __rule_simMaf
File "/anaconda3/envs/2020plus/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message

from 2020plus.

This is an issue with scipy, which changed its api. Try a scipy version below 1.0.0.

from 2020plus.

Shouldn't the correct modules and versions be installed into the environment by using environment_python.yml? I find that version numbers of required modules are very different from those listed in the requirements_dev file. Downgrading to versions listed in the requirements file is proving to be difficult as there are many dependancies

from 2020plus.

Do not use requirements_dev. That is an old file from original development

from 2020plus.