ctokheim
commented
5 years ago 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.
Open orochimarupap opened 5 years ago
ctokheim
commented
5 years ago 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.
orochimarupap
commented
5 years ago By uninstalling and reinstalling probabilistic2020 I found an error building wheel for probabilistic2020
ctokheim
commented
5 years ago Can you paste what the problem is? I do not get any installation problems on a clean python version.
orochimarupap
commented
4 years ago 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
mutannotate --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
ctokheim
commented
4 years ago This is an issue with scipy, which changed its api. Try a scipy version below 1.0.0.
orochimarupap
commented
4 years ago 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
ctokheim
commented
4 years ago Do not use requirements_dev. That is an old file from original development
We've gotten through the quick start and have trained our classifier. Now, while trying to run 2020plus an error is thrown, goes as follows:
Command: /anaconda3/envs/2020plus/bin/mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data/bladder.txt -p 0 -n 1 --maf --seed=378 -r 3 --unique -o output_bladder/simulated_summary/chasm_sim_maf9.txt There were 832 indels identified. Kept 33771 mutations after droping mutations with missing information (Droped: 0) Dropped 832 mutations after only keeping Missense_Mutation, Silent, Nonsense_Mutation, Splice_Site, Nonstop_Mutation, Translation_Start_Site. Indels are processed separately. Dropped 182 mutations after only keeping valid SNVs Dropped 0 mutations when removing duplicates Working on chromosome: chr1 . . . 'N' Traceback (most recent call last): File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/utils.py", line 131, in wrapper result = f(*args, *kwds) File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/console/annotate.py", line 209, in singleprocess_permutation drop_silent=opts['drop_silent']) File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/permutation.py", line 732, in maf_permutation num_permutations) File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/sequence_context.py", line 226, in random_pos pos_array = self.random_context_pos(n, num_permutations, contxt) File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/sequence_context.py", line 204, in random_context_pos random_pos = self.prng_dict[context].choice(available_pos, (num_permutations, num)) KeyError: 'N' Traceback (most recent call last): File "/anaconda3/envs/2020plus/bin/mut_annotate", line 10, in
sys.exit(cli_main())
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/console/annotate.py", line 432, in cli_main
main(opts)
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/console/annotate.py", line 417, in main
multiprocess_permutation(bed_dict, mut_df, opts, indel_df)
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/console/annotate.py", line 136, in multiprocess_permutation
chrom_results = singleprocess_permutation(info)
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/utils.py", line 131, in wrapper
result = f( args, *kwds)
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/console/annotate.py", line 209, in singleprocess_permutation
drop_silent=opts['drop_silent'])
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/permutation.py", line 732, in maf_permutation
num_permutations)
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/sequence_context.py", line 226, in random_pos
pos_array = self.random_context_pos(n, num_permutations, contxt)
File "/anaconda3/envs/2020plus/lib/python3.6/site-packages/prob2020/python/sequence_context.py", line 204, in random_context_pos
random_pos = self.prng_dict[context].choice(available_pos, (num_permutations, num))
KeyError: 'N'
Error in job simMaf while creating output file output_bladder/simulated_summary/chasm_sim_maf9.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/bladder.txt -p 0 -n 1 --maf --seed=$((942)) -r 3 --unique -o output_bladder/simulated_summary/chasm_sim_maf9.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
Removing output files of failed job simMaf since they might be corrupted:
output_bladder/simulated_summary/chasm_sim_maf9.txt
Will exit after finishing currently running jobs.