Error in rule SimSummary: /bin/bash: mut_annotate: command not found

[yasirniazi]

Kindly help me to resolve said issue

I run following command

snakemake -s Snakefile pretrained_predict -p --cores 1 --config mutations="data/bladder.txt" output_dir="output_bladder" trained_classifier="data/2020plus_10k.Rdata"

and find the following error

/bin/bash: mut_annotate: command not found

Error in rule simSummary:
jobid: 17
output: output_bladder/simulated_summary/chasm_sim_summary1.txt
shell:
mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data/bladder.txt -p 0 -n 1 --summary --seed=$((1*42)) --score-dir=data//scores --unique -r 3 -o output_bladder/simulated_summary/chasm_sim_summary1.txt
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[ctokheim]

This indicates that command line tools from the probabilistic2020 python package could not be found in your PATH environment variable. There are two possibilities: 1) the probabilistic2020 python package is not installed or 2) it is installed but the command line tool is not found in your path.

Regarding the first point, you can check if it is installed by the following:

$ python
>>> import prob2020  # this will fail if the python package is not installed

Regarding the second point, you can check outside of snakemake whether the command mut_annotate is on your path:

$ which mut_annotate

If the command could not be found, you might want to check where the bin folder for python is located.

$ which python

If you find mut_annotate is in the same bin folder as the main python you are using, then you likely need to add that directory to your PATH environment variable.

[yasirniazi]

Thanks for replying.
I am working on 2020plus not in prob2020
and according to given tutorial 2020plus all packages install using conda but prob2020 used pip. may b this variance is the reason for the issue.
secondly
I have checked the path. the following path is set in a bash file.

>>> conda initialize >>>

!! Contents within this block are managed by 'conda init' !!

__conda_setup="$('/home/yasir/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
eval "$__conda_setup"
else
if [ -f "/home/yasir/anaconda3/etc/profile.d/conda.sh" ]; then
. "/home/yasir/anaconda3/etc/profile.d/conda.sh"
else
export PATH="/home/yasir/anaconda3/bin:$PATH"
fi
fi

and the mut_annotate is located at
(base) yasir@YasirHP:~$ which mut_annotate
/home/yasir/anaconda3/bin/mut_annotate

it means there is no path issue.

[yasirniazi]

complete command run. maybe it will more clear to understand

(2020plus) yasir@YasirHP:~/Downloads/2020plus-1.2.3$ snakemake -s Snakefile pretrained_predict -p --cores 1 --config mutations="data/bladder.txt" output_dir="output_bladder" trained_classifier="data/2020plus_10k.Rdata"
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/bladder.txt
output: output_bladder/simulated_summary/chasm_sim_maf9.txt
jobid: 53
wildcards: iter=9

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=$((942)) -r 3 --unique -o output_bladder/simulated_summary/chasm_sim_maf9.txt
/bin/bash: mut_annotate: command not found
Error in job simMaf while creating output file output_bladder/simulated_summary/chasm_sim_maf9.txt.
RuleException:
CalledProcessError in line 135 of /home/yasir/Downloads/2020plus-1.2.3/Snakefile:
Command 'mut_annotate --log-level=INFO -b data//snvboxGenes.bed -i data//snvboxGenes.fa -c 1.5 -m data/bladder.txt -p 0 -n 1 --maf --seed=$((942)) -r 3 --unique -o output_bladder/simulated_summary/chasm_sim_maf9.txt' returned non-zero exit status 127.
File "/home/yasir/Downloads/2020plus-1.2.3/Snakefile", line 135, in __rule_simMaf
File "/home/yasir/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

[ctokheim]

Maybe there is an issue because mut_annotate is in your "base" conda environment and not within the 2020plus conda environment. Could you check the bin folder for the 2020plus conda environment?

[yasirniazi]

hi,
after lots of struggle. I didn't find an appropriate solution then I decided to remake the environment. I reinstall Ubuntu and then started to make the environment. but this type of error occurs.

yasirniazi@yasirniazi:~/2020plus-1.2.3$ conda env create -f environment_python.yml
Warning: you have pip-installed dependencies in your environment file, but you do not list pip itself as one of your conda dependencies. Conda may not use the correct pip to install your packages, and they may end up in the wrong place. Please add an explicit pip dependency. I'm adding one for you, but still nagging you.

CondaValueError: prefix already exists: /home/yasirniazi/anaconda3/envs/2020plu