Can't open file 'features': [Errno 2] No such file or directory

Question

[David_emir]

Hi All,

I am using 20/20 plus algorithms for the identification of driver mutations in my sample. while creating Simulated features I am facing an error.

rule simFeatures:
    input: output_soma_freebayes/simulated_summary/chasm_sim_summary3.txt, output_soma_freebayes/simulated_summary/oncogene_sim3.txt, output_soma_freebayes/simulated_summary/tsg_sim3.txt
    output: output_soma_freebayes/simulated_summary/simulated_features3.txt
    jobid: 11
    wildcards: iter=3

python `which 2020plus.py` features   -s output_soma_freebayes/simulated_summary/chasm_sim_summary3.txt --tsg-test output_soma_freebayes/simulated_summary/tsg_sim3.txt -og-test output_soma_freebayes/simulated_summary/oncogene_sim3.txt   -o output_soma_freebayes/simulated_summary/simulated_features3.txt
which: no 2020plus.py in (/home/ateeqanees/anaconda3/bin:/home/ateeqanees/miniconda3/envs/2020plus/bin:/home/ateeqanees/miniconda3/condabin:/home/ateeqanees/anaconda3/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/ateeqanees/.local/bin:/home/ateeqanees/bin)
***python: can't open file 'features': [Errno 2] No such file or directory***
Error in job simFeatures while creating output file output_soma_freebayes/simulated_summary/simulated_features3.txt.
RuleException:
CalledProcessError in line 202 of /home/ateeqanees/Desktop/20_20/2020plus-1.2.2/Snakefile:
Command 'python `which 2020plus.py` features   -s output_soma_freebayes/simulated_summary/chasm_sim_summary3.txt --tsg-test output_soma_freebayes/simulated_summary/tsg_sim3.txt -og-test output_soma_freebayes/simulated_summary/oncogene_sim3.txt   -o output_soma_freebayes/simulated_summary/simulated_features3.txt' returned non-zero exit status 2.
  File "/home/ateeqanees/Desktop/20_20/2020plus-1.2.2/Snakefile", line 202, in __rule_simFeatures
  File "/home/ateeqanees/miniconda3/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

I am not sure how to solve this I am referring to the Tutorial Documentation from here. Please let me know how to solve this issue.

Answer 1

[Collin]

I think the 2020plus.py scripts is not found in your current PATH. Enter something like this into your command line or .bash_rc file:

export PATH=$PATH:/path/to/2020plus

Where /path/to/2020plus is where you downloaded 2020plus on your system. If successful you should be able to type which 2020plus.py into a terminal and it will print out the correct path to the 2020plus.py script. See here for more details. Hopefully this fixes your issue.

[David_emir]

Hi Collin, Thanks a lot for the quick reply, I have added the path for 20/20+ as follows export PATH=$PATH:/home/ateeqanees/Desktop/20_20/2020plus-1.2.2 and when i say "echo $PATH" :

/home/ateeqanees/anaconda3/bin:/home/ateeqanees/miniconda3/envs/2020plus/bin:/home/ateeqanees/miniconda3/condabin:/home/ateeqanees/anaconda3/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/home/ateeqanees/.local/bin:/home/ateeqanees/bin:/home/ateeqanees/Desktop/20_20/2020plus-1.2.2/2020plus.py

Still I am have the same error. Please let me know how to solve the same. Thanks a lot for your kind help.

[Collin]

Try adding only the path to the directory (i.e. "/home/ateeqanees/Desktop/20_20/2020plus-1.2.2/") instead of the full path to the script.

[David_emir]

Thanks a lot, Collin, it is Perfectly working now! Thanks again for helping. Dave