Question: Can't open file 'features': [Errno 2] No such file or directory
1
gravatar for David_emir
11 months ago by
David_emir380
India
David_emir380 wrote:

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.

ADD COMMENTlink modified 11 months ago by Collin860 • written 11 months ago by David_emir380
2
gravatar for Collin
11 months ago by
Collin860
United States
Collin860 wrote:

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.

ADD COMMENTlink written 11 months ago by Collin860

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.

ADD REPLYlink modified 11 months ago • written 11 months ago by David_emir380
1

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.

ADD REPLYlink written 11 months ago by Collin860

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

ADD REPLYlink written 11 months ago by David_emir380
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