Dear G2P maintainer,
I would like to mention unexpected behavior, in which G2P produces no output files and no error. I suggest it should give an error.
I can successfully run the examples to simulate phenotypes as shown at https://github.com/XiaoleiLiuBio/G2P#linuxmac-3 :
cp ../data/AG.map . ; java -jar kG2P.jar --ped ../data/AG.ped --outgen my_output --rep 100 --dis geo 0.99 --h2 0.5 --nqtn 100 --QTNarea 1-500,1000-1500
Note that I copy the AG.map file from the data folder and use the AG.ped file which is present there as well. The output is clear:
Phenotype simulation
Congratulations! Simulation files are generated successfully!
Now, I do the same thing without the .ped file:
richel@N141CU:~/GitHubs/G2P/kG2P_linux_x86_64$ cp ../data/AG.map . ; java -jar kG2P.jar --outgen my_output_again --rep 100 --dis geo 0.99 --h2 0.5 --nqtn 100 --QTNarea 1-500,1000-1500
Which produces no output. I guess that that file is really important, so I expect an error message in text or as an exit code.
I check the exit code of the program:
Which returns:
Zero is the exit code if a program ends OK, so, also here, the program signals that everything went fine.
Looking at all content of the my_output_again folder ...
... shows that no files have been created:
my_output_again/
my_output_again/210510104415
So, no files, no error, no output.
I assume I should have received an error message.
I suggest that G2P gives a proper error message when it is asked to simulate phenotypes without a pedigree file, as well as have a non-zero exit code.
Dear G2P maintainer,
I would like to mention unexpected behavior, in which G2P produces no output files and no error. I suggest it should give an error.
I can successfully run the examples to simulate phenotypes as shown at https://github.com/XiaoleiLiuBio/G2P#linuxmac-3 :
Note that I copy the AG.map file from the data folder and use the AG.ped file which is present there as well. The output is clear:
Now, I do the same thing without the
.pedfile:Which produces no output. I guess that that file is really important, so I expect an error message in text or as an exit code.
I check the exit code of the program:
Which returns:
Zero is the exit code if a program ends OK, so, also here, the program signals that everything went fine.
Looking at all content of the
my_output_againfolder ...... shows that no files have been created:
So, no files, no error, no output.
I assume I should have received an error message.
I suggest that G2P gives a proper error message when it is asked to simulate phenotypes without a pedigree file, as well as have a non-zero exit code.