Where are the results printed?

[abrozzi]

Hi all,

I run

user% ./NERVE.sh -epp False -vir True -rz True -p1 UP000000625 -wd /Users/ab/Applications/NERVE/docker/nerve/workdir/ecoli -g n -m True

and got :

wrote config file /root/.config/epitopepredict/default.conf
Start NERVE 2.0
10% done
20% done
30% done
40% done
50% done
60% done
70% done
80% done
90% done
trained model: HLA-A*01:01 3074 9
trained model: HLA-A*01:01 547 10
trained model: HLA-A*02:01 9805 9
trained model: HLA-A*02:01 3806 10
trained model: HLA-A*02:01 141 11
trained model: HLA-A*03:01 4569 9
trained model: HLA-A*03:01 1515 10
trained model: HLA-A*24:02 1668 9
trained model: HLA-A*24:02 456 10
trained model: HLA-B*07:02 3178 9
trained model: HLA-B*07:02 522 10
trained model: HLA-B*44:03 570 9
trained model: HLA-B*44:03 439 10
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
predictions done for 1 sequences in 6 alleles
predictions done for 1 sequences in 8 alleles
100% done
End NERVE computation successfully.
user% 

but I don't find the results. I looked into my folder where is NERVE /Users/ab/Applications/NERVE/docker/nerve/workdir , but nothing. I also tried to set another folder by option -wd but again is empty.

Where are the results saved?

[FranceCosta]

Hi Alessandro. Sorry for the absence of documentation. This is still work in progress. If you want to have a more user-friendly interface to the results, you can visit NERVE-web. In the command line version, the results should be saved in the working directory, in your case "/Users/ab/Applications/NERVE/docker/nerve/workdir/ecoli". Is this folder empty? The filtered table containing vaccine candidates data is called "vaccine_candidates.csv" while proteins discarded because did not pass the selection tresholds are saved in "discarded_proteins.csv".

[FranceCosta]

Hi Alessandro. I was able to reproduce this behaviour and you are right, NERVE idoes not output the results if Docker is not added as user group. Try following this to do so: Docker post-installation procedure. Moreover, you should specify a relative path for the working directory. Your command would become:

user% ./NERVE.sh -epp False -vir True -rz True -p1 UP000000625 -wd ./docker/nerve/workdir/ecoli -g n -m True

I rekon this is totally not clear for a new user. We are working on the documentation.