final performance testing of vep (at merge)

averyniceday commented 4 years ago

curl submission to the 350000 variant set previous used for testing ... into vep_wrapper image via api call.

averyniceday commented 4 years ago

Testing results bad input into VEP commandline tool:

First Test (Bogus lines/string & writing to output file)

e.g BLHABA BAD STRING
Result: Bad records skipped and excluded from the output file.

Second Test (Bogus chromosome/bogus nucleotides/empty line & writing to output file)

e.g 99:1234-123456...
Result: Bad records skipped. Output file has annotatate-able records. Warning file generated with warnings such as "invalid range, record skipped".

Third Test (Bogus chromosome/bogus nucleotides/empty line & writing to STDOUT)

same result as second test

Fourth Test (Kill VEP CLT process early)

record is not suddenly cut off (possibility it cut off at end of record by chance?)

mandawilson commented 4 years ago

Deployed with kops, see Testing VEP Wrapper in Kubernetes

[ ] Modify docker image name in https://github.com/knowledgesystems/knowledgesystems-k8s-deployment/pull/58

mandawilson commented 4 years ago

RESULT: 28 minutes and 30 seconds.

vep@gn-vep-test-d45475d4c-wv5kv:~/src/ensembl-vep/input$ date; curl -X POST --header 'Content-Type: application/json' --header 'Accept: application/json' -d @- 'http://localhost:8888/vep/human/region' < ~/src/ensembl-vep/input/impact.sorted.for_vep_350000_exact.txt > impact.sorted.for_vep_350000_exact.out1.json; date
Mon Mar  9 15:02:28 UTC 2020
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 2018M    0 2009M  100 9163k  1203k   5487  0:28:30  0:28:29  0:00:01 5508k
Mon Mar  9 15:30:58 UTC 2020

genome-nexus / genome-nexus-vep

final performance testing of vep (at merge) #2