Precompute not being done when both OMIM and ORPHA passed as databases

[namratasp20]

Hi Team,

When I perform precompute with debug using (-db OMIM,ORPHA), the precomputation occurs , but uses 0 world objects instead of 50 world objects, for IC calculation. Hence, precomputation afor all query terms (1 to 10) also occurs with 0 world objects

Command used :
java -jar phenomiser-cli.jar precompute
-db OMIM,ORPHA
-hpo ${path to}hp.obo
-da ${path to}phenotype.hpoa
--debug

Display on terminal during precompute step ( -db OMIM,ORPHA)

INFO - 2022-02-14 10:33:44 - Computing IC of 16290 terms using 0 labels...
INFO - 2022-02-14 10:33:44 - Computing IC is complete.
INFO - 2022-02-14 10:35:12 - Done precomputing pairwise scores. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 1 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 2 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 3 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 4 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 5 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 6 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 7 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 8 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 9 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation. INFO - 2022-02-14 10:35:12 - Running precomputation for 0 world objects using 10 query terms... Resnik precomputation done by 0% (0 of 0 done, step elapsed: 0.0 s, elapsed: 0.0 s, processing "0.0 objects/s, estimated to go: NaN s).
INFO - 2022-02-14 10:35:12 - Done running precomputation.

What could be going wrong when including paramter "-db OMIM,ORPHA" ?

[pnrobinson]

It makes no sense to precompute for both OMIM and ORPHA together because the majority of diseases are represented in both databases. Please choose either OMIM or ORPHA or just do the calculations separately!

[namratasp20]

Hi,
Thanks for the response.

I probably misunderstood -db [OMIM,ORPHA] indicating we can use both databases.

Is there any link or method by which I could check number of diseases coming from OMIM and ORPHA individually vs the diseases found in both OMIM and ORPHA

I want to understand / view the list of diseases being picked up when db is OMIM and ORPHA respectively.

**

If one would run precompute without debug, the output stored under Phenomiser_data would require how many gbs of storage space ?

Thanks