monarch-initiative / exomiser-phenotype-data-revised Goto Github PK

OWLTOOLS_MEMORY=80G owltools --no-logging data/original_a/hp_hp.owl --sim-save-phenodigm-class-scores -m 2.5 -x HP,HP -a data/original_a/hp_hp_phenodigm_2_5.txt

For example here.

After 12 hours this command does not move on. On a hunch, a checked that data/original_a/hp_hp.owl is coherent (no unsatisfiable classes), and it is. What other reason could there be for the process to run 12 hours +.

In the original config, 14 GB of memory was sufficient!

0. Study the README.md and all documents linked from the "Important links" section
1. Document all dependencies
2. Identify inputs and outputs of the process in a nice diagram, review with group
3. make the entire pipeline executable
4. Compare outputs of current process with the outputs of the last time Damian ran it

Currently the phenodigm score generation relies on some old datasets located in monarch-initiative/monarch-owlsim-data.

@kshefchek What should these be replaced with:

# OWLSIM DATA
MONARCH_OWLSIM_DATA=https://raw.githubusercontent.com/monarch-initiative/monarch-owlsim-data/master/data
URL_MP_G2P=$(MONARCH_OWLSIM_DATA)/Mus_musculus/Mm_gene_phenotype.txt
URL_MP_GL=$(MONARCH_OWLSIM_DATA)/Mus_musculus/Mm_gene_labels.txt
URL_HP_D2P=$(MONARCH_OWLSIM_DATA)/Homo_sapiens/Hs_disease_phenotype.txt
URL_HP_DL=$(MONARCH_OWLSIM_DATA)/Homo_sapiens/Hs_disease_labels.txt
URL_ZP_G2P=$(MONARCH_OWLSIM_DATA)/Danio_rerio/Dr_gene_phenotype.txt
URL_ZP_GL=$(MONARCH_OWLSIM_DATA)/Danio_rerio/Dr_gene_labels.txt