I am running Achilles from R using:
DatabaseConnector JDBC drivers downloaded to ‘/application/jdbcDrivers’.
connectionDetails ← createConnectionDetails(
- dbms=“postgresql”,
- server=“hsc-ctsc-achilles.health.unm.edu/truven”,
- user=“achuser”,
- password=‘s0mepassord’,
- port=“5432”)
achilles(connectionDetails,
- cdmDatabaseSchema = “mdcr2003_2016”,
- resultsDatabaseSchema = “atlas_results”,
- scratchDatabaseSchema = “achilles_scratch”,
- vocabDatabaseSchema = “mdcr2003_2016”,
- numThreads = 1,
- sourceName = “AchilesAtlas”,
- cdmVersion = “5.0.1”,
- runHeel = FALSE,
- runCostAnalysis = FALSE,
- tempAchillesPrefix = ‘ta’,
- optimizeAtlasCache = TRUE,
- createIndices = TRUE)
Connecting using PostgreSQL driver
2021-10-11 21:55:13 Beginning single-threaded execution
Connecting using PostgreSQL driver
And I am getting messages like:
|======================================================================| 100%
Executing SQL took 9.99 mins
2021-10-13 19:21:13 [Main Analysis] [COMPLETE] 603 (9.990297 mins)
2021-10-13 19:21:13 Analysis 604 (Number of persons with at least one procedure occurrence, by procedure_concept_id by calendar year by gender by age decile) – START
|======================================================================| 100%
Executing SQL took 6.59 hours
2021-10-14 01:56:50 [Main Analysis] [COMPLETE] 604 (6.593505 hours)
2021-10-14 01:56:50 Analysis 605 (Number of procedure occurrence records, by procedure_concept_id by procedure_type_concept_id) – START
|======================================================================| 100%
Executing SQL took 2.55 hours
2021-10-14 04:29:37 [Main Analysis] [COMPLETE] 605 (2.546464 hours)
2021-10-14 04:29:37 Analysis 606 (Distribution of age by procedure_concept_id) – START
|======================================================================| 100%
Executing SQL took 45.5 mins
2021-10-14 05:15:06 [Main Analysis] [COMPLETE] 606 (45.475603 mins)
2021-10-14 05:15:06 Analysis 609 (Number of procedure occurrence records with invalid person_id) – START
|======================================================================| 100%
Executing SQL took 8.57 mins
2021-10-14 05:23:40 [Main Analysis] [COMPLETE] 609 (8.570902 mins)
2021-10-14 05:23:40 Analysis 610 (Number of procedure occurrence records outside valid observation period) – START
|======================================================================| 100%
Executing SQL took 6.67 mins
2021-10-14 05:30:20 [Main Analysis] [COMPLETE] 610 (6.665055 mins)
2021-10-14 05:30:20 Analysis 612 (Number of procedure occurrence records with invalid provider_id) – START
|======================================================================| 100%
Executing SQL took 4.66 mins
2021-10-14 05:34:59 [Main Analysis] [COMPLETE] 612 (4.655296 mins)
2021-10-14 05:34:59 Analysis 613 (Number of procedure occurrence records with invalid visit_id) – START
|======================================================================| 100%
Executing SQL took 1.72 hours
2021-10-14 07:18:29 [Main Analysis] [COMPLETE] 613 (1.724967 hours)
2021-10-14 07:18:29 Analysis 620 (Number of procedure occurrence records by procedure occurrence start month) – START
|======================================================================| 100%
Executing SQL took 13.8 mins
2021-10-14 07:32:16 [Main Analysis] [COMPLETE] 620 (13.781878 mins)
2021-10-14 07:32:16 Analysis 625 (Number of procedure_occurrence records by procedure_source_concept_id) – START
|======================================================================| 100%
Executing SQL took 9.97 mins
2021-10-14 07:42:15 [Main Analysis] [COMPLETE] 625 (9.974973 mins)
2021-10-14 07:42:15 Analysis 630 (Number of procedure_occurrence records inside a valid observation period) – START
|======================================================================| 100%
Executing SQL took 7.85 mins
2021-10-14 07:50:06 [Main Analysis] [COMPLETE] 630 (7.854032 mins)
2021-10-14 07:50:06 Analysis 631 (Proportion of people with at least one procedure_occurrence record outside a valid observation period) – START
|======================================================================| 100%
Executing SQL took 29.6 mins
2021-10-14 08:19:39 [Main Analysis] [COMPLETE] 631 (29.558354 mins)
2021-10-14 08:19:39 Analysis 632 (Proportion of procedure_occurrence records outside a valid observation period) – START
|======================================================================| 100%
Executing SQL took 8.85 mins
2021-10-14 08:28:31 [Main Analysis] [COMPLETE] 632 (8.852741 mins)
2021-10-14 08:28:31 Analysis 691 (Percentage of total persons that have at least x procedures) – START
|======================================================================| 100%
Executing SQL took 25.1 mins
2021-10-14 08:53:37 [Main Analysis] [COMPLETE] 691 (25.101722 mins)
2021-10-14 08:53:37 Analysis 700 (Number of persons with at least one drug exposure, by drug_concept_id) – START
|======================================================================| 100%
Executing SQL took 2.25 hours
2021-10-14 11:08:22 [Main Analysis] [COMPLETE] 700 (2.246009 hours)
2021-10-14 11:08:22 Analysis 701 (Number of drug exposure records, by drug_concept_id) – START
|======================================================================| 100%
Executing SQL took 9.11 mins
2021-10-14 11:17:29 [Main Analysis] [COMPLETE] 701 (9.113189 mins)
2021-10-14 11:17:29 Analysis 702 (Number of persons by drug exposure start month, by drug_concept_id) – START
|======================================================================| 100%
Executing SQL took 3.56 hours
2021-10-14 14:50:56 [Main Analysis] [COMPLETE] 702 (3.557406 hours)
2021-10-14 14:50:56 Analysis 703 (Number of distinct drug exposure concepts per person) – START
|======================================================================| 100%
Executing SQL took 9.32 mins
2021-10-14 15:00:15 [Main Analysis] [COMPLETE] 703 (9.321584 mins)
2021-10-14 15:00:15 Analysis 704 (Number of persons with at least one drug exposure, by drug_concept_id by calendar year by gender by age decile) – START
| | 0%
Of all these results, which ones will be useful for Atlas?
Is there a way to tell Achilles to get only those results important for Atlas? If so, which ones should I get?
Thanks