When I successfully run the treeWAS, but some Note and Warning for me.....
Reconstruction type must be 'ML' when variable is 'continuous'. Setting type to 'ML'.
Note: Updating n.snps.sim to match 10x the number of loci after data cleaning.
Input: 60950 -->
Updated: 57620
[1] "treeWAS snps sim done @ 2024-03-13 12:44:32.081081"
[1] "Reconstructions completed @ 2024-03-13 12:44:33.779422"
[1] "Started running terminal test @ 2024-03-13 12:44:33.78039"
[1] "Real data scores completed for terminal test @ 2024-03-13 12:44:33.782839"
[1] "Simulated data scores completed for terminal test @ 2024-03-13 12:44:33.795843"
[1] "Started running simultaneous test @ 2024-03-13 12:44:33.79743"
[1] "Real data scores completed for simultaneous test @ 2024-03-13 12:44:33.800595"
[1] "Simulated data scores completed for simultaneous test @ 2024-03-13 12:44:33.813231"
[1] "Started running subsequent test @ 2024-03-13 12:44:33.815669"
[1] "Real data scores completed for subsequent test @ 2024-03-13 12:44:33.822123"
[1] "Simulated data scores completed for subsequent test @ 2024-03-13 12:44:33.852223"
[1] "Finished running terminal test @ 2024-03-13 12:44:33.904884"
[1] "Finished running simultaneous test @ 2024-03-13 12:44:33.914732"
[1] "Finished running subsequent test @ 2024-03-13 12:44:33.926163"
[1] "ID of significant loci completed @ 2024-03-13 12:44:33.92651"
Warning message:
In phyDat.default(data, levels = levels, return.index = return.index, :
Found unknown characters (not supplied in levels). Deleted sites with unknown states.
When I successfully run the treeWAS, but some Note and Warning for me..... Reconstruction type must be 'ML' when variable is 'continuous'. Setting type to 'ML'. Note: Updating n.snps.sim to match 10x the number of loci after data cleaning. Input: 60950 --> Updated: 57620 [1] "treeWAS snps sim done @ 2024-03-13 12:44:32.081081" [1] "Reconstructions completed @ 2024-03-13 12:44:33.779422" [1] "Started running terminal test @ 2024-03-13 12:44:33.78039" [1] "Real data scores completed for terminal test @ 2024-03-13 12:44:33.782839" [1] "Simulated data scores completed for terminal test @ 2024-03-13 12:44:33.795843" [1] "Started running simultaneous test @ 2024-03-13 12:44:33.79743" [1] "Real data scores completed for simultaneous test @ 2024-03-13 12:44:33.800595" [1] "Simulated data scores completed for simultaneous test @ 2024-03-13 12:44:33.813231" [1] "Started running subsequent test @ 2024-03-13 12:44:33.815669" [1] "Real data scores completed for subsequent test @ 2024-03-13 12:44:33.822123" [1] "Simulated data scores completed for subsequent test @ 2024-03-13 12:44:33.852223" [1] "Finished running terminal test @ 2024-03-13 12:44:33.904884" [1] "Finished running simultaneous test @ 2024-03-13 12:44:33.914732" [1] "Finished running subsequent test @ 2024-03-13 12:44:33.926163" [1] "ID of significant loci completed @ 2024-03-13 12:44:33.92651" Warning message: In phyDat.default(data, levels = levels, return.index = return.index, : Found unknown characters (not supplied in levels). Deleted sites with unknown states.