umap full run

Author: quentinblampey

novae_benchmark/pan_tissue_umap.py

@@ -60,13 +60,7 @@ def main():
 
     print("adata:", adata_full)
 
-    for n_obs in [5_000_000, None]:
-        if n_obs is not None and n_obs < adata_full.n_obs:
-            adata = sc.pp.subsample(adata_full, n_obs=n_obs, copy=True)
-        else:
-            adata = adata_full
-
-        compute_and_save_umap(adata, res_path)
+    compute_and_save_umap(adata_full, res_path)
 
 
 if __name__ == "__main__":

remote/umaps.sh

@@ -1,9 +1,9 @@
 #!/bin/bash
 #SBATCH --job-name=novae
 #SBATCH --output=/gpfs/workdir/blampeyq/.jobs_outputs/%j
-#SBATCH --mem=128G
+#SBATCH --mem=512G
 #SBATCH --time=7-00:00:00
-#SBATCH --cpus-per-task=2
+#SBATCH --cpus-per-task=1
 #SBATCH --partition=cpu_long
 
 module purge