Changes between Version 2 and Version 3 of cypress/Cellranger-ARC

Timestamp:

09/04/2026 03:49:35 PM (3 days ago)

Author:

fuji

Comment:

--

cypress/Cellranger-ARC

@@ -5 +5 @@
 {{{
 #!/bin/bash
-#SBATCH --qos=normal            # Quality of Service
+#SBATCH --partition=centos7     # Partition
+#SBATCH --qos=normal            # Quality of Service
 #SBATCH --job-name=mkFASTQ # Job Name
-#SBATCH --time=24:00:00 # WallTime
-#SBATCH --nodes=1               # Number of Nodes = 1
-#SBATCH --ntasks-per-node=1     # Number of tasks (MPI presseces) = 1
-#SBATCH --cpus-per-task=1       # Number of processors per task OpenMP threads() = 1 
-#SBATCH --gres=mic:0            # Number of Co-Processors
+#SBATCH --time=24:00:00 # WallTime
+#SBATCH --nodes=1               # Number of Nodes
+#SBATCH --ntasks-per-node=1     # Number of tasks (MPI presseces)
+#SBATCH --cpus-per-task=20      # Number of processors per task OpenMP threads()
+#SBATCH --gres=mic:0            # Number of Co-Processors
 #SBATCH --export=ALL
+#SBATCH --mem=256000
 #SBATCH --mail-type=ALL
-#SBATCH --mail-user='USERID'@tulane.edu # SET YOUR EMAIL ADDRESS
+#SBATCH --mail-user=[email protected] # YOUR EMAIL ADDRESS
 
-module load cellranger-arc/1.0.1
+
+module load cellranger-arc/2.2.0
 
 cellranger-arc mkfastq --id=tiny-bcl-atac \
                  --run=./cellranger-arc-tiny-bcl-atac-1.0.0 \
                  --csv=./cellranger-arc-tiny-bcl-atac-simple-1.0.0.csv \
-                 --jobmode=slurm \
-                 --maxjobs=4 \
+                 --jobmode=slurm \
+                 --localmem=240 \
+                 --localcores=20 \
+                 --maxjobs=4 \
                  --jobinterval=1000
 }}}
@@ -28 +33 @@
 
 {{{
-                 --maxjobs=18 \
+                 --maxjobs=25 \
 }}}