Add toggle for db_load_mode

bin/run_msa_tool.py

@@ -51,6 +51,9 @@
 parser.add_argument(
     "--max_accept", default=100000, help="MMseqs2 max accepted alignments"
 )
+parser.add_argument("--db_load_mode", type=int, default=0,
+                    help="Database preload mode 0: auto, 1: fread, 2: mmap, 3: mmap+touch")
+
 
 args = parser.parse_args()
 
@@ -97,6 +100,7 @@
         gpu=args.gpu,
         gpu_server=args.gpu_server,
         max_accept=args.max_accept,
+        db_load_mode=args.db_load_mode,
     )
 
 

modules/local/common/main.nf

@@ -74,6 +74,7 @@ process mmseqs_align {
                         --mmseqs ${params.mmseqs_bin} \\
                         --out_dir ./ \\
                         --n_cpu ${n_cpu} \\
+                        --db_load_mode ${params.mmseqs_db_load_mode} \\
                         ${use_gpu} \\
                         ${use_env}
     fi

nextflow.config

@@ -31,6 +31,7 @@ params {
     mmseqs_db = "${projectDir}/database/"           // path to colabfold dbs. If installation was done as on README, no need to change anything
     mmseqs_bin = 'mmseqs'
     mmseqs_use_env = true                       // whether the environmental sequences DB should also be searched with MMseqs2
+    mmseqs_db_load_mode = 0                     // Database preload mode 0: auto, 1: fread, 2: mmap, 3: mmap+touch
 
     // general AF parameters
     af_n_gpu = 1

tests/nextflow.config

@@ -31,6 +31,7 @@ params {
     mmseqs_db = "${projectDir}/database/"           // path to colabfold dbs. If installation was done as on README, no need to change anything
     mmseqs_bin = 'mmseqs'
     mmseqs_use_env = true                       // whether the environmental sequences DB should also be searched with MMseqs2
+    mmseqs_db_load_mode = 0                     // Database preload mode 0: auto, 1: fread, 2: mmap, 3: mmap+touch
 
     // general AF parameters
     af_n_gpu = 1