include run_time

src/loaders/compute_tools/checkm2/checkm2.py

@@ -46,10 +46,6 @@ def _run_checkm2(
     # checkm2 will clear output_dir before it starts, which will delete any log files
     log_dir = output_dir.parent / ("checkm2_log_" + output_dir.parts[-1])
     run_command(command, log_dir if debug else None)
-    end_time = time.time()
-    print(f"Used {round((end_time - start) / 60, 2)} minutes to execute checkM2 predict "
-          + f"for {size} genomes"
-          )
 
     tool_file_name, genome_id_col = 'quality_report.tsv', 'Name'
     genome_attri_docs = process_genome_attri_result(output_dir,
@@ -70,14 +66,23 @@ def _run_checkm2(
         fatal_tuples.append(fatal_tuple)
     write_fatal_tuples_to_dict(fatal_tuples, output_dir)
 
+    end_time = time.time()
+    run_time = end_time - start
+    print(f"Used {round(run_time / 60, 2)} minutes to execute checkM2 predict "
+          + f"for {size} genomes"
+          )
+
     metadata = {'tool_name': 'checkm2',
                 'version': '1.0.1',
                 'command': command,
                 "reference_db": {
                     "version": None,
                     "comment": "diamond_db, ver unknown",
                     },
-                'ids_to_files': make_json_serializable(ids_to_files)}
+                'ids_to_files': make_json_serializable(ids_to_files),
+                'run_time': run_time,
+                'batch_size': size,
+                }
     create_tool_metadata(output_dir, metadata)
 
 

src/loaders/compute_tools/checkm2/versions.yaml

@@ -38,6 +38,7 @@ versions:
       - Create metadata file after running CheckM2
       - Fix a typo for 'tool_name' metadata field
       - Add method to ensure 'ids_to_files' is JSON serializable
+      - Include execution time in metadata
     reference_db_version: 1.0.1
 
 #Please keep this reminder at the end of this file

src/loaders/compute_tools/eggnog/eggnog.py

@@ -5,6 +5,7 @@
 Therefore, the parser program is not compatible with data generated by this tool.
 
 """
+import time
 from pathlib import Path
 
 from src.loaders.common.loader_common_names import TOOL_METADATA
@@ -21,6 +22,9 @@ def _run_eggnog_single(
         threads_per_tool_run: int,
         debug: bool) -> None:
 
+    start = time.time()
+    print(f'Start executing EggNog for {data_id}')
+
     metadata_file = output_dir / TOOL_METADATA
     if metadata_file.exists():
         print(f"Skipping {source_file} as it has already been processed.")
@@ -41,6 +45,11 @@ def _run_eggnog_single(
 
     run_command(command, output_dir if debug else None)
 
+    end_time = time.time()
+    run_time = end_time - start
+    print(
+        f'Used {round(run_time / 60, 2)} minutes to execute EggNog for {data_id}')
+
     # Save run info to a metadata file in the output directory for parsing later
     metadata = {'source_file': str(source_file),
                 'input_type': INPUT_TYPE,
@@ -51,6 +60,8 @@ def _run_eggnog_single(
                 "reference_db": {
                     "version": "5.0.2",
                     },
+                'run_time': run_time,
+                'batch_size': 1,
                 }
     create_tool_metadata(output_dir, metadata)
 

src/loaders/compute_tools/eggnog/versions.yaml

@@ -27,6 +27,7 @@ versions:
     date: 2024-08-16
     notes: |
       - Create metadata file after running Eggnog
+      - Include execution time in metadata
     reference_db_version: 5.0.2
 
 #Please keep this reminder at the end of this file

src/loaders/compute_tools/gtdb_tk/gtdb_tk.py

@@ -98,11 +98,6 @@ def _run_gtdb_tk(
     print(f'running {" ".join(command)}')
     run_command(command, output_dir / "classify_wf_log" if debug else None)
 
-    end_time = time.time()
-    print(
-        f'Used {round((end_time - start) / 60, 2)} minutes to execute gtdbtk classify_wf for '
-        f'{len(ids_to_files)} genomes')
-
     summary_files = find_gtdbtk_summary_files(output_dir)
     if not summary_files:
         raise ValueError(f"No summary files exist for gtdb-tk in the specified "
@@ -152,13 +147,21 @@ def _run_gtdb_tk(
                                 summary_files,
                                 )
 
+    end_time = time.time()
+    run_time = end_time - start
+    print(
+        f'Used {round(run_time / 60, 2)} minutes to execute gtdbtk classify_wf for '
+        f'{size} genomes')
+
     metadata = {'tool_name': 'gtdb_tk',
                 'version': '2.3.2',
                 'command': command,
                 "reference_db": {
                     "version": "release214",
                     },
-                'ids_to_files': make_json_serializable(ids_to_files)}
+                'ids_to_files': make_json_serializable(ids_to_files),
+                'run_time': run_time,
+                'batch_size': size,}
     create_tool_metadata(output_dir, metadata)
 
 

src/loaders/compute_tools/gtdb_tk/versions.yaml

@@ -47,6 +47,7 @@ versions:
       - Create metadata file after running GTDB-Tk
       - Fix a typo for 'tool_name' metadata field
       - Add method to ensure 'ids_to_files' is JSON serializable
+      - Include execution time in metadata
     reference_db_version: release214
 
 #Please keep this reminder at the end of this file

src/loaders/compute_tools/mash/mash.py

@@ -1,6 +1,7 @@
 """
 Run Mash on a set of assemblies.
 """
+import time
 from pathlib import Path
 
 from src.loaders.compute_tools.tool_common import ToolRunner, run_command, create_tool_metadata
@@ -18,6 +19,10 @@ def _run_mash_single(
         debug: bool,
         kmer_size: int = KMER_SIZE,
         sketch_size: int = SKETCH_SIZE) -> None:
+
+    start = time.time()
+    print(f'Start executing Mash for {data_id}')
+
     # RUN mash sketch for a single genome
     command = ['mash', 'sketch',
                '-o', source_file,  # Output prefix.
@@ -29,6 +34,11 @@ def _run_mash_single(
 
     run_command(command, output_dir if debug else None)
 
+    end_time = time.time()
+    run_time = end_time - start
+    print(
+        f'Used {round(run_time / 60, 2)} minutes to execute Mash for {data_id}')
+
     # Save run info to a metadata file in the output directory for parsing later
     metadata = {'source_file': str(source_file),
                 # Append '.msh' to the source file name to generate the sketch file name (default by Mash sketch)
@@ -38,7 +48,10 @@ def _run_mash_single(
                 'data_id': data_id,
                 'tool_name': 'mash',
                 'version': '2.0',
-                'command': command}
+                'command': command,
+                'run_time': run_time,
+                'batch_size': 1,
+                }
     create_tool_metadata(output_dir, metadata)
 
 

src/loaders/compute_tools/mash/versions.yaml

@@ -20,4 +20,5 @@ versions:
   - version: 0.1.5
     date: 2024-08-16
     notes: |
-      - Create metadata file after running Mash
+      - Create metadata file after running Mash
+      - Include execution time in metadata

src/loaders/compute_tools/microtrait/microtrait.py

@@ -2,6 +2,7 @@
 Runs microtrait on a set of assemblies.
 """
 import os
+import time
 import uuid
 from pathlib import Path
 from typing import Any
@@ -28,6 +29,7 @@
     FatalTuple,
     ToolRunner,
     write_fatal_tuples_to_dict,
+    create_tool_metadata,
 )
 from src.loaders.compute_tools.tool_result_parser import (
     create_jsonl_files,
@@ -208,6 +210,9 @@ def _run_microtrait(
     # since extract_traits function doesn't take the number of threads as an argument
     # https://github.com/ukaraoz/microtrait/blob/master/R/extract_traits.R#L22-L26
 
+    start = time.time()
+    print(f'Start executing Microtrait for {data_id}')
+
     # Load the R script as an R function
     r_script = """
         library(microtrait)
@@ -262,6 +267,22 @@ def _run_microtrait(
     create_jsonl_files(genome_dir / MICROTRAIT_CELLS, cells_meta)
     create_jsonl_files(genome_dir / MICROTRAIT_DATA, heatmap_row)
 
+    end_time = time.time()
+    run_time = end_time - start
+    print(
+        f'Used {round(run_time / 60, 2)} minutes to execute Microtrait for {data_id}')
+
+    # Save run info to a metadata file in the output directory for parsing later
+    metadata = {'source_file': str(fna_file),
+                'data_id': data_id,
+                'tool_name': 'microtrait',
+                'version': 'None',
+                'command': 'None - R script',
+                'run_time': run_time,
+                'batch_size': 1,
+                }
+    create_tool_metadata(genome_dir, metadata)
+
 
 def main():
     runner = ToolRunner("microtrait")

src/loaders/compute_tools/microtrait/versions.yaml

@@ -22,4 +22,9 @@ versions:
   - version: 0.1.5
     date: 2024-06-25
     notes: |
-      - Bug fix: tool_common.py - Converted Data IDs to string format to ensure proper comparison with associated folder names
+      - Bug fix: tool_common.py - Converted Data IDs to string format to ensure proper comparison with associated folder names
+  - version: 0.1.6
+    date: 2024-08-16
+    notes: |
+      - Create metadata file after running Microtrait
+      - Include execution time in metadata