rdrpcatch 0.0.5__tar.gz → 0.0.6__tar.gz

{rdrpcatch-0.0.5 → rdrpcatch-0.0.6}/.idea/workspace.xml

@@ -4,7 +4,11 @@
     <option name="autoReloadType" value="SELECTIVE" />
   </component>
   <component name="ChangeListManager">
-    <list default="true" id="d849e6fa-87f9-4e92-9c33-abef7cc975d3" name="Changes" comment="Updates:&#10;Fixed bug that crushed the script when at least one  pHMM DB does not have a match against the sequence database also for nuc branch" />
+    <list default="true" id="d849e6fa-87f9-4e92-9c33-abef7cc975d3" name="Changes" comment="Updates:&#10;Fixed bug that crushed the script when at least one  pHMM DB does not have a match against the sequence database also for nuc branch">
+      <change beforePath="$PROJECT_DIR$/pyproject.toml" beforeDir="false" afterPath="$PROJECT_DIR$/pyproject.toml" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/rdrpcatch/cli/args.py" beforeDir="false" afterPath="$PROJECT_DIR$/rdrpcatch/cli/args.py" afterDir="false" />
+      <change beforePath="$PROJECT_DIR$/rdrpcatch/rdrpcatch_wrapper.py" beforeDir="false" afterPath="$PROJECT_DIR$/rdrpcatch/rdrpcatch_wrapper.py" afterDir="false" />
+    </list>
     <option name="SHOW_DIALOG" value="false" />
     <option name="HIGHLIGHT_CONFLICTS" value="true" />
     <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
@@ -36,22 +40,22 @@
     <option name="hideEmptyMiddlePackages" value="true" />
     <option name="showLibraryContents" value="true" />
   </component>
-  <component name="PropertiesComponent"><![CDATA[{
-  "keyToString": {
-    "ASKED_ADD_EXTERNAL_FILES": "true",
-    "RunOnceActivity.OpenProjectViewOnStart": "true",
-    "RunOnceActivity.ShowReadmeOnStart": "true",
-    "ignore.virus.scanning.warn.message": "true",
-    "last_opened_file_path": "C:/Users/karso/PycharmProjects/rdrpcatch_benchmarks",
-    "node.js.detected.package.eslint": "true",
-    "node.js.detected.package.tslint": "true",
-    "node.js.selected.package.eslint": "(autodetect)",
-    "node.js.selected.package.tslint": "(autodetect)",
-    "nodejs_package_manager_path": "npm",
-    "settings.editor.selected.configurable": "preferences.pluginManager",
-    "vue.rearranger.settings.migration": "true"
+  <component name="PropertiesComponent">{
+  &quot;keyToString&quot;: {
+    &quot;ASKED_ADD_EXTERNAL_FILES&quot;: &quot;true&quot;,
+    &quot;RunOnceActivity.OpenProjectViewOnStart&quot;: &quot;true&quot;,
+    &quot;RunOnceActivity.ShowReadmeOnStart&quot;: &quot;true&quot;,
+    &quot;ignore.virus.scanning.warn.message&quot;: &quot;true&quot;,
+    &quot;last_opened_file_path&quot;: &quot;C:/Users/karso/PycharmProjects/rdrpcatch_benchmarks&quot;,
+    &quot;node.js.detected.package.eslint&quot;: &quot;true&quot;,
+    &quot;node.js.detected.package.tslint&quot;: &quot;true&quot;,
+    &quot;node.js.selected.package.eslint&quot;: &quot;(autodetect)&quot;,
+    &quot;node.js.selected.package.tslint&quot;: &quot;(autodetect)&quot;,
+    &quot;nodejs_package_manager_path&quot;: &quot;npm&quot;,
+    &quot;settings.editor.selected.configurable&quot;: &quot;preferences.pluginManager&quot;,
+    &quot;vue.rearranger.settings.migration&quot;: &quot;true&quot;
   }
-}]]></component>
+}</component>
   <component name="RecentsManager">
     <key name="CopyFile.RECENT_KEYS">
       <recent name="C:\Users\karso\PycharmProjects\ColaB-Scan\testing" />
@@ -116,7 +120,8 @@
       <workItem from="1743683517488" duration="7013000" />
       <workItem from="1743714892367" duration="21775000" />
       <workItem from="1744200654491" duration="635000" />
-      <workItem from="1744241097621" duration="28249000" />
+      <workItem from="1744241097621" duration="28847000" />
+      <workItem from="1745576502650" duration="11360000" />
     </task>
     <task id="LOCAL-00001" summary="First commit: Script for benchmark">
       <option name="closed" value="true" />

{rdrpcatch-0.0.5 → rdrpcatch-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdrpcatch
-Version: 0.0.5
+Version: 0.0.6
 Dynamic: Summary
 Project-URL: Home, https://github.com/dimitris-karapliafis/RdRpCATCH
 Project-URL: Source, https://github.com/dimitris-karapliafis/RdRpCATCH
@@ -205,7 +205,6 @@ Dimitris Karapliafis (dimitris.karapliafis@wur.nl), potentially via slack/teams
 
 ##TODO:
 - [ ] loud logging is linking to the utils.py file, not the actual line of code causing the error.
-- [ ] Add `overwrite` flag
 - [ ] drop `db_dir` argument and use global/environment/config variable that is set after running the `download` command
 
 

{rdrpcatch-0.0.5 → rdrpcatch-0.0.6}/README.md

@@ -183,7 +183,6 @@ Dimitris Karapliafis (dimitris.karapliafis@wur.nl), potentially via slack/teams
 
 ##TODO:
 - [ ] loud logging is linking to the utils.py file, not the actual line of code causing the error.
-- [ ] Add `overwrite` flag
 - [ ] drop `db_dir` argument and use global/environment/config variable that is set after running the `download` command
 
 

{rdrpcatch-0.0.5 → rdrpcatch-0.0.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "rdrpcatch"
-version = "0.0.5"
+version = "0.0.6"
 authors = [
     {name = "Dimitris Karapliafis", email = "dimitris.karapliafis@wur.nl"},
     {name = "Uri Neri", email = "uneri@lbl.gov"},

{rdrpcatch-0.0.5 → rdrpcatch-0.0.6}/rdrpcatch/cli/args.py

@@ -115,30 +115,30 @@ def cli():
 @click.option('-gen_code', '--gen_code',
               type=click.INT,
               default=1,
-              help='Genetic code to use for translation. (default: 1) Possible genetic codes (supported by seqkit translate) :      1: The Standard Code       \n'
-                     '2: The Vertebrate Mitochondrial Code      \n'
-                     '3: The Yeast Mitochondrial Code       \n'
-                     '4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code        \n'
-                     '5: The Invertebrate Mitochondrial Code        \n'
-                     '6: The Ciliate, Dasycladacean and Hexamita Nuclear Code       \n'
-                     '9: The Echinoderm and Flatworm Mitochondrial Code     \n'
-                    '10: The Euplotid Nuclear Code      \n'
-                    '11: The Bacterial, Archaeal and Plant Plastid Code     \n'
-                    '12: The Alternative Yeast Nuclear Code     \n'
-                    '13: The Ascidian Mitochondrial Code        \n'
-                    '14: The Alternative Flatworm Mitochondrial Code        \n'
-                    '16: Chlorophycean Mitochondrial Code       \n'
-                    '21: Trematode Mitochondrial Code       \n'
-                    '22: Scenedesmus obliquus Mitochondrial Code        \n'
-                    '23: Thraustochytrium Mitochondrial Code        \n'
-                    '24: Pterobranchia Mitochondrial Code       \n'
-                    '25: Candidate Division SR1 and Gracilibacteria Code        \n'
-                    '26: Pachysolen tannophilus Nuclear Code        \n'
-                    '27: Karyorelict Nuclear        \n'
-                    '28: Condylostoma Nuclear       \n'
-                    '29: Mesodinium Nuclear     \n'
-                    '30: Peritrich Nuclear      \n'
-                    '31: Blastocrithidia Nuclear        \n')
+              help='Genetic code to use for translation. (default: 1) Possible genetic codes (supported by seqkit translate) : 1: The Standard Code, '
+                     '2: The Vertebrate Mitochondrial Code, '
+                     '3: The Yeast Mitochondrial Code, '
+                     '4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code, '
+                     '5: The Invertebrate Mitochondrial Code, '
+                     '6: The Ciliate, Dasycladacean and Hexamita Nuclear Code, '
+                     '9: The Echinoderm and Flatworm Mitochondrial Code, '
+                    '10: The Euplotid Nuclear Code, '
+                    '11: The Bacterial, Archaeal and Plant Plastid Code, '
+                    '12: The Alternative Yeast Nuclear Code, '
+                    '13: The Ascidian Mitochondrial Code, '
+                    '14: The Alternative Flatworm Mitochondrial Code, '
+                    '16: Chlorophycean Mitochondrial Code, '
+                    '21: Trematode Mitochondrial Code, '
+                    '22: Scenedesmus obliquus Mitochondrial Code, '
+                    '23: Thraustochytrium Mitochondrial Code, '
+                    '24: Pterobranchia Mitochondrial Code, '
+                    '25: Candidate Division SR1 and Gracilibacteria Code, '
+                    '26: Pachysolen tannophilus Nuclear Code, '
+                    '27: Karyorelict Nuclear, '
+                    '28: Condylostoma Nuclear, '
+                    '29: Mesodinium Nuclear, '
+                    '30: Peritrich Nuclear, '
+                    '31: Blastocrithidia Nuclear, ')
 @click.option('-bundle', '--bundle',
               is_flag=True,
               default=False,
@@ -147,9 +147,14 @@ def cli():
               is_flag=True,
               default=False,
               help="Keep temporary files (Expert users) (default: False)")
+@click.option('-overwrite', '--overwrite',
+              is_flag=True,
+              default=False,
+              help="Force overwrite of existing output directory. (default: False)")
+
 @click.pass_context
 def scan(ctx, input, output, db_options, db_dir, custom_dbs, seq_type, verbose, evalue,
-         incevalue, domevalue, incdomevalue, zvalue, cpus, length_thr, gen_code, bundle, keep_tmp):
+         incevalue, domevalue, incdomevalue, zvalue, cpus, length_thr, gen_code, bundle, keep_tmp, overwrite):
     """Scan sequences for RdRps."""
 
     # Create a rich table for displaying parameters
@@ -175,6 +180,7 @@ def scan(ctx, input, output, db_options, db_dir, custom_dbs, seq_type, verbose,
     table.add_row("Genetic Code", str(gen_code))
     table.add_row("Bundle Output", "ON" if bundle else "OFF")
     table.add_row("Save Temporary Files", "ON" if keep_tmp else "OFF")
+    table.add_row("Force Overwrite", "ON" if overwrite else "OFF")
 
     console.print(Panel(table, title="Scan Configuration"))
 
@@ -207,7 +213,8 @@ def scan(ctx, input, output, db_options, db_dir, custom_dbs, seq_type, verbose,
         length_thr=length_thr,
         gen_code=gen_code,
         bundle=bundle,
-        keep_tmp=keep_tmp
+        keep_tmp=keep_tmp,
+        overwrite=overwrite
     )
 
 # @cli.command("download", help="Download RdRpCATCH databases.")

{rdrpcatch-0.0.5 → rdrpcatch-0.0.6}/rdrpcatch/rdrpcatch_wrapper.py

@@ -53,7 +53,7 @@ def bundle_results(output_dir, prefix):
     
     return archive_path
 
-def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,incdomE,domE,incE,z, cpus, length_thr, gen_code, bundle, keep_tmp):
+def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,incdomE,domE,incE,z, cpus, length_thr, gen_code, bundle, keep_tmp, overwrite):
     """
     Run RdRpCATCH scan.
 
@@ -110,8 +110,16 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
     log_file = outputs.log_file
     if not os.path.exists(outputs.output_dir):
         os.makedirs(outputs.output_dir)
+    elif os.path.exists(outputs.output_dir) and overwrite:
+        # If the output directory already exists and force_overwrite is True, remove the existing directory
+        import shutil
+        shutil.rmtree(outputs.output_dir)
+        os.makedirs(outputs.output_dir)
+        outputs = paths.rdrpcatch_output(prefix, Path(output_dir))
     else:
-        raise FileExistsError(f"Output directory already exists: {outputs.output_dir}, Please choose a different directory.")
+        raise FileExistsError(f"Output directory already exists: {outputs.output_dir}, Please choose a different directory"
+                              f" or activate the -overwrite flag to overwrite the contents of the directory.")
+
     if not os.path.exists(outputs.log_dir):
         os.makedirs(outputs.log_dir)
 
@@ -160,6 +168,8 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
     if seq_type == 'prot':
         utils.fasta_checker(input_file, logger).check_seq_length(100000)
 
+    logger.loud_log("Fetching HMM databases...")
+
     ## Fetch HMM databases- RVMT, NeoRdRp, NeoRdRp.2.1, TSA_Olendraite, RDRP-scan, Lucaprot
     rvmt_hmm_db = fetch_dbs.db_fetcher(db_dir).fetch_hmm_db_path("RVMT")
     if verbose:
@@ -234,10 +244,9 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
 
     # Fetch mmseqs database
 
-    if verbose:
-        logger.loud_log("Fetching mmseqs databases.")
-    else:
-        logger.silent_log("Fetching mmseqs databases.")
+
+    logger.loud_log("Fetching Mmseqs2 databases...")
+
     mmseqs_db_path = fetch_dbs.db_fetcher(db_dir).fetch_mmseqs_db_path("mmseqs_refseq_riboviria_20250211")
 
     if verbose:
@@ -260,21 +269,17 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
     if not os.path.exists(outputs.tmp_dir):
         outputs.tmp_dir.mkdir(parents=True)
 
+    logger.loud_log("Databases fetched successfully.")
+
     if seq_type == 'nuc':
-        if verbose:
-            logger.loud_log("Nucleotide sequence detected.")
-        else:
-            logger.silent_log("Nucleotide sequence detected.")
+        logger.loud_log("Nucleotide sequence detected.")
 
         set_dict = {}
         translated_set_dict = {}
         df_list = []
 
         ## Filter out sequences with length less than 400 bp with seqkit
-        if verbose:
-            logger.loud_log("Filtering out sequences with length less than 400 bp.")
-        else:
-            logger.silent_log("Filtering out sequences with length less than 400 bp.")
+        logger.loud_log("Filtering out sequences with length less than 400 bp.")
 
         if not os.path.exists(outputs.seqkit_seq_output_dir):
             outputs.seqkit_seq_output_dir.mkdir(parents=True)
@@ -286,10 +291,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
             logger.silent_log(f"Filtered sequence written to: { outputs.seqkit_seq_output_path}")
 
         ## Translate nucleotide sequences to protein sequences with seqkit
-        if verbose:
-            logger.loud_log("Translating nucleotide sequences to protein sequences.")
-        else:
-            logger.silent_log("Translating nucleotide sequences to protein sequences.")
+        logger.loud_log("Translating nucleotide sequences to protein sequences.")
 
         if not os.path.exists(outputs.seqkit_translate_output_dir):
             outputs.seqkit_translate_output_dir.mkdir(parents=True)
@@ -302,6 +304,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
             logger.silent_log(f"Translated sequence written to: {outputs.seqkit_translate_output_path}")
 
         for db_name,db_path in zip(db_name_list, db_path_list):
+            logger.loud_log(f"Running HMMsearch for {db_name} database.")
 
             if verbose:
                 logger.loud_log(f"HMM output path: {outputs.hmm_output_path(db_name)}")
@@ -353,7 +356,9 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
             ])
             df_list.append(df)
 
+            logger.loud_log(f"HMMsearch for {db_name} completed.")
 
+        logger.loud_log("HMMsearch completed.")
 
         if not os.path.exists(outputs.plot_outdir):
             outputs.plot_outdir.mkdir(parents=True)
@@ -361,6 +366,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
         if not os.path.exists(outputs.tsv_outdir):
             outputs.tsv_outdir.mkdir(parents=True)
 
+        logger.loud_log("Consolidating results.")
 
         # Combine all the dataframes in the list
         combined_df = pl.concat(df_list, how='vertical_relaxed')
@@ -379,6 +385,8 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
             logger.loud_log("No hits found by RdRpCATCH. Exiting.")
             return None
 
+        # Generate upset plot
+        logger.loud_log("Generating plots.")
 
         if len(db_name_list) > 1:
             if verbose:
@@ -411,6 +419,8 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
         combined_set = set.union(*[value for value in set_dict.values()])
         translated_combined_set = set.union(*[value for value in translated_set_dict.values()])
 
+        logger.loud_log("Extracting RdRp contigs from the input file.")
+
         # Write a fasta file with all the contigs
         if not os.path.exists(outputs.fasta_output_dir):
             outputs.fasta_output_dir.mkdir(parents=True)
@@ -430,25 +440,21 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
         if verbose:
             logger.loud_log(f"Contigs written to: {outputs.fasta_nuc_out_path}")
             logger.loud_log(f"Translated contigs written to: {outputs.fasta_prot_out_path}")
+            logger.loud_log(f"Trimmed contigs written to: {outputs.fasta_trimmed_out_path}")
         else:
             logger.silent_log(f"Contigs written to: {outputs.fasta_nuc_out_path}")
             logger.silent_log(f"Translated contigs written to: {outputs.fasta_prot_out_path}")
+            logger.silent_log(f"Trimmed contigs written to: {outputs.fasta_trimmed_out_path}")
 
         if not os.path.exists(outputs.mmseqs_tax_output_dir):
             outputs.mmseqs_tax_output_dir.mkdir(parents=True)
 
-        if verbose:
-            logger.loud_log("Running mmseqs easy-taxonomy for taxonomic annotation.")
-        else:
-            logger.silent_log("Running mmseqs easy-taxonomy for taxonomic annotation.")
+        logger.loud_log("Running mmseqs easy-taxonomy for taxonomic annotation.")
 
         mmseqs_tax.mmseqs(outputs.fasta_prot_out_path, mmseqs_db_path, outputs.mmseqs_tax_output_prefix,
                           outputs.mmseqs_tax_output_dir, 7, cpus, outputs.mmseqs_tax_log_path).run_mmseqs_easy_tax_lca()
 
-        if verbose:
-            logger.loud_log("Running mmseqs easy-search for taxonomic annotation.")
-        else:
-            logger.silent_log("Running mmseqs easy-search for taxonomic annotation.")
+        logger.loud_log("Running mmseqs easy-search for taxonomic annotation.")
 
         if not os.path.exists(outputs.mmseqs_e_search_output_dir):
             outputs.mmseqs_e_search_output_dir.mkdir(parents=True)
@@ -460,18 +466,17 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
         utils.mmseqs_parser(outputs.mmseqs_tax_output_lca_path, outputs.mmseqs_e_search_output_path).tax_to_rdrpcatch(
             outputs.rdrpcatch_output_tsv, outputs.extended_rdrpcatch_output, seq_type)
 
+        logger.loud_log("Taxonomic annotation completed.")
 
     elif seq_type == 'prot':
 
-        if verbose:
-            logger.loud_log("Protein sequence detected.")
-        else:
-            logger.silent_log("Protein sequence detected.")
+        logger.loud_log("Protein sequence detected.")
 
         set_dict = {}
         df_list = []
 
         for db_name,db_path in zip (db_name_list, db_path_list):
+            logger.loud_log(f"Running HMMsearch for {db_name} database.")
 
             if verbose:
                 logger.loud_log(f"HMM output path: {outputs.hmm_output_path(db_name)}")
@@ -519,12 +524,17 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
             ])
             df_list.append(df)
 
+            logger.loud_log(f"HMMsearch for {db_name} completed.")
+
+        logger.loud_log("HMMsearch completed.")
+
         if not os.path.exists(outputs.plot_outdir):
             outputs.plot_outdir.mkdir(parents=True)
 
         if not os.path.exists(outputs.tsv_outdir):
             outputs.tsv_outdir.mkdir(parents=True)
 
+        logger.loud_log("Consolidating results.")
 
         # Combine all the dataframes in the list
         combined_df = pl.concat(df_list, how='vertical_relaxed')
@@ -542,6 +552,9 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
             logger.loud_log("No hits found by RdRpCATCH. Exiting.")
             return None
 
+        # Generate upset plot
+        logger.loud_log("Generating plots.")
+
         if len(db_name_list) > 1:
             if verbose:
                 logger.loud_log("Generating upset plot.")
@@ -574,6 +587,9 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
         # Extract all the contigs
         combined_set = set.union(*[value for value in set_dict.values()])
         # Write a fasta file with all the contigs
+
+        logger.loud_log("Extracting RdRp contigs from the input file.")
+
         if not os.path.exists(outputs.fasta_output_dir):
             outputs.fasta_output_dir.mkdir(parents=True)
 
@@ -600,11 +616,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
         if not os.path.exists(outputs.mmseqs_tax_output_dir):
             outputs.mmseqs_tax_output_dir.mkdir(parents=True)
 
-        if verbose:
-            logger.loud_log("Running mmseqs easy-taxonomy for taxonomic annotation.")
-        else:
-            logger.silent_log("Running mmseqs easy-taxonomy for taxonomic annotation.")
-
+        logger.loud_log("Running mmseqs easy-taxonomy for taxonomic annotation.")
 
         mmseqs_tax.mmseqs(outputs.fasta_prot_out_path, mmseqs_db_path, outputs.mmseqs_tax_output_prefix,
                           outputs.mmseqs_tax_output_dir, 7, cpus, outputs.mmseqs_tax_log_path).run_mmseqs_easy_tax_lca()
@@ -612,10 +624,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
         if not os.path.exists(outputs.mmseqs_e_search_output_dir):
             outputs.mmseqs_e_search_output_dir.mkdir(parents=True)
 
-        if verbose:
-            logger.loud_log("Running mmseqs easy-search for taxonomic annotation.")
-        else:
-            logger.silent_log("Running mmseqs easy-search for taxonomic annotation.")
+        logger.loud_log("Running mmseqs easy-search for taxonomic annotation.")
 
         mmseqs_tax.mmseqs(outputs.fasta_prot_out_path, mmseqs_db_path, outputs.mmseqs_e_search_output_dir,
                           outputs.mmseqs_e_search_output_path, 7, cpus, outputs.mmseqs_e_search_log_path).run_mmseqs_e_search()
@@ -624,11 +633,7 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
             outputs.rdrpcatch_output_tsv, outputs.extended_rdrpcatch_output, seq_type)
 
 
-    end_time = logger.stop_timer(start_time, verbose)
-    if verbose:
-        logger.loud_log(f"Total Runtime: {end_time}")
-    else:
-        logger.silent_log(f"Total Runtime: {end_time}")
+
 
 
 
@@ -657,6 +662,11 @@ def run_scan(input_file, output_dir, db_options, db_dir, seq_type, verbose, e,in
         else:
             logger.silent_log(f"Results bundled into: {archive_path}")
 
+    end_time = logger.stop_timer(start_time, verbose)
+
+    logger.loud_log(f"Total Runtime: {end_time}")
+
+    logger.loud_log("RdRpCATCH completed successfully.")
 
 
     return outputs.extended_rdrpcatch_output