diff --git a/conf/modules.config b/conf/modules.config
index 21666d6d..d298a828 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -808,12 +808,12 @@ process {
 
     withName: GANON_CLASSIFY {
         tag = {"${meta.db_name}|${meta.id}"}
-        ext.args = params.ganon_save_readclassifications ? { "${meta.db_params} --output-all --output-lca --output-unclassified" } : { "${meta.db_params}" }
+        ext.args = params.ganon_save_readclassifications ? { "${meta.db_params} --output-all --output-unclassified" } : { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.ganon" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.ganon" }
         publishDir = [
             path: { "${params.outdir}/ganon/${meta.db_name}/" },
             mode: params.publish_dir_mode,
-            pattern: '*.{tre,rep,lca,all,unc,log}'
+            pattern: '*.{tre,rep,one,all,unc,log}'
         ]
     }
 
diff --git a/docs/output.md b/docs/output.md
index baf5d292..89cafb8f 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -618,9 +618,9 @@ The main taxonomic classification file from KMCP is the `*kmcp.profile` which is
     - `<sample_id>_report.tre`: output of `ganon report` containing taxonomic classifications with possible formatting and/or filtering depending on options specified.
     - `<sample_id>`.tre: output of `ganon classify` containing raw taxonomic classifications and abundance estimations with no additional formatting or filtering.
     - `<sample_id>`.rep: 'raw' report of counts against each taxon.
-    - `<sample_id>`.all: per-read summary of all hits of each reads.
-    - `<sample_id>`.lca: per-read summary of the best single hit after LCA for each read.
-    - `<sample_id>`.unc: list of read IDs with no hits.
+    - `<sample_id>`.all: per-read summary of all hits of each read. Only generated if `--ganon_save_readclassifications` specified.
+    - `<sample_id>`.one: per-read summary of the best single hit after the selection by the user specified multiple match method for each read. Only generated if `--ganon_save_readclassifications` specified.
+    - `<sample_id>`.unc: list of read IDs with no hits. Only generated if `--ganon_save_readclassifications` specified.
     - `<sample_id>`.log: the stdout console messages printed by `ganon classify`, containing some classification summary information
 
   - `ganon_<db_name>_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by `ganon table`)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6d1c702c..4fb4ba40 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -589,7 +589,7 @@
                     "type": "boolean",
                     "description": "Turn on saving of ganon per-read taxonomic assignment file(s).",
                     "fa_icon": "fas fa-save",
-                    "help_text": "Saves `.lca`, `.all`, and `.unc` text files that contains a list of each read that had a taxonomic assignment, with information on specific taxonomic assignment that the read received.\n\n> Modifies tool parameter(s):\n- ganon classify: `--output-all --output-lca --output-unclassified`"
+                    "help_text": "Saves `.one`, `.all`, and `.unc` text files that contains a list of each read that had a taxonomic assignment, with information on specific taxonomic assignment that the read received.\n\n> Modifies tool parameter(s):\n- ganon classify: `--output-all --output-unclassified`"
                 },
                 "ganon_report_type": {
                     "type": "string",