diff --git a/covidRefSequences/PacBioHiFi.mmi b/covidRefSequences/PacBioHiFi.mmi
new file mode 100755
index 0000000..054cfb2
Binary files /dev/null and b/covidRefSequences/PacBioHiFi.mmi differ
diff --git a/nextflow.config b/nextflow.config
index f023e1e..27480a3 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -60,9 +60,10 @@ process {
     }
 
     withName: 'freyjaVariantCaller' {
-        time = '2 h'
+        time = '3 h'
         maxForks = 20
         cpus = 15
+        // cpus = 20 
         memory = '24 GB'
     }
     
diff --git a/startWorkflow.nf b/startWorkflow.nf
index ad0fb5a..b0ce8b1 100755
--- a/startWorkflow.nf
+++ b/startWorkflow.nf
@@ -152,7 +152,7 @@ process referenceAlignment {
                 minimap2 -a --sam-hit-only -2 -x map-ont ${refSeqBasename}.mmi R1.fastq.gz -t \$numThreads -o aligned.sam
                 ;;
             PacBio)
-                minimap2 -a --sam-hit-only -2 -x map-hifi ${refSeqBasename}.mmi R1.fastq.gz -t \$numThreads -o aligned.sam
+                minimap2 -a --sam-hit-only -2 -x map-hifi $projectDir/covidRefSequences/PacBioHiFi.mmi R1.fastq.gz -t \$numThreads -o aligned.sam
                 ;;
         esac
     """