diff --git a/bin/check_hcid.py b/bin/check_hcid.py
index 3e34a71a..0f0c2b7b 100755
--- a/bin/check_hcid.py
+++ b/bin/check_hcid.py
@@ -189,17 +189,39 @@ def report_findings(hcid_dict, read_file, prefix):
             w.writerow({key: hcid_dict[taxid][key] for key in keys})
 
     found = []
-    records = pyfastx.Fastq(read_file, full_name=False, build_index=True)
+    needed = {
+        name
+        for taxid in hcid_dict
+        if hcid_dict[taxid]["mapped_found"]
+        for name in hcid_dict[taxid]["mapped_read_ids"]
+    }
+
+    read_records = {}
+    for name, seq, qual in pyfastx.Fastq(read_file, full_name=False, build_index=False):
+        if name in needed:
+            read_records[name] = (seq, qual)
+
+        if needed - set(read_records.keys()) == set():
+            break
+
     for taxid in hcid_dict:
         if hcid_dict[taxid]["mapped_found"]:
             quals = []
             lens = []
             with open("%s.reads.fq" % taxid, "w") as f_reads:
                 for mapped_name in hcid_dict[taxid]["mapped_read_ids"]:
-                    record = records[mapped_name]
-                    f_reads.write(record.raw)
-                    quals.append(stats.fmean(record.quali) if record.quali else 0)
-                    lens.append(len(record.seq))
+                    record = read_records.get(mapped_name)
+                    if record is None:
+                        print(
+                            f"WARNING: read {mapped_name} not found in FASTQ, skipping",
+                            file=sys.stderr,
+                        )
+                        continue
+                    seq, qual = record
+                    f_reads.write(f"@{mapped_name}\n{seq}\n+\n{qual}\n")
+                    phred = [ord(c) - 33 for c in qual]
+                    quals.append(stats.fmean(phred) if phred else 0)
+                    lens.append(len(seq))
             with open("%s.warning.json" % taxid, "w") as f_warn:
                 msg1 = f"WARNING: Found {hcid_dict[taxid]['classified_count']} classified reads ({hcid_dict[taxid]['mapped_count']} mapped reads) of {hcid_dict[taxid]['name']} and {hcid_dict[taxid]['classified_parent_count']} classified reads for the parent taxon.\n"
                 msg2 = f"Mapping details for required references (ref_accession:mapped_read_count:fraction_ref_covered) {hcid_dict[taxid]['mapped_required_details']}.\n"
diff --git a/nextflow.config b/nextflow.config
index af207bfc..e6a33b27 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -25,7 +25,7 @@ manifest {
     description     = 'Classify metagenomic sequence data from human respiratory infections.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = 'v2.2.0'
+    version         = 'v2.2.1'
 }
 
 profiles {