diff --git a/mibios/omics/managers.py b/mibios/omics/managers.py
index 05bc0d33..4713f04c 100644
--- a/mibios/omics/managers.py
+++ b/mibios/omics/managers.py
@@ -2,6 +2,7 @@
 Module for data load managers
 """
 from collections import defaultdict
+from contextlib import ExitStack
 from datetime import date
 from functools import partial
 from itertools import groupby, islice
@@ -702,46 +703,51 @@ def update_from_pipeline_registry(
             (SUCCESS, 'import_success'),
         )
 
-        # setup log file output
-        if log_dir := getattr(settings, 'IMPORT_LOG_DIR', ''):
-            # find a unique log file name and set up the log handler
-            path = Path(log_dir) / 'omics_status_update'
-            today = date.today()
-            suffix = f'.{today}.log'
-            num = 0
-            while path.with_suffix(suffix).exists():
-                num += 1
-                suffix = f'.{today}.{num}.log'
-
-            log_file = path.with_suffix(suffix).open('w')
-            print(f'Logging to: {log_file.name}')
-        else:
-            log_file = sys.stdout
+        # ExitStack: To cleanly close log file (if needed) and input file as
+        # there is some interaction with the atomic_dry wrapper
+        with ExitStack() as estack:
+
+            # setup log file output
+            if log_dir := getattr(settings, 'IMPORT_LOG_DIR', ''):
+                # find a unique log file name and set up the log handler
+                log_file_base = Path(log_dir) / 'omics_status_update'
+                today = date.today()
+                suffix = f'.{today}.log'
+                num = 0
+                while (log_file := log_file_base.with_suffix(suffix)).exists():
+                    num += 1
+                    suffix = f'.{today}.{num}.log'
+
+                log_file = estack.enter_context(log_file.open('w'))
+                print(f'Logging to: {log_file.name}')
+            else:
+                log_file = sys.stdout
 
-        def log(msg):
-            if quiet and msg.startswith('INFO'):
-                return
-            print(msg, file=log_file)
+            def log(msg):
+                if quiet and msg.startswith('INFO'):
+                    return
+                print(msg, file=log_file)
 
-        def err(msg):
-            msg = f'ERROR: {msg}'
-            if skip_on_error:
-                log(msg)
-            else:
-                raise RuntimeError(msg)
+            def err(msg):
+                msg = f'ERROR: {msg}'
+                if skip_on_error:
+                    log(msg)
+                else:
+                    raise RuntimeError(msg)
 
-        objs = self.select_related('dataset').in_bulk(field_name='sample_id')
+            objs = self.select_related('dataset') \
+                       .in_bulk(field_name='sample_id')
 
-        if source_file is None:
-            source_file = self.get_omics_import_file()
+            if source_file is None:
+                source_file = self.get_omics_import_file()
 
-        with open(source_file) as f:
             print(f'Reading {source_file} ...')
-            head = f.readline().rstrip('\n').split('\t')
+            srcf = estack.enter_context(open(source_file))
+            head = srcf.readline().rstrip('\n').split('\t')
             for index, column in COLUMN_NAMES:
                 if head[index] != column:
                     raise RuntimeError(
-                        f'unexpected header in {f.name}: 0-based column '
+                        f'unexpected header in {srcf.name}: 0-based column '
                         f'{index} is "{head[index]}" but expected "{column}"'
                     )
 
@@ -751,7 +757,7 @@ def err(msg):
             unchanged = 0
             notfound = 0
             nosuccess = 0
-            for lineno, line in enumerate(f, start=1):
+            for lineno, line in enumerate(srcf, start=1):
                 row = line.rstrip('\n').split('\t')
                 sample_id = row[SAMPLE_ID]
                 dataset = row[STUDY_ID]
@@ -827,30 +833,33 @@ def err(msg):
                 if not new:
                     tr.save()  # update timestamp
 
-        log('Summary:')
-        log(f'  records read from file: {lineno}')
-        log(f'  (unique) samples listed: {len(samp_id_seen)}')
-        log(f'  samples updated: {changed}')
-        if notfound:
-            log(f'WARNING Samples missing from database (or hidden): '
-                f'{notfound}')
-
-        if nosuccess:
-            log(f'WARNING Samples not marked "import_success": {nosuccess}')
-
-        if unchanged:
-            log(f'Data for {unchanged} listed samples remain unchanged.')
-
-        missing_or_bad = self.exclude(pk__in=good_seen)
-        if missing_or_bad.exists():
-            log(f'WARNING The DB has {missing_or_bad.count()} samples '
-                f'which are missing from {source_file} or which had '
-                f'to be skipped for other reasons.')
-
-        missing = self.exclude(sample_id__in=samp_id_seen)
-        if missing.exists():
-            log(f'WARNING The DB has {missing.count()} samples not at all '
-                f'listed in {source_file}')
+            srcf.close()
+
+            log('Summary:')
+            log(f'  records read from file: {lineno}')
+            log(f'  (unique) samples listed: {len(samp_id_seen)}')
+            log(f'  samples updated: {changed}')
+            if notfound:
+                log(f'WARNING Samples missing from database (or hidden): '
+                    f'{notfound}')
+
+            if nosuccess:
+                log(f'WARNING Samples not marked "import_success": '
+                    f'{nosuccess}')
+
+            if unchanged:
+                log(f'Data for {unchanged} listed samples remain unchanged.')
+
+            missing_or_bad = self.exclude(pk__in=good_seen)
+            if missing_or_bad.exists():
+                log(f'WARNING The DB has {missing_or_bad.count()} samples '
+                    f'which are missing from {source_file} or which had '
+                    f'to be skipped for other reasons.')
+
+            missing = self.exclude(sample_id__in=samp_id_seen)
+            if missing.exists():
+                log(f'WARNING The DB has {missing.count()} samples not at all '
+                    f'listed in {source_file}')
 
     def get_metagenomic_loader_script(self):
         """