diff --git a/python/obitools3/commands/alignpairedend.pyx b/python/obitools3/commands/alignpairedend.pyx
index e012c99..5b5bd32 100755
--- a/python/obitools3/commands/alignpairedend.pyx
+++ b/python/obitools3/commands/alignpairedend.pyx
@@ -205,19 +205,25 @@ def run(config):
     if type(entries) == list:
         forward = entries[0]
         reverse = entries[1]
-        aligner = Kmer_similarity(forward, \
-                                  view2=reverse, \
-                                  kmer_size=config['alignpairedend']['kmersize'], \
-                                  reversed_column=None)
+        if len(forward) == 0 or len(reverse) == 0:
+            aligner = None
+        else:
+            aligner = Kmer_similarity(forward, \
+                                      view2=reverse, \
+                                      kmer_size=config['alignpairedend']['kmersize'], \
+                                      reversed_column=None)
     else:
-        aligner = Kmer_similarity(entries, \
-                                  column2=entries[REVERSE_SEQUENCE_COLUMN], \
-                                  qual_column2=entries[REVERSE_QUALITY_COLUMN], \
-                                  kmer_size=config['alignpairedend']['kmersize'], \
-                                  reversed_column=entries[b'reversed'])  # column created by the ngsfilter tool
+        if len(entries) == 0:
+            aligner = None
+        else:
+            aligner = Kmer_similarity(entries, \
+                                      column2=entries[REVERSE_SEQUENCE_COLUMN], \
+                                      qual_column2=entries[REVERSE_QUALITY_COLUMN], \
+                                      kmer_size=config['alignpairedend']['kmersize'], \
+                                      reversed_column=entries[b'reversed'])  # column created by the ngsfilter tool
         
     ba = alignmentIterator(entries, aligner)
-
+    
     i = 0
     for ali in ba:
         
@@ -251,7 +257,7 @@ def run(config):
         pb(i, force=True)
         print("", file=sys.stderr)
 
-    if kmer_ali :
+    if kmer_ali and aligner is not None:
         aligner.free()
 
     # Save command config in View and DMS comments
diff --git a/python/obitools3/commands/ngsfilter.pyx b/python/obitools3/commands/ngsfilter.pyx
index 9ffdf01..959210f 100644
--- a/python/obitools3/commands/ngsfilter.pyx
+++ b/python/obitools3/commands/ngsfilter.pyx
@@ -645,6 +645,7 @@ def run(config):
     
     g = 0
     u = 0
+    i = 0
     no_tags = config['ngsfilter']['notags']
     try:
         for i in range(entries_len):
diff --git a/python/obitools3/parsers/universal.pyx b/python/obitools3/parsers/universal.pyx
index 4ef828f..c3fd80b 100755
--- a/python/obitools3/parsers/universal.pyx
+++ b/python/obitools3/parsers/universal.pyx
@@ -53,7 +53,11 @@ def entryIteratorFactory(lineiterator,
 
     i = iterator
         
-    first=next(i)    
+    try:
+        first=next(i)
+    except StopIteration:
+        first=""
+        pass
 
     format=b"tabular"
     
diff --git a/src/obi_clean.c b/src/obi_clean.c
index d94850c..8521c02 100755
--- a/src/obi_clean.c
+++ b/src/obi_clean.c
@@ -229,6 +229,8 @@ int obi_clean(const char* dms_name,
 		return -1;
 	}
 
+	seq_count = (i_view->infos)->line_count;
+
 	// Open the sequence column
 	if (strcmp((i_view->infos)->view_type, VIEW_TYPE_NUC_SEQS) == 0)
 		iseq_column = obi_view_get_column(i_view, NUC_SEQUENCE_COLUMN);
@@ -245,7 +247,7 @@ int obi_clean(const char* dms_name,
 	}
 
 	// Open the sample column if there is one
-	if ((strcmp(sample_column_name, "") == 0) || (sample_column_name == NULL))
+	if ((strcmp(sample_column_name, "") == 0) || (sample_column_name == NULL) || (seq_count == 0))
 	{
 		fprintf(stderr, "Info: No sample information provided, assuming one sample.\n");
 		sample_column = obi_view_get_column(i_view, COUNT_COLUMN);
@@ -340,66 +342,67 @@ int obi_clean(const char* dms_name,
 		return -1;
 	}
 
-	// Build kmer tables
-	ktable = hash_seq_column(i_view, iseq_column, 0);
-	if (ktable == NULL)
+	if (seq_count > 0)
 	{
-		obi_set_errno(OBI_CLEAN_ERROR);
-		obidebug(1, "\nError building kmer tables before aligning");
-		return -1;
-	}
+		// Build kmer tables
+		ktable = hash_seq_column(i_view, iseq_column, 0);
+		if (ktable == NULL)
+		{
+			obi_set_errno(OBI_CLEAN_ERROR);
+			obidebug(1, "\nError building kmer tables before aligning");
+			return -1;
+		}
 
-	seq_count = (i_view->infos)->line_count;
-
-	// Allocate arrays for sample counts otherwise reading in mapped files takes longer
-	complete_sample_count_array = (int*) malloc(seq_count * sample_count * sizeof(int));
-	if (complete_sample_count_array == NULL)
-	{
-		obi_set_errno(OBI_MALLOC_ERROR);
-		obidebug(1, "\nError allocating memory for the array of sample counts, size: %lld", seq_count * sample_count * sizeof(int));
-		return -1;
-	}
-	for (samp=0; samp < sample_count; samp++)
-	{
-		for (k=0; k<seq_count; k++)
-			complete_sample_count_array[k+(samp*seq_count)] = obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, k, samp);
-	}
-
-	// Allocate arrays for blobs otherwise reading in mapped files takes longer
-	blob_array = (Obi_blob_p*) malloc(seq_count * sizeof(Obi_blob_p));
-	if (blob_array == NULL)
-	{
-		obi_set_errno(OBI_MALLOC_ERROR);
-		obidebug(1, "\nError allocating memory for the array of blobs");
-		return -1;
-	}
-	for (k=0; k<seq_count; k++)
-	{
-		blob_array[k] = obi_get_blob_with_elt_idx_and_col_p_in_view(i_view, iseq_column, k, 0);
-	}
-
-	// Allocate alignment result array (byte at 0 if not aligned yet,
-	//											1 if sequence at index has a similarity above the threshold with the current sequence,
-	//											2 if sequence at index has a similarity below the threshold with the current sequence)
-	alignment_result_array = (byte_t*) calloc(seq_count, sizeof(byte_t));
-	if (alignment_result_array == NULL)
-	{
-		obi_set_errno(OBI_MALLOC_ERROR);
-		obidebug(1, "\nError allocating memory for alignment result array");
-		return -1;
-	}
-
-	// Initialize all sequences to singletons or NA if no sequences in that sample
-	for (k=0; k<seq_count; k++)
-	{
+		// Allocate arrays for sample counts otherwise reading in mapped files takes longer
+		complete_sample_count_array = (int*) malloc(seq_count * sample_count * sizeof(int));
+		if (complete_sample_count_array == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for the array of sample counts, size: %lld", seq_count * sample_count * sizeof(int));
+			return -1;
+		}
 		for (samp=0; samp < sample_count; samp++)
 		{
-			if (obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, k, samp) != OBIInt_NA)  // Only initialize samples where there are some sequences
+			for (k=0; k<seq_count; k++)
+				complete_sample_count_array[k+(samp*seq_count)] = obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, k, samp);
+		}
+
+		// Allocate arrays for blobs otherwise reading in mapped files takes longer
+		blob_array = (Obi_blob_p*) malloc(seq_count * sizeof(Obi_blob_p));
+		if (blob_array == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for the array of blobs");
+			return -1;
+		}
+		for (k=0; k<seq_count; k++)
+		{
+			blob_array[k] = obi_get_blob_with_elt_idx_and_col_p_in_view(i_view, iseq_column, k, 0);
+		}
+
+		// Allocate alignment result array (byte at 0 if not aligned yet,
+		//											1 if sequence at index has a similarity above the threshold with the current sequence,
+		//											2 if sequence at index has a similarity below the threshold with the current sequence)
+		alignment_result_array = (byte_t*) calloc(seq_count, sizeof(byte_t));
+		if (alignment_result_array == NULL)
+		{
+			obi_set_errno(OBI_MALLOC_ERROR);
+			obidebug(1, "\nError allocating memory for alignment result array");
+			return -1;
+		}
+
+		// Initialize all sequences to singletons or NA if no sequences in that sample
+		for (k=0; k<seq_count; k++)
+		{
+			for (samp=0; samp < sample_count; samp++)
 			{
-				if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, k, samp, 's') < 0)
+				if (obi_get_int_with_elt_idx_and_col_p_in_view(i_view, sample_column, k, samp) != OBIInt_NA)  // Only initialize samples where there are some sequences
 				{
-					obidebug(1, "\nError initializing all sequences to singletons");
-					return -1;
+					if (obi_set_char_with_elt_idx_and_col_p_in_view(o_view, status_column, k, samp, 's') < 0)
+					{
+						obidebug(1, "\nError initializing all sequences to singletons");
+						return -1;
+					}
 				}
 			}
 		}
@@ -551,17 +554,20 @@ int obi_clean(const char* dms_name,
 		}
 	}
 
-	free_kmer_tables(ktable, seq_count);
-	free(complete_sample_count_array);
-	free(blob_array);
-	free(alignment_result_array);
+	if (seq_count > 0)
+	{
+		free_kmer_tables(ktable, seq_count);
+		free(complete_sample_count_array);
+		free(blob_array);
+		free(alignment_result_array);
+	}
 
 	fprintf(stderr, "\n");
 
 	if (stop)
 		return -1;
 
-	if (heads_only)
+	if (heads_only && (seq_count > 0))
 	{
 		line_selection = malloc((((o_view->infos)->line_count) + 1) * sizeof(index_t));
 		if (line_selection == NULL)
@@ -635,7 +641,7 @@ int obi_clean(const char* dms_name,
 	}
 
 	// Flag the end of the line selection
-	if (heads_only)
+	if (heads_only && (seq_count > 0))
 		line_selection[l] = -1;
 
 	// Create new view with line selection if heads only