v1.7.5.3

Kinggerm · Jan 21, 2022 · 0a931c6 · 0a931c6
1 parent caa29f1
commit 0a931c6
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/GetOrganelleLib/versions.py b/GetOrganelleLib/versions.py
@@ -10,9 +10,10 @@ def get_versions():
         "features": [
             "1. get_organelle_from_reads.py: fix a bug when no qualified reads found (issue 123)",
             "2. get_organelle_from_reads.py: pass --spades-options to pre-assembly for Mac M1 (issue 127)",
-            "3. Update README.md: input read qc; issues->discussions",
+            "3. get_organelle_from_reads.py:slim_spades_result: avoid ValueError",
+            "4. Update README.md: input read qc; issues->discussions",
         ],
-        "time": "2022-01-19 21:00 UTC-5"
+        "time": "2022-01-21 11:20 UTC-5"
     },
     {
         "number": "1.7.5.2",

diff --git a/get_organelle_from_reads.py b/get_organelle_from_reads.py
@@ -3263,6 +3263,8 @@ def slim_spades_result(organelle_types, in_custom, ex_custom, spades_output, ign
                           and kmer_d.startswith("K")
                           and os.path.exists(os.path.join(spades_output, kmer_d, "assembly_graph.fastg"))],
                          reverse=True)
+    if not kmer_values:
+        return [], ignore_kmer_res  # to avoid "ValueError: max() arg is an empty sequence"
     if max(kmer_values) <= ignore_kmer_res:
         log_handler.info("Small kmer values, resetting \"--ignore-k -1\"")
         ignore_kmer_res = -1