From 0a931c61d6aad0a0ceac2190a5ccf91008370634 Mon Sep 17 00:00:00 2001 From: Kinggerm Date: Fri, 21 Jan 2022 11:20:51 -0500 Subject: [PATCH] v1.7.5.3 --- GetOrganelleLib/versions.py | 5 +++-- get_organelle_from_reads.py | 2 ++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/GetOrganelleLib/versions.py b/GetOrganelleLib/versions.py index e8ca3c7..6a6e58b 100644 --- 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 index 3ccdb65..3c4be76 100755 --- 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