8cd2af3f5f15571eb78ae62c1a470e492aecf22d
hiram
  Fri Jul 24 14:13:13 2026 -0700
temporary field count error in assembly_summary_refseq.txt ignore bad records refs #31811

diff --git src/hg/hubApi/assemblyList.py src/hg/hubApi/assemblyList.py
index dc73bdc62c9..ff83fe4bdfc 100755
--- src/hg/hubApi/assemblyList.py
+++ src/hg/hubApi/assemblyList.py
@@ -311,32 +311,32 @@
             if refSeqCategory == "na":
                refSeqCategory = ""
             if versionStatus == "na":
                versionStatus = ""
             if assemblyLevel == "na":
                assemblyLevel = ""
             thisStat = {
                 "refSeqCategory": refSeqCategory,
                 "versionStatus": versionStatus,
                 "assemblyLevel": assemblyLevel,
             }
             statusDict[gcAccession] = thisStat
             if gcAccession in prioExists:
                continue
             if len(row) != 38:
-                print(f"ERROR: incorrect number of fields in {file}")
-                sys.exit(255)
+                print(f"WARNING: incorrect number of fields: 38 != {len(row)} in {filePath}")
+                continue
             strain = re.sub(r'breed=', '', row[8])
             s0 = re.sub(r'cultivar=', '', strain)
             strain = re.sub(r'ecotype=', '', s0)
             s0 = re.sub(r'strain=', '', strain)
             strain = re.sub(r'na', '', s0)
             asmId = gcAccession + "_" + asmName
             asmSubmitter = row[16]
             asmType = row[23]
             commonName = "n/a"
             if gcAccession in comNames:
                 commonName = comNames[gcAccession]
             clade = row[24]	# almost like GenArk clades
             if asmId in asmIdClade:	# specific GenArk clade
                 clade = asmIdClade[asmId]
             if clade == "plant":