ERROR in parsing gene gapmm2_4 #44
Description
Hello, I always get this error every time I include my Orthofuser-assembled transcriptome as transcript input for the funannotate2 predict command. I tried transcriptome reduction via mmseqs as a post-processing step just to see if it might help, but to no avail.
I would appreciate any help to overcome this problem.
ERROR in parsing gene gapmm2_4
[('partialStart', [], 0), ('partialStop', [], 0)]
{'name': 'TRINITY_DN6892_c1_g1_i1', 'type': ['mRNA'], 'transcript':
...
'cds_transcript': [''], 'protein': [''], '5UTR': [[]], '3UTR': [[]], 'gene_synonym': [], 'codon_start': [1], 'ids': ['gapmm2_4'], 'CDS': [[(2107953, 2107952)]], 'mRNA': [[(2107953, 2108017), (2100799, 2100924), (2099727, 2099943), (2099194, 2099318), (2098536, 2098598), (2097910, 2097987), (2097318, 2097422), (2096780, 2096866), (2095876, 2095953), (2095391, 2095448), (2095015, 2095112), (2094430, 2094591), (2093405, 2093461), (2093261, 2093294), (2092902, 2092965), (2092595, 2092701), (2091818, 2091942), (2091379, 2091507), (2090542, 2090679), (2089696, 2089808), (2089258, 2089406), (2087544, 2088307)]], 'strand': '-', 'EC_number': [[]], 'location': (2087544, 2108017), 'contig': 'contig_67', 'product': ['transcript alignment'], 'source': 'gapmm2', 'phase': [['?']], 'db_xref': [[]], 'go_terms': [[]], 'note': [[]], 'partialStart': [], 'partialStop': [], 'pseudo': False, 'score': [99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69, 99.69], 'target': ['TRINITY_DN6892_c1_g1_i1 2188 2952', 'TRINITY_DN6892_c1_g1_i1 2039 2187', 'TRINITY_DN6892_c1_g1_i1 1926 2038', 'TRINITY_DN6892_c1_g1_i1 1788 1925', 'TRINITY_DN6892_c1_g1_i1 1659 1787', 'TRINITY_DN6892_c1_g1_i1 1534 1658', 'TRINITY_DN6892_c1_g1_i1 1427 1533', 'TRINITY_DN6892_c1_g1_i1 1363 1426', 'TRINITY_DN6892_c1_g1_i1 1329 1362', 'TRINITY_DN6892_c1_g1_i1 1272 1328', 'TRINITY_DN6892_c1_g1_i1 1110 1271', 'TRINITY_DN6892_c1_g1_i1 1012 1109', 'TRINITY_DN6892_c1_g1_i1 954 1011', 'TRINITY_DN6892_c1_g1_i1 876 953', 'TRINITY_DN6892_c1_g1_i1 789 875', 'TRINITY_DN6892_c1_g1_i1 684 788', 'TRINITY_DN6892_c1_g1_i1 606 683', 'TRINITY_DN6892_c1_g1_i1 543 60(funannotate2)