-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_10423348-10685244

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_23-snap.2060-T1
Valid prediction for snap_scaffold_23-snap.2007-T1
Valid prediction for GlimmerHMM_glimmerT_51726-T1
Valid prediction for snap_scaffold_23-snap.2051-T1
Valid prediction for GlimmerHMM_glimmerT_51745-T1
Valid prediction for snap_scaffold_23-snap.2050-T1
Valid prediction for GlimmerHMM_glimmerT_51752-T1
Valid prediction for snap_scaffold_23-snap.2061-T1
Valid prediction for GlimmerHMM_glimmerT_51725-T1
Valid prediction for GlimmerHMM_glimmerT_51746-T1
Valid prediction for snap_scaffold_23-snap.2028-T1
Valid prediction for GlimmerHMM_glimmerT_51757-T1
Valid prediction for snap_scaffold_23-snap.2048-T1
Valid prediction for snap_scaffold_23-snap.2032-T1
Valid prediction for snap_scaffold_23-snap.2025-T1
Valid prediction for snap_scaffold_23-snap.2031-T1
Valid prediction for snap_scaffold_23-snap.2057-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.2020-T1
Valid prediction for snap_scaffold_23-snap.2035-T1
Valid prediction for GlimmerHMM_glimmerT_51742-T1
Valid prediction for GlimmerHMM_glimmerT_51749-T1
Valid prediction for snap_scaffold_23-snap.2019-T1
Valid prediction for snap_scaffold_23-snap.2015-T1
Valid prediction for snap_scaffold_23-snap.2017-T1
Valid prediction for snap_scaffold_23-snap.2030-T1
Valid prediction for snap_scaffold_23-snap.2054-T1
Valid prediction for snap_scaffold_23-snap.2009-T1
Valid prediction for snap_scaffold_23-snap.2044-T1
Valid prediction for GlimmerHMM_glimmerT_51730-T1
Valid prediction for snap_scaffold_23-snap.2022-T1
Valid prediction for GlimmerHMM_glimmerT_51751-T1
Valid prediction for snap_scaffold_23-snap.2036-T1
Valid prediction for snap_scaffold_23-snap.2038-T1
Valid prediction for snap_scaffold_23-snap.2010-T1
Valid prediction for snap_scaffold_23-snap.2040-T1
Valid prediction for GlimmerHMM_glimmerT_51739-T1
Valid prediction for snap_scaffold_23-snap.2052-T1
Valid prediction for GlimmerHMM_glimmerT_51748-T1
Valid prediction for GlimmerHMM_glimmerT_51750-T1
Valid prediction for snap_scaffold_23-snap.2047-T1
Valid prediction for snap_scaffold_23-snap.2014-T1
Valid prediction for GlimmerHMM_glimmerT_51743-T1
Valid prediction for snap_scaffold_23-snap.2034-T1
Valid prediction for GlimmerHMM_glimmerT_51737-T1
Valid prediction for GlimmerHMM_glimmerT_51731-T1
Valid prediction for GlimmerHMM_glimmerT_51753-T1
Valid prediction for snap_scaffold_23-snap.2046-T1
Valid prediction for snap_scaffold_23-snap.2021-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 176767, 176850
Couldn't classify 179262, 179374
Sorry, prediction pasa_asmbl_31864.p1 fails validation.
(CTC)	 TT	176767-176850	GT	AGG
(ATA)	 AG	177867-177943	GT	AGG
(GAA)	 AG	178369-178526	GT	AGG
(ACT)	 AG	179262-179374	GC	AGG
-recovered pasa_asmbl_31864.p1, internal, 177867, 177943
-recovered pasa_asmbl_31864.p1, internal, 178369, 178526
-recovered pasa_asmbl_31864.p1, internal, 179262, 179374
Valid prediction for GlimmerHMM_glimmerT_51728-T1
Valid prediction for snap_scaffold_23-snap.2041-T1
Couldn't classify 179855, 179899
Sorry, prediction pasa_asmbl_31865.p1 fails validation.
(TCG)	 GG	179855-179899	GT	AGG
(GGC)	 AG	180965-181393	AC	AGA
-recovered pasa_asmbl_31865.p1, terminal, 180965, 181393
Valid prediction for snap_scaffold_23-snap.2012-T1
Valid prediction for Augustus_model.g34567.t1
Valid prediction for GlimmerHMM_glimmerT_51756-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for snap_scaffold_23-snap.2049-T1
Couldn't classify 11306, 11379
Sorry, prediction pasa_asmbl_31269.p1 fails validation.
(ATG)	 CA	5737-5847	GT	CCG
(ACC)	 AG	6180-6306	GT	GGG
(GTC)	 AG	6658-6728	GT	GGG
(ACC)	 AG	6954-7142	GT	AGG
(TTG)	 AG	7909-8000	GT	ATG
(AAT)	 AG	8306-8401	GT	AGG
(GCT)	 AG	8687-8808	GT	AGG
(GGT)	 AG	8984-9045	GT	AGG
(CTC)	 AG	9702-9833	GT	AGG
(CTG)	 AG	10188-10398	GT	CGG
(GTC)	 AG	10562-10693	GT	AGG
(ATG)	 AG	10819-11040	GT	GGG
(GGT)	 AG	11306-11379	GT	CTG
-recovered pasa_asmbl_31269.p1, initial, 5737, 5847
add_exon() Sorry, pasa_asmbl_31269.p1 10819-11040-initial-1 is invalid.
-recovered pasa_asmbl_31269.p1, initial, 10819, 11040
-recovered pasa_asmbl_31269.p1, internal, 6180, 6306
-recovered pasa_asmbl_31269.p1, internal, 6658, 6728
-recovered pasa_asmbl_31269.p1, internal, 6954, 7142
-recovered pasa_asmbl_31269.p1, internal, 7909, 8000
-recovered pasa_asmbl_31269.p1, internal, 8306, 8401
-recovered pasa_asmbl_31269.p1, internal, 8687, 8808
-recovered pasa_asmbl_31269.p1, internal, 8984, 9045
-recovered pasa_asmbl_31269.p1, internal, 9702, 9833
-recovered pasa_asmbl_31269.p1, internal, 10188, 10398
-recovered pasa_asmbl_31269.p1, internal, 10562, 10693
-recovered pasa_asmbl_31269.p1, internal, 10819, 11040
-recovered pasa_asmbl_31269.p1, internal, 11306, 11379
Valid prediction for snap_scaffold_23-snap.2026-T1
Valid prediction for snap_scaffold_23-snap.2024-T1
Valid prediction for snap_scaffold_23-snap.2037-T1
Valid prediction for snap_scaffold_23-snap.2058-T1
Valid prediction for GlimmerHMM_glimmerT_51727-T1
Valid prediction for GlimmerHMM_glimmerT_51738-T1
Valid prediction for snap_scaffold_23-snap.2016-T1
Valid prediction for snap_scaffold_23-snap.2039-T1
Valid prediction for GlimmerHMM_glimmerT_51734-T1
Valid prediction for GlimmerHMM_glimmerT_51740-T1
Valid prediction for snap_scaffold_23-snap.2043-T1
Valid prediction for snap_scaffold_23-snap.2042-T1
Valid prediction for snap_scaffold_23-snap.2011-T1
Valid prediction for GlimmerHMM_glimmerT_51747-T1
Valid prediction for GlimmerHMM_glimmerT_51732-T1
Valid prediction for GlimmerHMM_glimmerT_51735-T1
Valid prediction for GlimmerHMM_glimmerT_51755-T1
Valid prediction for GlimmerHMM_glimmerT_51736-T1
Valid prediction for snap_scaffold_23-snap.2033-T1
Valid prediction for GlimmerHMM_glimmerT_51754-T1
Valid prediction for GlimmerHMM_glimmerT_51758-T1
Valid prediction for snap_scaffold_23-snap.2018-T1
Valid prediction for snap_scaffold_23-snap.2027-T1
Valid prediction for GlimmerHMM_glimmerT_51733-T1
Valid prediction for snap_scaffold_23-snap.2045-T1
Valid prediction for snap_scaffold_23-snap.2059-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g34568.t1
Valid prediction for snap_scaffold_23-snap.2008-T1
Valid prediction for CodingQuarry_transcript_35800-T1
Valid prediction for snap_scaffold_23-snap.2053-T1
Valid prediction for snap_scaffold_23-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_51744-T1
Valid prediction for GlimmerHMM_glimmerT_51741-T1
Valid prediction for GlimmerHMM_glimmerT_51729-T1
Valid prediction for snap_scaffold_23-snap.2013-T1
Couldn't classify 13574, 13683
Sorry, prediction pasa_asmbl_31146.p1 fails validation.
(AGG)	 GC	13574-13683	GT	TTG
(CTA)	 AG	13893-14125	GT	AGG
(GTC)	 AG	14294-14529	GG	GAG
-recovered pasa_asmbl_31146.p1, terminal, 14294, 14529
-recovered pasa_asmbl_31146.p1, internal, 13893, 14125
Valid prediction for snap_scaffold_23-snap.2023-T1
Valid prediction for snap_scaffold_23-snap.2029-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.2055-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 146994, rend_intergenic: 146991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 156946, rend_intergenic: 156943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14404, rend_intergenic: 14186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16676, rend_intergenic: 14664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17067, rend_intergenic: 16693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25679, rend_intergenic: 17226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30701, rend_intergenic: 27064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41248, rend_intergenic: 32209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47141, rend_intergenic: 42688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54967, rend_intergenic: 47907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65889, rend_intergenic: 55054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70766, rend_intergenic: 66521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74081, rend_intergenic: 72286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87705, rend_intergenic: 75069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91469, rend_intergenic: 88432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99221, rend_intergenic: 91532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117698, rend_intergenic: 116788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126662, rend_intergenic: 118279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135732, rend_intergenic: 126944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146829, rend_intergenic: 140178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153048, rend_intergenic: 146991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158585, rend_intergenic: 154769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159381, rend_intergenic: 159137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161815, rend_intergenic: 160204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194102, rend_intergenic: 189129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228714, rend_intergenic: 219448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234609, rend_intergenic: 229272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243450, rend_intergenic: 239003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253244, rend_intergenic: 243464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256161, rend_intergenic: 253625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 261897
-exon list size: 358


building trellis

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3.6    
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12.2    
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14.7    
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15.6    
15.8    
16.1    
16.4    
16.7    
16.9    
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17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.2    
19.4    
19.7    
20.0    
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21.4    
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21.9    
22.2    
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23.3    
23.6    
23.9    
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24.4    
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25.6    
25.8    
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26.4    
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26.9    
27.2    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.3    
30.6    
30.8    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.2    
39.4    
39.7    
40.0    
40.3    
40.6    
40.8    
41.1    
41.4    
41.7    
41.9    
42.2    
42.5    
42.8    
43.1    
43.3    
43.6    
43.9    
44.2    
44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.7    
46.9    
47.2    
47.5    
47.8    
48.1    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
51.9    
52.2    
52.5    
52.8    
53.1    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.8    
56.1    
56.4    
56.7    
56.9    
57.2    
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57.8    
58.1    
58.3    
58.6    
58.9    
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59.7    
60.0    
60.3    
60.6    
60.8    
61.1    
61.4    
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62.2    
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63.1    
63.3    
63.6    
63.9    
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64.4    
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65.3    
65.6    
65.8    
66.1    
66.4    
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66.9    
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67.5    
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78.1    
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78.6    
78.9    
79.2    
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80.0    
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80.6    
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86.1    
86.4    
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88.1    
88.3    
88.6    
88.9    
89.2    
89.4    
89.7    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.7    
91.9    
92.2    
92.5    
92.8    
93.1    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
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95.3    
95.6    
95.8    
96.1    
96.4    
96.7    
96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 146994, rend_intergenic: 146991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 156946, rend_intergenic: 156943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14404, rend_intergenic: 14186  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16676, rend_intergenic: 14664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17067, rend_intergenic: 16693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25679, rend_intergenic: 17226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30701, rend_intergenic: 27064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41248, rend_intergenic: 32209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47141, rend_intergenic: 42688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54967, rend_intergenic: 47907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65889, rend_intergenic: 55054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70766, rend_intergenic: 66521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74081, rend_intergenic: 72286  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87705, rend_intergenic: 75069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91469, rend_intergenic: 88432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99221, rend_intergenic: 91532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117698, rend_intergenic: 116788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126662, rend_intergenic: 118279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135732, rend_intergenic: 126944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146829, rend_intergenic: 140178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153048, rend_intergenic: 146991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158585, rend_intergenic: 154769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159381, rend_intergenic: 159137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161815, rend_intergenic: 160204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194102, rend_intergenic: 189129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228714, rend_intergenic: 219448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234609, rend_intergenic: 229272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243450, rend_intergenic: 239003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253244, rend_intergenic: 243464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256161, rend_intergenic: 253625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15495
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14663
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 4036 - 14663
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support