-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_8030711-8202487

-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 GlimmerHMM_glimmerT_59204-T1
Valid prediction for GlimmerHMM_glimmerT_59208-T1
Valid prediction for GlimmerHMM_glimmerT_59214-T1
Valid prediction for snap_scaffold_28-snap.1825-T1
Couldn't classify 73122, 73272
Couldn't classify 77688, 77793
Sorry, prediction pasa_asmbl_37845.p1 fails validation.
(ACG)	 TG	73122-73272	GT	GGG
(CTA)	 AG	75274-75388	GT	AGG
(GGG)	 AG	77688-77793	GA	GAG
-recovered pasa_asmbl_37845.p1, internal, 75274, 75388
Valid prediction for snap_scaffold_28-snap.1837-T1
Valid prediction for snap_scaffold_28-snap.1840-T1
Valid prediction for snap_scaffold_28-snap.1829-T1
Valid prediction for GlimmerHMM_glimmerT_59212-T1
Valid prediction for snap_scaffold_28-snap.1824-T1
Valid prediction for GlimmerHMM_glimmerT_59217-T1
Valid prediction for HiQ_model.g39239.t1
Valid prediction for GlimmerHMM_glimmerT_59227-T1
Valid prediction for GlimmerHMM_glimmerT_59210-T1
Valid prediction for GlimmerHMM_glimmerT_59211-T1
Valid prediction for snap_scaffold_28-snap.1834-T1
Valid prediction for snap_scaffold_28-snap.1845-T1
Valid prediction for Augustus_model.g39236.t1
Valid prediction for CodingQuarry_transcript_43734-T1
Valid prediction for snap_scaffold_28-snap.1847-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1818-T1
Couldn't classify 36330, 36381
Sorry, prediction pasa_asmbl_37721.p1 fails validation.
(TCC)	 TC	36330-36381	GT	CGG
(GAC)	 AG	36591-36691	GT	TGG
(TGT)	 AG	37293-37463	GT	AGG
(AGG)	 AG	38507-38617	TG	AGT
-recovered pasa_asmbl_37721.p1, terminal, 38507, 38617
-recovered pasa_asmbl_37721.p1, internal, 36591, 36691
-recovered pasa_asmbl_37721.p1, internal, 37293, 37463
Valid prediction for snap_scaffold_28-snap.1811-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_59228-T1
Valid prediction for Augustus_model.g39234.t1
Valid prediction for GlimmerHMM_glimmerT_59216-T1
Valid prediction for Augustus_model.g39245.t1
Valid prediction for GlimmerHMM_glimmerT_59207-T1
Valid prediction for snap_scaffold_28-snap.1839-T1
Valid prediction for GlimmerHMM_glimmerT_59213-T1
Valid prediction for GlimmerHMM_glimmerT_59222-T1
Valid prediction for snap_scaffold_28-snap.1813-T1
Valid prediction for CodingQuarry_transcript_43735-T1
Couldn't classify 28515, 28726
Couldn't classify 29478, 29601
Sorry, prediction pasa_asmbl_37843.p1 fails validation.
(GGT)	 CA	28515-28726	GT	GAG
(TCA)	 AG	29478-29601	AC	CCA
Valid prediction for snap_scaffold_28-snap.1833-T1
Valid prediction for snap_scaffold_28-snap.1814-T1
Valid prediction for snap_scaffold_28-snap.1810-T1
Couldn't classify 84049, 84392
Sorry, prediction pasa_asmbl_37723.p1 fails validation.
(ATG)	 AC	79633-79647	GT	AGG
(GAG)	 AG	80114-80288	GT	AGG
(ATA)	 AG	80753-80917	GT	AGG
(GGT)	 AG	81223-81423	GT	AGG
(AGT)	 AG	84049-84392	CC	GAC
-recovered pasa_asmbl_37723.p1, initial, 79633, 79647
-recovered pasa_asmbl_37723.p1, internal, 80114, 80288
-recovered pasa_asmbl_37723.p1, internal, 80753, 80917
-recovered pasa_asmbl_37723.p1, internal, 81223, 81423
Valid prediction for snap_scaffold_28-snap.1849-T1
Valid prediction for snap_scaffold_28-snap.1815-T1
Valid prediction for GlimmerHMM_glimmerT_59209-T1
Valid prediction for GlimmerHMM_glimmerT_59220-T1
Valid prediction for snap_scaffold_28-snap.1819-T1
Valid prediction for HiQ_model.g39242.t1
Valid prediction for snap_scaffold_28-snap.1842-T1
Valid prediction for pasa_asmbl_37725.p1
Valid prediction for CodingQuarry_transcript_43731-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 GlimmerHMM_glimmerT_59219-T1
Valid prediction for Augustus_model.g39246.t1
Valid prediction for GlimmerHMM_glimmerT_59215-T1
Valid prediction for snap_scaffold_28-snap.1841-T1
Valid prediction for GlimmerHMM_glimmerT_59229-T1
Valid prediction for snap_scaffold_28-snap.1821-T1
Valid prediction for Augustus_model.g39233.t1
Couldn't classify 31512, 31641
Couldn't classify 34605, 34847
Sorry, prediction pasa_asmbl_38443.p2 fails validation.
(GTG)	 AG	31512-31641	GT	TGG
(GCT)	 AG	32526-32707	GT	CGG
(GAG)	 AG	32810-32929	GT	CGG
(CAA)	 AG	33114-33218	GT	AGG
(GGC)	 AG	33359-33504	GT	AGG
(GTT)	 AG	33888-33945	GT	AGG
(AGC)	 AG	34605-34847	GT	TCG
-recovered pasa_asmbl_38443.p2, internal, 31512, 31641
-recovered pasa_asmbl_38443.p2, internal, 32526, 32707
-recovered pasa_asmbl_38443.p2, internal, 32810, 32929
-recovered pasa_asmbl_38443.p2, internal, 33114, 33218
-recovered pasa_asmbl_38443.p2, internal, 33359, 33504
-recovered pasa_asmbl_38443.p2, internal, 33888, 33945
-recovered pasa_asmbl_38443.p2, internal, 34605, 34847
Valid prediction for snap_scaffold_28-snap.1823-T1
Valid prediction for snap_scaffold_28-snap.1822-T1
Valid prediction for Augustus_model.g39237.t1
Valid prediction for Augustus_model.g39249.t1
Valid prediction for snap_scaffold_28-snap.1830-T1
Valid prediction for Augustus_model.g39247.t1
Valid prediction for Augustus_model.g39243.t1
Valid prediction for CodingQuarry_transcript_43733-T1
Valid prediction for Augustus_model.g39241.t1
Valid prediction for Augustus_model.g39244.t1
Valid prediction for snap_scaffold_28-snap.1843-T1
Valid prediction for GlimmerHMM_glimmerT_59205-T1
Valid prediction for snap_scaffold_28-snap.1816-T1
Valid prediction for snap_scaffold_28-snap.1832-T1
Valid prediction for snap_scaffold_28-snap.1844-T1
Valid prediction for snap_scaffold_28-snap.1827-T1
Valid prediction for snap_scaffold_28-snap.1835-T1
Valid prediction for snap_scaffold_28-snap.1846-T1
Valid prediction for snap_scaffold_28-snap.1809-T1
Valid prediction for GlimmerHMM_glimmerT_59206-T1
Valid prediction for snap_scaffold_28-snap.1817-T1
Valid prediction for snap_scaffold_28-snap.1838-T1
Valid prediction for snap_scaffold_28-snap.1812-T1
Valid prediction for snap_scaffold_28-snap.1831-T1
Valid prediction for snap_scaffold_28-snap.1836-T1
Valid prediction for snap_scaffold_28-snap.1828-T1
Couldn't classify 165084, 165236
Couldn't classify 167604, 167669
Sorry, prediction pasa_asmbl_38437.p1 fails validation.
(ACG)	 CC	165084-165236	GT	AGG
(GTG)	 AG	165438-165524	GT	AGG
(GTT)	 AG	166094-166225	GT	TGG
(GAC)	 AG	166813-166869	GT	TGG
(ACG)	 AG	167604-167669	GT	TGG
-recovered pasa_asmbl_38437.p1, internal, 165438, 165524
-recovered pasa_asmbl_38437.p1, internal, 166094, 166225
-recovered pasa_asmbl_38437.p1, internal, 166813, 166869
-recovered pasa_asmbl_38437.p1, internal, 167604, 167669
Valid prediction for snap_scaffold_28-snap.1848-T1
Valid prediction for Augustus_model.g39248.t1
Couldn't classify 58511, 58912
Couldn't classify 59570, 59752
Sorry, prediction pasa_asmbl_38440.p1 fails validation.
(GAG)	 GC	58511-58912	GT	AGG
(GTG)	 AG	59037-59189	GT	AGG
(GGT)	 AG	59570-59752	TG	CGT
-recovered pasa_asmbl_38440.p1, internal, 59037, 59189
Valid prediction for GlimmerHMM_glimmerT_59226-T1
Valid prediction for GlimmerHMM_glimmerT_59224-T1
Valid prediction for GlimmerHMM_glimmerT_59221-T1
Valid prediction for GlimmerHMM_glimmerT_59218-T1
Valid prediction for Augustus_model.g39235.t1
Valid prediction for Augustus_model.g39238.t1
Couldn't classify 53784, 53825
Couldn't classify 58143, 58304
Sorry, prediction pasa_asmbl_38441.p1 fails validation.
(AGA)	 GC	53784-53825	GT	AGG
(GAC)	 AG	54664-54802	GT	TGG
(ATG)	 AG	54939-55046	GT	AGG
(AGT)	 AG	55650-55727	GT	GAG
(GGT)	 AG	56333-56391	GT	AGG
(GCA)	 AG	56879-56988	GT	AGG
(GTC)	 AG	57080-57192	GT	GGG
(GCT)	 AG	57575-57651	GT	AGG
(GTG)	 AG	58143-58304	GA	ATG
add_exon() Sorry, pasa_asmbl_38441.p1 54939-55046-initial-1 is invalid.
-recovered pasa_asmbl_38441.p1, initial, 54939, 55046
-recovered pasa_asmbl_38441.p1, internal, 54664, 54802
-recovered pasa_asmbl_38441.p1, internal, 54939, 55046
-recovered pasa_asmbl_38441.p1, internal, 55650, 55727
-recovered pasa_asmbl_38441.p1, internal, 56333, 56391
-recovered pasa_asmbl_38441.p1, internal, 56879, 56988
-recovered pasa_asmbl_38441.p1, internal, 57080, 57192
-recovered pasa_asmbl_38441.p1, internal, 57575, 57651
Valid prediction for snap_scaffold_28-snap.1820-T1
Valid prediction for Augustus_model.g39240.t1
Valid prediction for GlimmerHMM_glimmerT_59223-T1
Valid prediction for GlimmerHMM_glimmerT_59225-T1
Valid prediction for snap_scaffold_28-snap.1826-T1
Couldn't classify 82565, 82915
Sorry, prediction pasa_asmbl_38438.p1 fails validation.
(CTG)	 GG	82565-82915	AC	AAA

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11822, rend_intergenic: 4953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13413, rend_intergenic: 12412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18663, rend_intergenic: 14628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38617, rend_intergenic: 28592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67774, rend_intergenic: 58051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73583, rend_intergenic: 70983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84900, rend_intergenic: 76831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118466, rend_intergenic: 105636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120280, rend_intergenic: 118627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129747, rend_intergenic: 128197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131649, rend_intergenic: 130061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138992, rend_intergenic: 136289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141233, rend_intergenic: 139020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154868, rend_intergenic: 152965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161512, rend_intergenic: 155010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166667, rend_intergenic: 161729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171407, rend_intergenic: 167432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171777
-exon list size: 338


building trellis

0.3    
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2.9    
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3.5    
3.8    
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8.5    
8.8    
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10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.8    
27.1    
27.4    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
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66.8    
67.1    
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67.6    
67.9    
68.2    
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69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
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72.1    
72.4    
72.6    
72.9    
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73.8    
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74.4    
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75.0    
75.3    
75.6    
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78.2    
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81.2    
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82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 11822, rend_intergenic: 4953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13413, rend_intergenic: 12412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18663, rend_intergenic: 14628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38617, rend_intergenic: 28592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67774, rend_intergenic: 58051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73583, rend_intergenic: 70983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84900, rend_intergenic: 76831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118466, rend_intergenic: 105636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120280, rend_intergenic: 118627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129747, rend_intergenic: 128197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131649, rend_intergenic: 130061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138992, rend_intergenic: 136289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141233, rend_intergenic: 139020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154868, rend_intergenic: 152965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161512, rend_intergenic: 155010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166667, rend_intergenic: 161729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171407, rend_intergenic: 167432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support