-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_7487231-7615080

-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_56101-T1
Valid prediction for GlimmerHMM_glimmerT_56091-T1
Couldn't classify 55364, 55551
Couldn't classify 55830, 56007
Sorry, prediction pasa_asmbl_35352.p2 fails validation.
(AGA)	 GC	55364-55551	GT	AAG
(ACC)	 AG	55830-56007	CT	ACC
Valid prediction for snap_scaffold_26-snap.1768-T1
Valid prediction for Augustus_model.g37184.t1
Valid prediction for snap_scaffold_26-snap.1760-T1
Valid prediction for CodingQuarry_transcript_40403-T1
Valid prediction for snap_scaffold_26-snap.1761-T1
Valid prediction for snap_scaffold_26-snap.1755-T1
Valid prediction for snap_scaffold_26-snap.1763-T1
Valid prediction for snap_scaffold_26-snap.1756-T1
Valid prediction for CodingQuarry_transcript_40404-T1
Valid prediction for GlimmerHMM_glimmerT_56088-T1
Valid prediction for GlimmerHMM_glimmerT_56107-T1
Valid prediction for snap_scaffold_26-snap.1775-T1
Valid prediction for snap_scaffold_26-snap.1766-T1
Valid prediction for GlimmerHMM_glimmerT_56092-T1
Valid prediction for snap_scaffold_26-snap.1748-T1
Valid prediction for GlimmerHMM_glimmerT_56102-T1
Valid prediction for Augustus_model.g37189.t1
Couldn't classify 62903, 63053
Sorry, prediction pasa_asmbl_35127.p1 fails validation.
(GTG)	 AG	62903-63053	GT	CGG
(AGA)	 AG	63178-63266	GT	AGG
(TTC)	 AG	63370-63475	GT	AGG
(AGA)	 AG	63821-63999	AG	GAA
-recovered pasa_asmbl_35127.p1, terminal, 63821, 63999
-recovered pasa_asmbl_35127.p1, internal, 62903, 63053
-recovered pasa_asmbl_35127.p1, internal, 63178, 63266
-recovered pasa_asmbl_35127.p1, internal, 63370, 63475
Valid prediction for Augustus_model.g37183.t1
Valid prediction for snap_scaffold_26-snap.1746-T1
Valid prediction for Augustus_model.g37186.t1
Couldn't classify 98286, 98420
Couldn't classify 99319, 99366
Sorry, prediction pasa_asmbl_35130.p1 fails validation.
(GCT)	 AA	98286-98420	GT	TGG
(GGT)	 AG	98651-98728	GT	AGG
(CGC)	 AG	98842-98993	GT	AGG
(AAG)	 AG	99148-99202	GT	GGG
(GTG)	 AG	99319-99366	CG	GAC
-recovered pasa_asmbl_35130.p1, internal, 98651, 98728
-recovered pasa_asmbl_35130.p1, internal, 98842, 98993
-recovered pasa_asmbl_35130.p1, internal, 99148, 99202
Valid prediction for GlimmerHMM_glimmerT_56098-T1
Couldn't classify 100154, 100352
Sorry, prediction pasa_asmbl_35131.p1 fails validation.
(CCT)	 CT	100154-100352	GT	AGG
(AGC)	 AG	100484-100825	GT	AGG
(ATT)	 AG	100913-101020	GT	AGG
(AAG)	 AG	101136-101260	GT	AGG
(GTT)	 AG	101423-101474	GT	TGG
(AGG)	 AG	101565-101701	AC	AGA
-recovered pasa_asmbl_35131.p1, terminal, 101565, 101701
-recovered pasa_asmbl_35131.p1, internal, 100484, 100825
-recovered pasa_asmbl_35131.p1, internal, 100913, 101020
-recovered pasa_asmbl_35131.p1, internal, 101136, 101260
-recovered pasa_asmbl_35131.p1, internal, 101423, 101474
Valid prediction for Augustus_model.g37181.t1
Valid prediction for GlimmerHMM_glimmerT_56093-T1
Valid prediction for snap_scaffold_26-snap.1752-T1
Valid prediction for Augustus_model.g37187.t1
Valid prediction for GlimmerHMM_glimmerT_56111-T1
Couldn't classify 56440, 56619
Couldn't classify 58009, 58089
Sorry, prediction pasa_asmbl_35124.p1 fails validation.
(ACT)	 GG	56440-56619	GT	AGG
(GCG)	 AG	56822-57041	GT	TGG
(ATG)	 AG	57755-57873	GT	AGG
(TAT)	 AG	58009-58089	CG	CAC
-recovered pasa_asmbl_35124.p1, initial, 57755, 57873
-recovered pasa_asmbl_35124.p1, internal, 56822, 57041
-recovered pasa_asmbl_35124.p1, internal, 57755, 57873
Valid prediction for GlimmerHMM_glimmerT_56096-T1
Valid prediction for snap_scaffold_26-snap.1769-T1
Valid prediction for GlimmerHMM_glimmerT_56109-T1
Valid prediction for Augustus_model.g37180.t1
Valid prediction for GlimmerHMM_glimmerT_56095-T1
Valid prediction for snap_scaffold_26-snap.1751-T1
Valid prediction for Augustus_model.g37178.t1
Valid prediction for Augustus_model.g37176.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_26-snap.1759-T1
Valid prediction for snap_scaffold_26-snap.1773-T1
Valid prediction for snap_scaffold_26-snap.1754-T1
Valid prediction for Augustus_model.g37177.t1
Valid prediction for Augustus_model.g37182.t1
Valid prediction for snap_scaffold_26-snap.1757-T1
Valid prediction for snap_scaffold_26-snap.1753-T1
Valid prediction for snap_scaffold_26-snap.1750-T1
Valid prediction for GlimmerHMM_glimmerT_56090-T1
Valid prediction for GlimmerHMM_glimmerT_56106-T1
Valid prediction for snap_scaffold_26-snap.1762-T1
Couldn't classify 119656, 119678
Couldn't classify 120858, 120985
Sorry, prediction pasa_asmbl_35712.p1 fails validation.
(GAA)	 GA	119656-119678	GT	AGG
(TAA)	 AG	120018-120090	GT	AGG
(GGA)	 AG	120162-120215	GT	AGG
(AGG)	 AG	120318-120429	GT	TGG
(ATG)	 AG	120611-120739	GT	AGG
(TGC)	 AG	120858-120985	CA	TAC
add_exon() Sorry, pasa_asmbl_35712.p1 120611-120739-initial-1 is invalid.
-recovered pasa_asmbl_35712.p1, initial, 120611, 120739
-recovered pasa_asmbl_35712.p1, internal, 120018, 120090
-recovered pasa_asmbl_35712.p1, internal, 120162, 120215
-recovered pasa_asmbl_35712.p1, internal, 120318, 120429
-recovered pasa_asmbl_35712.p1, internal, 120611, 120739
Valid prediction for GlimmerHMM_glimmerT_56104-T1
Valid prediction for GlimmerHMM_glimmerT_56103-T1
Valid prediction for HiQ_model.g37175.t1
Valid prediction for Augustus_model.g37174.t1
Valid prediction for Augustus_model.g37179.t1
Valid prediction for Augustus_model.g37188.t1
Valid prediction for snap_scaffold_26-snap.1765-T1
Valid prediction for snap_scaffold_26-snap.1770-T1
Valid prediction for snap_scaffold_26-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_56108-T1
Valid prediction for pasa_asmbl_35713.p1
Couldn't classify 123050, 123159
Sorry, prediction pasa_asmbl_35711.p2 fails validation.
(TGG)	 AC	123050-123159	GT	AGG
(GGA)	 AG	123298-123427	GT	ACG
(ACC)	 AG	124285-124377	GT	GAG
-recovered pasa_asmbl_35711.p2, terminal, 124285, 124377
-recovered pasa_asmbl_35711.p2, internal, 123298, 123427
-recovered pasa_asmbl_35711.p2, internal, 124285, 124377
Valid prediction for GlimmerHMM_glimmerT_56099-T1
Valid prediction for GlimmerHMM_glimmerT_56100-T1
Couldn't classify 108810, 108884
Couldn't classify 109311, 109541
Sorry, prediction pasa_asmbl_35715.p1 fails validation.
(GTG)	 AG	108810-108884	GT	AGG
(CTA)	 AG	109005-109208	GT	AGG
(AAA)	 AG	109311-109541	CA	TAC
-recovered pasa_asmbl_35715.p1, internal, 108810, 108884
-recovered pasa_asmbl_35715.p1, internal, 109005, 109208
Valid prediction for snap_scaffold_26-snap.1767-T1
Valid prediction for GlimmerHMM_glimmerT_56097-T1
Valid prediction for snap_scaffold_26-snap.1758-T1
Valid prediction for snap_scaffold_26-snap.1747-T1
Valid prediction for GlimmerHMM_glimmerT_56089-T1
Valid prediction for GlimmerHMM_glimmerT_56105-T1
Valid prediction for snap_scaffold_26-snap.1771-T1
Valid prediction for snap_scaffold_26-snap.1749-T1
Valid prediction for Augustus_model.g37185.t1
Valid prediction for snap_scaffold_26-snap.1774-T1
Valid prediction for snap_scaffold_26-snap.1772-T1
Valid prediction for GlimmerHMM_glimmerT_56094-T1
Couldn't classify 25144, 25452
Sorry, prediction pasa_asmbl_35716.p1 fails validation.
(GCT)	 GT	25144-25452	TC	TCT
Valid prediction for GlimmerHMM_glimmerT_56110-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16695, rend_intergenic: 7927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27239, rend_intergenic: 20335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29007, rend_intergenic: 27480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37527, rend_intergenic: 33829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42733, rend_intergenic: 37567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55651, rend_intergenic: 47475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59927, rend_intergenic: 57780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81481, rend_intergenic: 79768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107004, rend_intergenic: 92503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 127850
-exon list size: 317


building trellis

0.3    
0.6    
0.9    
1.3    
1.6    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.2    
8.5    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.4    
98.7    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 16695, rend_intergenic: 7927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27239, rend_intergenic: 20335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29007, rend_intergenic: 27480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37527, rend_intergenic: 33829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42733, rend_intergenic: 37567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55651, rend_intergenic: 47475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59927, rend_intergenic: 57780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81481, rend_intergenic: 79768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107004, rend_intergenic: 92503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support