-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_643236-736508

-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_4-snap.147-T1
Valid prediction for GlimmerHMM_glimmerT_8655-T1
Valid prediction for snap_scaffold_4-snap.138-T1
Valid prediction for snap_scaffold_4-snap.144-T1
Valid prediction for snap_scaffold_4-snap.148-T1
Valid prediction for snap_scaffold_4-snap.146-T1
Valid prediction for snap_scaffold_4-snap.140-T1
Valid prediction for snap_scaffold_4-snap.143-T1
Valid prediction for GlimmerHMM_glimmerT_8660-T1
Valid prediction for snap_scaffold_4-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_8666-T1
Valid prediction for GlimmerHMM_glimmerT_8664-T1
Valid prediction for snap_scaffold_4-snap.134-T1
Valid prediction for Augustus_model.g5619.t1
Valid prediction for snap_scaffold_4-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_8662-T1
Valid prediction for snap_scaffold_4-snap.145-T1
Valid prediction for snap_scaffold_4-snap.141-T1
Valid prediction for snap_scaffold_4-snap.136-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 Augustus_model.g5625.t1
Valid prediction for snap_scaffold_4-snap.150-T1
Valid prediction for snap_scaffold_4-snap.151-T1
Valid prediction for snap_scaffold_4-snap.137-T1
Valid prediction for Augustus_model.g5623.t1
Valid prediction for snap_scaffold_4-snap.142-T1
Valid prediction for GlimmerHMM_glimmerT_8661-T1
Valid prediction for snap_scaffold_4-snap.139-T1
Valid prediction for GlimmerHMM_glimmerT_8656-T1
Couldn't classify 76971, 77112
Sorry, prediction pasa_asmbl_42337.p1 fails validation.
(GAA)	 CA	76971-77112	GT	CTG
(CCC)	 AG	77766-77938	GT	AGG
(TGC)	 AG	79296-79385	GT	AGG
(ACT)	 AG	79524-79574	TC	GAT
-recovered pasa_asmbl_42337.p1, terminal, 79524, 79574
-recovered pasa_asmbl_42337.p1, internal, 77766, 77938
-recovered pasa_asmbl_42337.p1, internal, 79296, 79385
Valid prediction for CodingQuarry_transcript_48869-T1
Valid prediction for GlimmerHMM_glimmerT_8658-T1
Valid prediction for GlimmerHMM_glimmerT_8663-T1
Valid prediction for GlimmerHMM_glimmerT_8659-T1
Valid prediction for HiQ_model.g5621.t1
Couldn't classify 59555, 59738
Couldn't classify 63229, 63354
Sorry, prediction pasa_asmbl_42343.p1 fails validation.
(TCT)	 AG	59555-59738	GT	GGG
(CTC)	 AG	60155-60329	GT	AGG
(GTT)	 AG	60600-60721	GT	CTG
(ACG)	 AG	61499-61686	GT	CGG
(GTA)	 AG	63229-63354	TG	GGT
-recovered pasa_asmbl_42343.p1, internal, 59555, 59738
-recovered pasa_asmbl_42343.p1, internal, 60155, 60329
-recovered pasa_asmbl_42343.p1, internal, 60600, 60721
-recovered pasa_asmbl_42343.p1, internal, 61499, 61686
Couldn't classify 64402, 64516
Couldn't classify 67021, 67046
Sorry, prediction pasa_asmbl_43557.p1 fails validation.
(GTG)	 AG	64402-64516	GT	AGG
(ACA)	 AG	64880-65036	GT	AGG
(GTG)	 AG	66380-66483	GT	GGG
(ATC)	 AG	67021-67046	TG	GCT
-recovered pasa_asmbl_43557.p1, internal, 64402, 64516
-recovered pasa_asmbl_43557.p1, internal, 64880, 65036
-recovered pasa_asmbl_43557.p1, internal, 66380, 66483
Valid prediction for Augustus_model.g5624.t1
Valid prediction for snap_scaffold_4-snap.152-T1
Valid prediction for GlimmerHMM_glimmerT_8665-T1
Valid prediction for Augustus_model.g5626.t1
Valid prediction for GlimmerHMM_glimmerT_8657-T1
Couldn't classify 47149, 47301
Couldn't classify 48839, 48926
Sorry, prediction pasa_asmbl_43661.p1 fails validation.
(GAG)	 GG	47149-47301	GT	AGG
(GCA)	 AG	47852-48009	GT	TGG
(GTA)	 AG	48501-48593	GT	AGG
(ATG)	 AG	48839-48926	TG	ACT
-recovered pasa_asmbl_43661.p1, internal, 47852, 48009
-recovered pasa_asmbl_43661.p1, internal, 48501, 48593
Couldn't classify 84185, 84404
Sorry, prediction pasa_asmbl_42336.p3 fails validation.
(ATG)	 AG	83451-83608	GT	GAG
(ATC)	 AG	83899-83949	GT	CGG
(GTA)	 AG	84185-84404	CG	CGC
-recovered pasa_asmbl_42336.p3, initial, 83451, 83608
-recovered pasa_asmbl_42336.p3, internal, 83451, 83608
-recovered pasa_asmbl_42336.p3, internal, 83899, 83949
Valid prediction for snap_scaffold_4-snap.156-T1
Valid prediction for HiQ_model.g5622.t1
Couldn't classify 68152, 68313
Sorry, prediction pasa_asmbl_42339.p1 fails validation.
(CCA)	 AC	68152-68313	GT	CGG
(ACC)	 AG	68892-69036	GT	GAG
(AGT)	 AG	69460-69519	GT	AGG
(GTC)	 AG	69711-69778	GT	GGG
(GTG)	 AG	70207-70317	GT	AGG
(GTG)	 AG	70993-71080	GT	AGG
(AAT)	 AG	71891-71929	GT	TGG
(CGC)	 AG	72222-72327	GT	CAG
(GGA)	 AG	72746-72909	GT	AGG
(TGT)	 AG	73264-73300	GT	AAG
(GCA)	 AG	73969-73991	GT	GAG
(ATT)	 AG	74371-74426	GT	AGG
(TCT)	 AG	74857-75126	TG	GAT
-recovered pasa_asmbl_42339.p1, terminal, 74857, 75126
-recovered pasa_asmbl_42339.p1, internal, 68892, 69036
-recovered pasa_asmbl_42339.p1, internal, 69460, 69519
-recovered pasa_asmbl_42339.p1, internal, 69711, 69778
-recovered pasa_asmbl_42339.p1, internal, 70207, 70317
-recovered pasa_asmbl_42339.p1, internal, 70993, 71080
-recovered pasa_asmbl_42339.p1, internal, 71891, 71929
-recovered pasa_asmbl_42339.p1, internal, 72222, 72327
-recovered pasa_asmbl_42339.p1, internal, 72746, 72909
-recovered pasa_asmbl_42339.p1, internal, 73264, 73300
-recovered pasa_asmbl_42339.p1, internal, 73969, 73991
-recovered pasa_asmbl_42339.p1, internal, 74371, 74426
Valid prediction for Augustus_model.g5620.t1
Valid prediction for snap_scaffold_4-snap.154-T1
Valid prediction for snap_scaffold_4-snap.135-T1
Couldn't classify 51067, 51208
Couldn't classify 56783, 56838
Sorry, prediction pasa_asmbl_42344.p1 fails validation.
(GGT)	 TA	51067-51208	GT	TGG
(GGG)	 AG	51321-51482	GT	AGG
(ATG)	 AG	54227-54368	GT	AGG
(GTG)	 AG	55962-56161	GT	GGG
(TTG)	 AG	56783-56838	GA	GTG
-recovered pasa_asmbl_42344.p1, initial, 54227, 54368
-recovered pasa_asmbl_42344.p1, internal, 51321, 51482
-recovered pasa_asmbl_42344.p1, internal, 54227, 54368
-recovered pasa_asmbl_42344.p1, internal, 55962, 56161

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18861, rend_intergenic: 13700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29457, rend_intergenic: 20943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37343, rend_intergenic: 31030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59295, rend_intergenic: 38179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73679, rend_intergenic: 62810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81807, rend_intergenic: 75123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84408, rend_intergenic: 81952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 93273
-exon list size: 207


building trellis

0.5    
1.0    
1.4    
1.9    
2.4    
2.9    
3.3    
3.8    
4.3    
4.8    
5.3    
5.7    
6.2    
6.7    
7.2    
7.7    
8.1    
8.6    
9.1    
9.6    
10.0    
10.5    
11.0    
11.5    
12.0    
12.4    
12.9    
13.4    
13.9    
14.4    
14.8    
15.3    
15.8    
16.3    
16.7    
17.2    
17.7    
18.2    
18.7    
19.1    
19.6    
20.1    
20.6    
21.1    
21.5    
22.0    
22.5    
23.0    
23.4    
23.9    
24.4    
24.9    
25.4    
25.8    
26.3    
26.8    
27.3    
27.8    
28.2    
28.7    
29.2    
29.7    
30.1    
30.6    
31.1    
31.6    
32.1    
32.5    
33.0    
33.5    
34.0    
34.4    
34.9    
35.4    
35.9    
36.4    
36.8    
37.3    
37.8    
38.3    
38.8    
39.2    
39.7    
40.2    
40.7    
41.1    
41.6    
42.1    
42.6    
43.1    
43.5    
44.0    
44.5    
45.0    
45.5    
45.9    
46.4    
46.9    
47.4    
47.8    
48.3    
48.8    
49.3    
49.8    
50.2    
50.7    
51.2    
51.7    
52.2    
52.6    
53.1    
53.6    
54.1    
54.5    
55.0    
55.5    
56.0    
56.5    
56.9    
57.4    
57.9    
58.4    
58.9    
59.3    
59.8    
60.3    
60.8    
61.2    
61.7    
62.2    
62.7    
63.2    
63.6    
64.1    
64.6    
65.1    
65.6    
66.0    
66.5    
67.0    
67.5    
67.9    
68.4    
68.9    
69.4    
69.9    
70.3    
70.8    
71.3    
71.8    
72.2    
72.7    
73.2    
73.7    
74.2    
74.6    
75.1    
75.6    
76.1    
76.6    
77.0    
77.5    
78.0    
78.5    
78.9    
79.4    
79.9    
80.4    
80.9    
81.3    
81.8    
82.3    
82.8    
83.3    
83.7    
84.2    
84.7    
85.2    
85.6    
86.1    
86.6    
87.1    
87.6    
88.0    
88.5    
89.0    
89.5    
90.0    
90.4    
90.9    
91.4    
91.9    
92.3    
92.8    
93.3    
93.8    
94.3    
94.7    
95.2    
95.7    
96.2    
96.7    
97.1    
97.6    
98.1    
98.6    
99.0    
99.5    
-found 10 predictions from path traversal
Error with prediction: snap lend_intergenic: 18861, rend_intergenic: 13700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29457, rend_intergenic: 20943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37343, rend_intergenic: 31030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59295, rend_intergenic: 38179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73679, rend_intergenic: 62810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81807, rend_intergenic: 75123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84408, rend_intergenic: 81952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 7 predictions persist after filtering for low support