-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_13475187-13671847

-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 Augustus_model.g12733.t1
Valid prediction for GeneMark_model.31508_t
Valid prediction for GlimmerHMM_glimmerT_18816-T1
Valid prediction for pasa_asmbl_51231.p1
Valid prediction for snap_scaffold_7-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_18819-T1
Valid prediction for snap_scaffold_7-snap.2553-T1
Valid prediction for CodingQuarry_transcript_57553-T1
Valid prediction for GeneMark_model.31519_t
Valid prediction for GlimmerHMM_glimmerT_18828-T1
Valid prediction for GlimmerHMM_glimmerT_18827-T1
Valid prediction for snap_scaffold_7-snap.2554-T1
Valid prediction for GlimmerHMM_glimmerT_18824-T1
Valid prediction for Augustus_model.g12734.t1
Valid prediction for GlimmerHMM_glimmerT_18830-T1
Valid prediction for Augustus_model.g12735.t1
Valid prediction for Augustus_model.g12732.t1
Valid prediction for GeneMark_model.31510_t
Couldn't classify 1853, 1957
Couldn't classify 3591, 3745
Sorry, prediction pasa_asmbl_51228.p1 fails validation.
(GGA)	 CA	1853-1957	GT	CGG
(AAG)	 AG	2165-2206	GT	ATG
(ATG)	 AG	2625-2709	GT	AGG
(ACC)	 AG	2944-3023	GT	AGG
(CTC)	 AG	3261-3321	GT	TGG
(GGA)	 AG	3591-3745	GG	AAG
-recovered pasa_asmbl_51228.p1, initial, 2625, 2709
-recovered pasa_asmbl_51228.p1, internal, 2165, 2206
-recovered pasa_asmbl_51228.p1, internal, 2625, 2709
-recovered pasa_asmbl_51228.p1, internal, 2944, 3023
-recovered pasa_asmbl_51228.p1, internal, 3261, 3321
Valid prediction for snap_scaffold_7-snap.2564-T1
Valid prediction for GeneMark_model.31514_t
Valid prediction for GeneMark_model.31520_t
Valid prediction for snap_scaffold_7-snap.2559-T1
Valid prediction for snap_scaffold_7-snap.2568-T1
Valid prediction for snap_scaffold_7-snap.2562-T1
Valid prediction for GeneMark_model.31501_t
Valid prediction for GeneMark_model.31516_t
Valid prediction for GeneMark_model.31518_t
Valid prediction for snap_scaffold_7-snap.2560-T1
Valid prediction for CodingQuarry_transcript_57550-T1
Valid prediction for GeneMark_model.31498_t
Valid prediction for GlimmerHMM_glimmerT_18826-T1
Valid prediction for GeneMark_model.31526_t
Valid prediction for GlimmerHMM_glimmerT_18812-T1
Valid prediction for GeneMark_model.31506_t
Valid prediction for snap_scaffold_7-snap.2555-T1
Valid prediction for GeneMark_model.31522_t
Valid prediction for CodingQuarry_transcript_57551-T1
Valid prediction for pasa_asmbl_51245.p1
Couldn't classify 134912, 134964
Sorry, prediction pasa_asmbl_51247.p1 fails validation.
(GCC)	 CT	134912-134964	GT	AGG
(GTA)	 AG	135067-135184	GT	AGG
(GAG)	 AG	136616-136693	GT	GGG
(ATT)	 AG	136832-136899	GT	GAG
(GTC)	 AG	137170-137308	GT	AGG
(CCT)	 AG	138374-138460	GT	ATG
(AGC)	 AG	138908-139003	GT	AGG
(GCG)	 AG	139308-139509	GT	AGG
(AAA)	 AG	139893-140027	GT	AGG
(GAA)	 AG	140289-140407	CG	GAC
-recovered pasa_asmbl_51247.p1, terminal, 140289, 140407
-recovered pasa_asmbl_51247.p1, internal, 135067, 135184
-recovered pasa_asmbl_51247.p1, internal, 136616, 136693
-recovered pasa_asmbl_51247.p1, internal, 136832, 136899
-recovered pasa_asmbl_51247.p1, internal, 137170, 137308
-recovered pasa_asmbl_51247.p1, internal, 138374, 138460
-recovered pasa_asmbl_51247.p1, internal, 138908, 139003
-recovered pasa_asmbl_51247.p1, internal, 139308, 139509
-recovered pasa_asmbl_51247.p1, internal, 139893, 140027
Valid prediction for Augustus_model.g12731.t1
Valid prediction for GeneMark_model.31512_t
Valid prediction for CodingQuarry_transcript_57554-T1
Valid prediction for GeneMark_model.31511_t
Valid prediction for GlimmerHMM_glimmerT_18817-T1
Valid prediction for Augustus_model.g12738.t1
Valid prediction for Augustus_model.g12740.t1
Valid prediction for snap_scaffold_7-snap.2550-T1
Valid prediction for GlimmerHMM_glimmerT_18815-T1
Valid prediction for snap_scaffold_7-snap.2571-T1
Valid prediction for GeneMark_model.31496_t
Valid prediction for GlimmerHMM_glimmerT_18820-T1
Valid prediction for snap_scaffold_7-snap.2552-T1
Valid prediction for HiQ_model.g12737.t1
Valid prediction for GeneMark_model.31504_t
Valid prediction for GlimmerHMM_glimmerT_18823-T1
Couldn't classify 25574, 25725
Sorry, prediction pasa_asmbl_51230.p1 fails validation.
(ATG)	 AT	20483-20669	GT	AGG
(GTT)	 AG	20924-21078	GT	AGG
(GTG)	 AG	22210-22416	GT	AGG
(GGC)	 AG	22995-23076	GT	TGG
(GCG)	 AG	25574-25725	TC	GGT
-recovered pasa_asmbl_51230.p1, initial, 20483, 20669
-recovered pasa_asmbl_51230.p1, internal, 20924, 21078
-recovered pasa_asmbl_51230.p1, internal, 22210, 22416
-recovered pasa_asmbl_51230.p1, internal, 22995, 23076
Valid prediction for pasa_asmbl_51240.p1
Couldn't classify 4217, 4373
Sorry, prediction pasa_asmbl_51229.p1 fails validation.
(CTG)	 CT	4217-4373	GT	CGG
(ACA)	 AG	4481-4549	GT	CCG
(GGT)	 AG	4653-4745	GT	AGG
(TGT)	 AG	4845-4915	GT	AGG
(ATC)	 AG	5032-5087	GT	AGG
(GGT)	 AG	5983-6070	GC	GAG
add_exon() Sorry, pasa_asmbl_51229.p1 4653-4745-terminal-1 is invalid.
-recovered pasa_asmbl_51229.p1, terminal, 4653, 4745
-recovered pasa_asmbl_51229.p1, terminal, 5983, 6070
-recovered pasa_asmbl_51229.p1, internal, 4481, 4549
-recovered pasa_asmbl_51229.p1, internal, 4653, 4745
-recovered pasa_asmbl_51229.p1, internal, 4845, 4915
-recovered pasa_asmbl_51229.p1, internal, 5032, 5087
-recovered pasa_asmbl_51229.p1, internal, 5983, 6070

-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.g12729.t1
Valid prediction for snap_scaffold_7-snap.2549-T1
Valid prediction for snap_scaffold_7-snap.2548-T1
Valid prediction for GeneMark_model.31502_t
Valid prediction for GeneMark_model.31513_t
Valid prediction for GeneMark_model.31515_t
Valid prediction for snap_scaffold_7-snap.2551-T1
Valid prediction for CodingQuarry_transcript_57552-T1
Valid prediction for GlimmerHMM_glimmerT_18814-T1
Valid prediction for GlimmerHMM_glimmerT_18829-T1
Valid prediction for GlimmerHMM_glimmerT_18813-T1
Valid prediction for snap_scaffold_7-snap.2566-T1
Valid prediction for GlimmerHMM_glimmerT_18831-T1
Valid prediction for GeneMark_model.31509_t
Valid prediction for GeneMark_model.31527_t
Valid prediction for CodingQuarry_transcript_57549-T1
Valid prediction for snap_scaffold_7-snap.2569-T1
Valid prediction for GeneMark_model.31500_t
Valid prediction for snap_scaffold_7-snap.2563-T1
Valid prediction for GeneMark_model.31521_t
Valid prediction for GeneMark_model.31505_t
Valid prediction for snap_scaffold_7-snap.2567-T1
Valid prediction for GeneMark_model.31499_t
Couldn't classify 186748, 187095
Sorry, prediction pasa_asmbl_50123.p1 fails validation.
(TAC)	 CC	186748-187095	GT	AGG
(GAA)	 AG	187254-187396	GT	AAG
(GTC)	 AG	187822-187933	TT	GAT
-recovered pasa_asmbl_50123.p1, terminal, 187822, 187933
-recovered pasa_asmbl_50123.p1, internal, 187254, 187396
Valid prediction for GlimmerHMM_glimmerT_18821-T1
Couldn't classify 182053, 182100
Couldn't classify 183327, 183454
Sorry, prediction pasa_asmbl_50125.p1 fails validation.
(GTG)	 AT	182053-182100	GT	AGG
(GAG)	 AG	182226-182347	GT	AGG
(GAA)	 AG	182515-182636	GT	GAG
(CCT)	 AG	182825-182953	GT	CAG
(GTA)	 AG	183327-183454	TA	GGT
-recovered pasa_asmbl_50125.p1, internal, 182226, 182347
-recovered pasa_asmbl_50125.p1, internal, 182515, 182636
-recovered pasa_asmbl_50125.p1, internal, 182825, 182953
Valid prediction for GeneMark_model.31517_t
Valid prediction for GlimmerHMM_glimmerT_18818-T1
Valid prediction for snap_scaffold_7-snap.2570-T1
Valid prediction for GlimmerHMM_glimmerT_18825-T1
Valid prediction for Augustus_model.g12742.t1
Valid prediction for GeneMark_model.31497_t
Valid prediction for snap_scaffold_7-snap.2565-T1
Valid prediction for GeneMark_model.31524_t
Valid prediction for HiQ_model.g12736.t1
Valid prediction for GeneMark_model.31523_t
Valid prediction for GeneMark_model.31525_t
Valid prediction for Augustus_model.g12739.t1
Valid prediction for GeneMark_model.31503_t
Valid prediction for snap_scaffold_7-snap.2561-T1
Valid prediction for snap_scaffold_7-snap.2558-T1
Valid prediction for Augustus_model.g12730.t1
Valid prediction for Augustus_model.g12741.t1
Valid prediction for snap_scaffold_7-snap.2556-T1
Valid prediction for pasa_asmbl_50128.p1
Valid prediction for CodingQuarry_transcript_57548-T1
Valid prediction for GlimmerHMM_glimmerT_18822-T1
Valid prediction for GeneMark_model.31507_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15477, rend_intergenic: 10257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71131, rend_intergenic: 67893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71469, rend_intergenic: 71194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129860, rend_intergenic: 121144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140407, rend_intergenic: 130455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177123, rend_intergenic: 174415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195499, rend_intergenic: 187005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196661
-exon list size: 486


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 15477, rend_intergenic: 10257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71131, rend_intergenic: 67893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71469, rend_intergenic: 71194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129860, rend_intergenic: 121144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140407, rend_intergenic: 130455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177123, rend_intergenic: 174415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195499, rend_intergenic: 187005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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