-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_2485961-2711408

-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_13-snap.479-T1
Valid prediction for snap_scaffold_13-snap.492-T1
Valid prediction for GeneMark_model.54829_t
Valid prediction for HiQ_model.g21350.t1
Valid prediction for GlimmerHMM_glimmerT_31925-T1
Valid prediction for snap_scaffold_13-snap.477-T1
Couldn't classify 160467, 160583
Sorry, prediction pasa_asmbl_10617.p1 fails validation.
(ACA)	 GT	160467-160583	GT	CTG
(GCG)	 AG	160969-161042	GT	AAG
(TGA)	 AG	161158-161218	GT	TTG
(GTA)	 AG	161358-161427	GT	AGG
(GCA)	 AG	161518-161636	GT	CGG
(AAC)	 AG	161744-161792	GT	TGG
(ATC)	 AG	161877-161972	GT	AGG
(GTT)	 AG	162075-162157	GT	AGG
(CAC)	 AG	162247-162320	GT	TGG
(CTC)	 AG	162441-162549	GT	AGG
(TAT)	 AG	162631-162765	GT	AGG
(CTG)	 AG	162884-162984	GT	AGG
(CTC)	 AG	163131-163197	GT	AGG
(CTC)	 AG	163305-163355	GT	AGG
(CAC)	 AG	163459-163529	GT	AGG
(ACC)	 AG	163671-163766	GT	AAG
(TGA)	 AG	163850-163915	GT	AGG
(GGA)	 AG	164026-164109	GT	AAG
(GGT)	 AG	164203-164350	GT	CTG
(AAG)	 AG	164462-164546	GT	CAG
(GCC)	 AG	164661-164938	AC	GAA
add_exon() Sorry, pasa_asmbl_10617.p1 164026-164109-terminal-1 is invalid.
-recovered pasa_asmbl_10617.p1, terminal, 164026, 164109
-recovered pasa_asmbl_10617.p1, terminal, 164661, 164938
-recovered pasa_asmbl_10617.p1, internal, 160969, 161042
-recovered pasa_asmbl_10617.p1, internal, 161158, 161218
-recovered pasa_asmbl_10617.p1, internal, 161358, 161427
-recovered pasa_asmbl_10617.p1, internal, 161518, 161636
-recovered pasa_asmbl_10617.p1, internal, 161744, 161792
-recovered pasa_asmbl_10617.p1, internal, 161877, 161972
-recovered pasa_asmbl_10617.p1, internal, 162075, 162157
-recovered pasa_asmbl_10617.p1, internal, 162247, 162320
-recovered pasa_asmbl_10617.p1, internal, 162441, 162549
-recovered pasa_asmbl_10617.p1, internal, 162631, 162765
-recovered pasa_asmbl_10617.p1, internal, 162884, 162984
-recovered pasa_asmbl_10617.p1, internal, 163131, 163197
-recovered pasa_asmbl_10617.p1, internal, 163305, 163355
-recovered pasa_asmbl_10617.p1, internal, 163459, 163529
-recovered pasa_asmbl_10617.p1, internal, 163671, 163766
-recovered pasa_asmbl_10617.p1, internal, 163850, 163915
-recovered pasa_asmbl_10617.p1, internal, 164026, 164109
-recovered pasa_asmbl_10617.p1, internal, 164203, 164350
-recovered pasa_asmbl_10617.p1, internal, 164462, 164546
Valid prediction for GeneMark_model.54819_t
Valid prediction for GeneMark_model.54823_t
Valid prediction for CodingQuarry_transcript_12862-T1
Couldn't classify 81008, 81045
Sorry, prediction pasa_asmbl_10609.p1 fails validation.
(CTG)	 AC	81008-81045	GT	AGG
(CCT)	 AG	81839-82085	GT	AGG
(CTA)	 AG	83804-83831	GT	AGG
(ACT)	 AG	84359-84508	GT	GGG
(ACA)	 AG	84644-84817	GT	GGG
(GGG)	 AG	84990-85067	GT	AGG
(CTT)	 AG	85214-85242	AG	AAA
-recovered pasa_asmbl_10609.p1, terminal, 85214, 85242
-recovered pasa_asmbl_10609.p1, internal, 81839, 82085
-recovered pasa_asmbl_10609.p1, internal, 83804, 83831
-recovered pasa_asmbl_10609.p1, internal, 84359, 84508
-recovered pasa_asmbl_10609.p1, internal, 84644, 84817
-recovered pasa_asmbl_10609.p1, internal, 84990, 85067
Valid prediction for GlimmerHMM_glimmerT_31926-T1
Valid prediction for snap_scaffold_13-snap.478-T1
Valid prediction for Augustus_model.g21349.t1
Valid prediction for GeneMark_model.54820_t
Valid prediction for snap_scaffold_13-snap.495-T1
Valid prediction for GlimmerHMM_glimmerT_31929-T1
Valid prediction for GeneMark_model.54834_t
Valid prediction for GlimmerHMM_glimmerT_31935-T1
Valid prediction for pasa_asmbl_10615.p1
Valid prediction for GlimmerHMM_glimmerT_31928-T1
Valid prediction for snap_scaffold_13-snap.484-T1
Valid prediction for HiQ_model.g21343.t1
Valid prediction for Augustus_model.g21345.t1
Valid prediction for GeneMark_model.54817_t
Valid prediction for CodingQuarry_transcript_12863-T1
Valid prediction for GlimmerHMM_glimmerT_31920-T1
Valid prediction for snap_scaffold_13-snap.480-T1
Valid prediction for HiQ_model.g21348.t1
Valid prediction for Augustus_model.g21347.t1
Valid prediction for snap_scaffold_13-snap.486-T1
Valid prediction for GeneMark_model.54827_t
Valid prediction for GlimmerHMM_glimmerT_31924-T1
Valid prediction for GlimmerHMM_glimmerT_31923-T1
Valid prediction for GeneMark_model.54831_t
Valid prediction for GlimmerHMM_glimmerT_31919-T1
Valid prediction for GeneMark_model.54828_t
Valid prediction for snap_scaffold_13-snap.483-T1
Valid prediction for Augustus_model.g21344.t1
Valid prediction for GeneMark_model.54836_t
Valid prediction for GeneMark_model.54822_t
Valid prediction for snap_scaffold_13-snap.493-T1
Valid prediction for snap_scaffold_13-snap.476-T1
Valid prediction for snap_scaffold_13-snap.490-T1
Valid prediction for snap_scaffold_13-snap.488-T1
Valid prediction for GlimmerHMM_glimmerT_31921-T1
Valid prediction for GeneMark_model.54821_t
Valid prediction for snap_scaffold_13-snap.485-T1
Valid prediction for GeneMark_model.54816_t

-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_13-snap.481-T1
Valid prediction for Augustus_model.g21341.t1
Valid prediction for GeneMark_model.54826_t
Valid prediction for GeneMark_model.54832_t
Valid prediction for GlimmerHMM_glimmerT_31932-T1
Couldn't classify 38829, 38915
Sorry, prediction pasa_asmbl_9430.p1 fails validation.
(AGT)	 TC	38829-38915	GT	TGG
(GTT)	 AG	39024-39161	GT	AGG
(CTG)	 AG	39320-39495	GT	CGG
(GGA)	 AG	39627-39711	GT	AGG
(GAT)	 AG	39915-40059	GT	CGG
(GCG)	 AG	40203-40341	GT	AGG
(AGA)	 AG	40680-40771	GT	GAG
(CGG)	 AG	41462-41621	GT	CAG
(GTT)	 AG	42092-42161	GT	ACG
(CTG)	 AG	42370-42458	GT	AGG
(GAC)	 AG	42657-42705	GT	AGG
(GCT)	 AG	42831-42966	GT	AGG
(TTT)	 AG	43291-43382	GT	AGG
(CTG)	 AG	43734-43980	GT	GGG
(CGC)	 AG	44587-44693	GT	AGG
(GAG)	 AG	44807-44957	GT	TGG
(CGG)	 AG	45520-45680	GT	AGG
(GTG)	 AG	45997-46181	GT	AAG
(GCA)	 AG	46685-46754	GT	CAG
(ACA)	 AG	46873-46976	GT	AGG
(GGA)	 AG	47080-47245	GT	GGG
(CTT)	 AG	47436-47529	GT	AGG
(AGT)	 AG	47617-47705	GT	AGG
(GCG)	 AG	47823-48014	GT	CGG
(CAA)	 AG	48250-48415	GT	CGG
(AAT)	 AG	50792-50862	GT	AGG
(TAC)	 AG	50978-51066	GT	GAG
(CAA)	 AG	51237-51315	GT	AGG
(ATC)	 AG	51393-51654	GT	AGG
(TGA)	 AG	51848-52055	GT	AGG
(CTA)	 AG	52740-52743	CC	AAC
-recovered pasa_asmbl_9430.p1, terminal, 52740, 52743
-recovered pasa_asmbl_9430.p1, internal, 39024, 39161
-recovered pasa_asmbl_9430.p1, internal, 39320, 39495
-recovered pasa_asmbl_9430.p1, internal, 39627, 39711
-recovered pasa_asmbl_9430.p1, internal, 39915, 40059
-recovered pasa_asmbl_9430.p1, internal, 40203, 40341
-recovered pasa_asmbl_9430.p1, internal, 40680, 40771
-recovered pasa_asmbl_9430.p1, internal, 41462, 41621
-recovered pasa_asmbl_9430.p1, internal, 42092, 42161
-recovered pasa_asmbl_9430.p1, internal, 42370, 42458
-recovered pasa_asmbl_9430.p1, internal, 42657, 42705
-recovered pasa_asmbl_9430.p1, internal, 42831, 42966
-recovered pasa_asmbl_9430.p1, internal, 43291, 43382
-recovered pasa_asmbl_9430.p1, internal, 43734, 43980
-recovered pasa_asmbl_9430.p1, internal, 44587, 44693
-recovered pasa_asmbl_9430.p1, internal, 44807, 44957
-recovered pasa_asmbl_9430.p1, internal, 45520, 45680
-recovered pasa_asmbl_9430.p1, internal, 45997, 46181
-recovered pasa_asmbl_9430.p1, internal, 46685, 46754
-recovered pasa_asmbl_9430.p1, internal, 46873, 46976
-recovered pasa_asmbl_9430.p1, internal, 47080, 47245
-recovered pasa_asmbl_9430.p1, internal, 47436, 47529
-recovered pasa_asmbl_9430.p1, internal, 47617, 47705
-recovered pasa_asmbl_9430.p1, internal, 47823, 48014
-recovered pasa_asmbl_9430.p1, internal, 48250, 48415
-recovered pasa_asmbl_9430.p1, internal, 50792, 50862
-recovered pasa_asmbl_9430.p1, internal, 50978, 51066
-recovered pasa_asmbl_9430.p1, internal, 51237, 51315
-recovered pasa_asmbl_9430.p1, internal, 51393, 51654
-recovered pasa_asmbl_9430.p1, internal, 51848, 52055
Valid prediction for GeneMark_model.54835_t
Valid prediction for Augustus_model.g21346.t1
Valid prediction for GlimmerHMM_glimmerT_31936-T1
Valid prediction for GlimmerHMM_glimmerT_31934-T1
Valid prediction for CodingQuarry_transcript_12864-T1
Valid prediction for snap_scaffold_13-snap.475-T1
Valid prediction for GeneMark_model.54837_t
Valid prediction for Augustus_model.g21342.t1
Valid prediction for GlimmerHMM_glimmerT_31930-T1
Valid prediction for GeneMark_model.54818_t
Valid prediction for GlimmerHMM_glimmerT_31917-T1
Valid prediction for HiQ_model.g21351.t1
Valid prediction for CodingQuarry_transcript_12865-T1
Valid prediction for GeneMark_model.54825_t
Valid prediction for GlimmerHMM_glimmerT_31937-T1
Valid prediction for snap_scaffold_13-snap.491-T1
Valid prediction for GeneMark_model.54815_t
Valid prediction for GlimmerHMM_glimmerT_31922-T1
Valid prediction for GlimmerHMM_glimmerT_31927-T1
Valid prediction for snap_scaffold_13-snap.487-T1
Valid prediction for GeneMark_model.54830_t
Valid prediction for snap_scaffold_13-snap.489-T1
Valid prediction for HiQ_model.g21352.t1
Valid prediction for snap_scaffold_13-snap.482-T1
Valid prediction for GeneMark_model.54824_t
Valid prediction for snap_scaffold_13-snap.496-T1
Valid prediction for GeneMark_model.54814_t
Valid prediction for snap_scaffold_13-snap.474-T1
Valid prediction for GlimmerHMM_glimmerT_31933-T1
Valid prediction for snap_scaffold_13-snap.473-T1
Valid prediction for GlimmerHMM_glimmerT_31918-T1
Valid prediction for pasa_asmbl_9425.p1
Valid prediction for HiQ_model.g21353.t1
Valid prediction for GeneMark_model.54833_t
Valid prediction for snap_scaffold_13-snap.494-T1
Valid prediction for GlimmerHMM_glimmerT_31931-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 164938, rend_intergenic: 164018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180033, rend_intergenic: 176539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192310, rend_intergenic: 181138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225448
-exon list size: 404


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
4.9    
5.2    
5.4    
5.7    
5.9    
6.2    
6.4    
6.7    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.1    
11.3    
11.6    
11.8    
12.1    
12.3    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 14 predictions from path traversal
Error with prediction: snap lend_intergenic: 164938, rend_intergenic: 164018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180033, rend_intergenic: 176539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192310, rend_intergenic: 181138  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 188849 - 225448
-exon list size: 81


building trellis

1.2    
2.4    
3.6    
4.8    
6.0    
7.2    
8.4    
9.6    
10.8    
12.0    
13.3    
14.5    
15.7    
16.9    
18.1    
19.3    
20.5    
21.7    
22.9    
24.1    
25.3    
26.5    
27.7    
28.9    
30.1    
31.3    
32.5    
33.7    
34.9    
36.1    
37.3    
38.6    
39.8    
41.0    
42.2    
43.4    
44.6    
45.8    
47.0    
48.2    
49.4    
50.6    
51.8    
53.0    
54.2    
55.4    
56.6    
57.8    
59.0    
60.2    
61.4    
62.7    
63.9    
65.1    
66.3    
67.5    
68.7    
69.9    
71.1    
72.3    
73.5    
74.7    
75.9    
77.1    
78.3    
79.5    
80.7    
81.9    
83.1    
84.3    
85.5    
86.7    
88.0    
89.2    
90.4    
91.6    
92.8    
94.0    
95.2    
96.4    
97.6    
98.8    
-found 5 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 2 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 188849 - 204365
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 189750 - 204365
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-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

-building DP trellis

-building trellis in range 189750 - 200512
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-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

-building DP trellis

-building trellis in range 189750 - 200257
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 189750 - 200206
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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

-building DP trellis

-building trellis in range 210743 - 225448
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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