-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_1727226-1933678

-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_10-snap.385-T1
Valid prediction for Augustus_model.g16108.t1
Valid prediction for GlimmerHMM_glimmerT_24176-T1
Valid prediction for GlimmerHMM_glimmerT_24163-T1
Valid prediction for Augustus_model.g16111.t1
Valid prediction for Augustus_model.g16112.t1
Valid prediction for GlimmerHMM_glimmerT_24173-T1
Valid prediction for Augustus_model.g16105.t1
Valid prediction for Augustus_model.g16107.t1
Valid prediction for snap_scaffold_10-snap.394-T1
Valid prediction for snap_scaffold_10-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_24172-T1
Valid prediction for GlimmerHMM_glimmerT_24167-T1
Valid prediction for snap_scaffold_10-snap.383-T1
Valid prediction for snap_scaffold_10-snap.396-T1
Valid prediction for GlimmerHMM_glimmerT_24161-T1
Valid prediction for Augustus_model.g16115.t1
Valid prediction for snap_scaffold_10-snap.400-T1
Valid prediction for GlimmerHMM_glimmerT_24168-T1
Valid prediction for GlimmerHMM_glimmerT_24179-T1
Valid prediction for GlimmerHMM_glimmerT_24169-T1
Valid prediction for GlimmerHMM_glimmerT_24170-T1
Valid prediction for snap_scaffold_10-snap.387-T1
Couldn't classify 63961, 64078
Sorry, prediction pasa_asmbl_3830.p1 fails validation.
(ATG)	 AG	60214-60302	GT	GTG
(GTC)	 AG	60646-60748	GT	AGG
(ACC)	 AG	60872-61003	GT	CTG
(ATG)	 AG	61334-61453	GT	AGG
(GGA)	 AG	61675-61893	GT	AGG
(AGG)	 AG	62070-62405	GT	TGG
(ACC)	 AG	62628-62848	GT	TGG
(CAT)	 AG	62934-63136	GT	ATG
(GTT)	 AG	63331-63416	GT	TGG
(AGT)	 AG	63510-63643	GT	AGG
(TGT)	 AG	63961-64078	GT	CGG
-recovered pasa_asmbl_3830.p1, initial, 60214, 60302
-recovered pasa_asmbl_3830.p1, initial, 61334, 61453
-recovered pasa_asmbl_3830.p1, internal, 60214, 60302
-recovered pasa_asmbl_3830.p1, internal, 60646, 60748
-recovered pasa_asmbl_3830.p1, internal, 60872, 61003
-recovered pasa_asmbl_3830.p1, internal, 61334, 61453
-recovered pasa_asmbl_3830.p1, internal, 61675, 61893
-recovered pasa_asmbl_3830.p1, internal, 62070, 62405
-recovered pasa_asmbl_3830.p1, internal, 62628, 62848
-recovered pasa_asmbl_3830.p1, internal, 62934, 63136
-recovered pasa_asmbl_3830.p1, internal, 63331, 63416
-recovered pasa_asmbl_3830.p1, internal, 63510, 63643
-recovered pasa_asmbl_3830.p1, internal, 63961, 64078
Valid prediction for GlimmerHMM_glimmerT_24180-T1
Valid prediction for snap_scaffold_10-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_24171-T1
Valid prediction for GlimmerHMM_glimmerT_24177-T1
Valid prediction for GlimmerHMM_glimmerT_24174-T1
Valid prediction for Augustus_model.g16114.t1
Valid prediction for GlimmerHMM_glimmerT_24181-T1
Valid prediction for GlimmerHMM_glimmerT_24165-T1
Couldn't classify 44017, 44121
Sorry, prediction pasa_asmbl_2956.p1 fails validation.
(ATG)	 CC	41396-41513	GT	CGG
(AAT)	 AG	41881-41898	GT	AGG
(GTA)	 AG	42011-42093	GT	TTG
(GTG)	 AG	44017-44121	GT	AGG
-recovered pasa_asmbl_2956.p1, initial, 41396, 41513
-recovered pasa_asmbl_2956.p1, internal, 41881, 41898
-recovered pasa_asmbl_2956.p1, internal, 42011, 42093
-recovered pasa_asmbl_2956.p1, internal, 44017, 44121
Valid prediction for snap_scaffold_10-snap.375-T1
Couldn't classify 134210, 134416
Couldn't classify 134540, 134680
Sorry, prediction pasa_asmbl_3866.p1 fails validation.
(AGG)	 GC	134210-134416	GT	AGG
(GCA)	 AG	134540-134680	AA	CCA
Valid prediction for Augustus_model.g16113.t1
Couldn't classify 55017, 55097
Couldn't classify 55741, 55907
Sorry, prediction pasa_asmbl_2958.p1 fails validation.
(TCA)	 AG	55017-55097	GT	CTG
(GGT)	 AG	55256-55553	GT	GGG
(GCC)	 AG	55741-55907	GT	GGG
-recovered pasa_asmbl_2958.p1, internal, 55017, 55097
-recovered pasa_asmbl_2958.p1, internal, 55256, 55553
-recovered pasa_asmbl_2958.p1, internal, 55741, 55907
Valid prediction for GlimmerHMM_glimmerT_24175-T1
Valid prediction for GlimmerHMM_glimmerT_24166-T1
Valid prediction for snap_scaffold_10-snap.376-T1
Valid prediction for snap_scaffold_10-snap.367-T1
Valid prediction for Augustus_model.g16117.t1
Valid prediction for snap_scaffold_10-snap.380-T1
Valid prediction for HiQ_model.g16116.t1
Valid prediction for Augustus_model.g16110.t1
Valid prediction for snap_scaffold_10-snap.395-T1
Couldn't classify 123025, 123064
Couldn't classify 124458, 124572
Sorry, prediction pasa_asmbl_2961.p1 fails validation.
(GCC)	 TG	123025-123064	GT	CAG
(ATA)	 AG	123892-124026	GT	AGG
(CCC)	 AG	124121-124226	GT	AGG
(GAT)	 AG	124458-124572	CA	CGC
add_exon() Sorry, pasa_asmbl_2961.p1 123892-124026-terminal-1 is invalid.
-recovered pasa_asmbl_2961.p1, terminal, 123892, 124026
-recovered pasa_asmbl_2961.p1, internal, 123892, 124026
-recovered pasa_asmbl_2961.p1, internal, 124121, 124226
Valid prediction for HiQ_model.g16106.t1
Valid prediction for Augustus_model.g16104.t1
Valid prediction for snap_scaffold_10-snap.398-T1
Valid prediction for snap_scaffold_10-snap.372-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g16109.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_10-snap.392-T1
Valid prediction for snap_scaffold_10-snap.401-T1
Valid prediction for snap_scaffold_10-snap.388-T1
Valid prediction for snap_scaffold_10-snap.377-T1
Couldn't classify 181219, 181308
Couldn't classify 182951, 182965
Sorry, prediction pasa_asmbl_5217.p1 fails validation.
(TTC)	 CC	181219-181308	GT	CGG
(GAG)	 AG	181777-181863	GT	AGG
(TGT)	 AG	182203-182310	GT	TGG
(CTC)	 AG	182951-182965	CC	AGC
-recovered pasa_asmbl_5217.p1, internal, 181777, 181863
-recovered pasa_asmbl_5217.p1, internal, 182203, 182310
Valid prediction for snap_scaffold_10-snap.370-T1
Valid prediction for snap_scaffold_10-snap.384-T1
Valid prediction for Augustus_model.g16102.t1
Valid prediction for snap_scaffold_10-snap.399-T1
Valid prediction for snap_scaffold_10-snap.366-T1
Valid prediction for Augustus_model.g16100.t1
Valid prediction for snap_scaffold_10-snap.373-T1
Valid prediction for Augustus_model.g16103.t1
Valid prediction for Augustus_model.g16101.t1
Valid prediction for GlimmerHMM_glimmerT_24184-T1
Valid prediction for GlimmerHMM_glimmerT_24178-T1
Valid prediction for snap_scaffold_10-snap.393-T1
Valid prediction for GlimmerHMM_glimmerT_24183-T1
Valid prediction for GlimmerHMM_glimmerT_24159-T1
Valid prediction for snap_scaffold_10-snap.381-T1
Valid prediction for snap_scaffold_10-snap.397-T1
Valid prediction for GlimmerHMM_glimmerT_24156-T1
Valid prediction for snap_scaffold_10-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_24157-T1
Valid prediction for snap_scaffold_10-snap.378-T1
Valid prediction for snap_scaffold_10-snap.368-T1
Valid prediction for snap_scaffold_10-snap.374-T1
Valid prediction for snap_scaffold_10-snap.389-T1
Valid prediction for GlimmerHMM_glimmerT_24158-T1
Valid prediction for GlimmerHMM_glimmerT_24160-T1
Valid prediction for GlimmerHMM_glimmerT_24164-T1
Valid prediction for CodingQuarry_transcript_5290-T1
Valid prediction for GlimmerHMM_glimmerT_24182-T1
Valid prediction for snap_scaffold_10-snap.382-T1
Valid prediction for snap_scaffold_10-snap.379-T1
Valid prediction for snap_scaffold_10-snap.371-T1
Valid prediction for snap_scaffold_10-snap.386-T1
Valid prediction for GlimmerHMM_glimmerT_24162-T1
Valid prediction for snap_scaffold_10-snap.365-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8819, rend_intergenic: 7022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29050, rend_intergenic: 24388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32032, rend_intergenic: 29117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64456, rend_intergenic: 47737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81421, rend_intergenic: 73227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96394, rend_intergenic: 84074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99812, rend_intergenic: 97806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100790, rend_intergenic: 100165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121059, rend_intergenic: 101356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122640, rend_intergenic: 121167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146201, rend_intergenic: 134505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184799, rend_intergenic: 176652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203168, rend_intergenic: 200787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206453
-exon list size: 436


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.7    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.3    
4.6    
4.8    
5.0    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.1    
7.3    
7.5    
7.8    
8.0    
8.2    
8.4    
8.7    
8.9    
9.1    
9.4    
9.6    
9.8    
10.0    
10.3    
10.5    
10.7    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.2    
13.5    
13.7    
13.9    
14.2    
14.4    
14.6    
14.8    
15.1    
15.3    
15.5    
15.8    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.8    
18.0    
18.3    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.5    
20.8    
21.0    
21.2    
21.5    
21.7    
21.9    
22.1    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 8819, rend_intergenic: 7022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29050, rend_intergenic: 24388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32032, rend_intergenic: 29117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64456, rend_intergenic: 47737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81421, rend_intergenic: 73227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96394, rend_intergenic: 84074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99812, rend_intergenic: 97806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100790, rend_intergenic: 100165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121059, rend_intergenic: 101356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122640, rend_intergenic: 121167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146201, rend_intergenic: 134505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184799, rend_intergenic: 176652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203168, rend_intergenic: 200787  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