-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_10747355-10926372

-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_7272-T1
Valid prediction for GlimmerHMM_glimmerT_7285-T1
Valid prediction for snap_scaffold_3-snap.2138-T1
Valid prediction for Augustus_model.g4734.t1
Valid prediction for snap_scaffold_3-snap.2159-T1
Couldn't classify 59295, 59447
Sorry, prediction pasa_asmbl_40299.p1 fails validation.
(CAG)	 TG	59295-59447	GT	AGG
(GCC)	 AG	59999-60158	GT	GGG
(GGT)	 AG	60298-60394	GT	GGG
(ATT)	 AG	60482-60535	GT	AGG
(GAA)	 AG	60702-60759	GT	ACG
(CCT)	 AG	61197-61294	GT	AGG
(GGT)	 AG	61416-61527	GT	AGG
(ATC)	 AG	61702-61764	GT	TTG
(GAC)	 AG	61877-62032	AC	AGA
-recovered pasa_asmbl_40299.p1, terminal, 61877, 62032
-recovered pasa_asmbl_40299.p1, internal, 59999, 60158
-recovered pasa_asmbl_40299.p1, internal, 60298, 60394
-recovered pasa_asmbl_40299.p1, internal, 60482, 60535
-recovered pasa_asmbl_40299.p1, internal, 60702, 60759
-recovered pasa_asmbl_40299.p1, internal, 61197, 61294
-recovered pasa_asmbl_40299.p1, internal, 61416, 61527
-recovered pasa_asmbl_40299.p1, internal, 61702, 61764
Valid prediction for GlimmerHMM_glimmerT_7270-T1
Valid prediction for Augustus_model.g4743.t1
Valid prediction for snap_scaffold_3-snap.2165-T1
Valid prediction for Augustus_model.g4741.t1
Valid prediction for Augustus_model.g4727.t1
Couldn't classify 55631, 55735
Couldn't classify 56056, 56194
Sorry, prediction pasa_asmbl_40298.p1 fails validation.
(GGG)	 AG	55631-55735	GT	AGG
(ATC)	 AG	55856-55947	GT	AGG
(CGC)	 AG	56056-56194	CA	GAC
-recovered pasa_asmbl_40298.p1, internal, 55631, 55735
-recovered pasa_asmbl_40298.p1, internal, 55856, 55947
Valid prediction for GlimmerHMM_glimmerT_7278-T1
Valid prediction for GlimmerHMM_glimmerT_7292-T1
Valid prediction for pasa_asmbl_40302.p1
Couldn't classify 118754, 119187
Couldn't classify 122071, 122150
Sorry, prediction pasa_asmbl_40313.p1 fails validation.
(CGA)	 GG	118754-119187	GT	CGG
(GAC)	 AG	119973-120079	GT	CTG
(TGG)	 AG	121763-121897	GT	AGG
(GTA)	 AG	122071-122150	GT	AGG
-recovered pasa_asmbl_40313.p1, internal, 119973, 120079
-recovered pasa_asmbl_40313.p1, internal, 121763, 121897
-recovered pasa_asmbl_40313.p1, internal, 122071, 122150
Valid prediction for GlimmerHMM_glimmerT_7287-T1
Valid prediction for GlimmerHMM_glimmerT_7273-T1
Valid prediction for CodingQuarry_transcript_46268-T1
Valid prediction for GlimmerHMM_glimmerT_7275-T1
Valid prediction for snap_scaffold_3-snap.2143-T1
Valid prediction for CodingQuarry_transcript_46264-T1
Valid prediction for Augustus_model.g4739.t1
Valid prediction for snap_scaffold_3-snap.2166-T1
Valid prediction for snap_scaffold_3-snap.2160-T1
Valid prediction for GlimmerHMM_glimmerT_7269-T1
Couldn't classify 86825, 86994
Sorry, prediction pasa_asmbl_40301.p1 fails validation.
(ATG)	 CT	82373-82432	GT	AGG
(GTG)	 AG	84795-84962	GT	AGG
(GTT)	 AG	85154-85283	GT	GGG
(TGG)	 AG	85407-85519	GT	AGG
(TCC)	 AG	85781-85971	GT	AGG
(CAT)	 AG	86403-86623	GT	AGG
(AGG)	 AG	86825-86994	TG	TGT
-recovered pasa_asmbl_40301.p1, initial, 82373, 82432
-recovered pasa_asmbl_40301.p1, internal, 84795, 84962
-recovered pasa_asmbl_40301.p1, internal, 85154, 85283
-recovered pasa_asmbl_40301.p1, internal, 85407, 85519
-recovered pasa_asmbl_40301.p1, internal, 85781, 85971
-recovered pasa_asmbl_40301.p1, internal, 86403, 86623
Couldn't classify 175500, 175755
Couldn't classify 176600, 176841
Sorry, prediction pasa_asmbl_40317.p1 fails validation.
(AGC)	 CC	175500-175755	GT	CGG
(GTC)	 AG	176600-176841	AT	AGA
Valid prediction for snap_scaffold_3-snap.2147-T1
Valid prediction for Augustus_model.g4733.t1
Valid prediction for snap_scaffold_3-snap.2152-T1
Valid prediction for snap_scaffold_3-snap.2161-T1
Valid prediction for GlimmerHMM_glimmerT_7289-T1
Valid prediction for snap_scaffold_3-snap.2145-T1
Valid prediction for snap_scaffold_3-snap.2139-T1
Valid prediction for Augustus_model.g4747.t1
Valid prediction for HiQ_model.g4748.t1
Valid prediction for GlimmerHMM_glimmerT_7288-T1
Valid prediction for GlimmerHMM_glimmerT_7268-T1
Valid prediction for Augustus_model.g4735.t1
Valid prediction for snap_scaffold_3-snap.2155-T1
Couldn't classify 91893, 92213
Sorry, prediction pasa_asmbl_40303.p1 fails validation.
(TCT)	 TC	91893-92213	TA	GAT
Valid prediction for snap_scaffold_3-snap.2157-T1
Valid prediction for snap_scaffold_3-snap.2167-T1
Valid prediction for GlimmerHMM_glimmerT_7284-T1
Valid prediction for pasa_asmbl_40314.p1
Valid prediction for CodingQuarry_transcript_46269-T1
Valid prediction for GlimmerHMM_glimmerT_7276-T1
Valid prediction for pasa_asmbl_40309.p1
Valid prediction for Augustus_model.g4744.t1
Valid prediction for snap_scaffold_3-snap.2141-T1
Valid prediction for Augustus_model.g4732.t1
Valid prediction for CodingQuarry_transcript_46263-T1
Valid prediction for snap_scaffold_3-snap.2163-T1
Valid prediction for snap_scaffold_3-snap.2168-T1
Valid prediction for Augustus_model.g4729.t1
Valid prediction for Augustus_model.g4728.t1
Valid prediction for GlimmerHMM_glimmerT_7282-T1
Couldn't classify 7927, 7960
Sorry, prediction pasa_asmbl_40295.p1 fails validation.
(TCA)	 AG	7927-7960	GT	GGG
(AGA)	 AG	8404-8554	GT	TGG
(GTG)	 AG	8674-8749	GT	AGG
(ATA)	 AG	8853-8981	GT	ACG
(TCC)	 AG	9076-9153	GT	AGG
-recovered pasa_asmbl_40295.p1, terminal, 9076, 9153
-recovered pasa_asmbl_40295.p1, internal, 7927, 7960
-recovered pasa_asmbl_40295.p1, internal, 8404, 8554
-recovered pasa_asmbl_40295.p1, internal, 8674, 8749
-recovered pasa_asmbl_40295.p1, internal, 8853, 8981
-recovered pasa_asmbl_40295.p1, internal, 9076, 9153

-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.g4737.t1
Valid prediction for pasa_asmbl_39119.p3
Valid prediction for pasa_asmbl_39118.p1
Valid prediction for snap_scaffold_3-snap.2153-T1
Valid prediction for GlimmerHMM_glimmerT_7281-T1
Valid prediction for snap_scaffold_3-snap.2146-T1
Valid prediction for Augustus_model.g4731.t1
Valid prediction for Augustus_model.g4736.t1
Valid prediction for snap_scaffold_3-snap.2156-T1
Couldn't classify 105862, 105930
Sorry, prediction pasa_asmbl_39111.p1 fails validation.
(CCC)	 CC	105862-105930	GC	AGG
(GTC)	 AG	106231-106518	CG	GAC
-recovered pasa_asmbl_39111.p1, terminal, 106231, 106518
Valid prediction for GlimmerHMM_glimmerT_7286-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.2162-T1
Valid prediction for snap_scaffold_3-snap.2148-T1
Valid prediction for pasa_asmbl_39707.p1
Valid prediction for GlimmerHMM_glimmerT_7283-T1
Couldn't classify 67312, 67365
Couldn't classify 67443, 68039
Sorry, prediction pasa_asmbl_39117.p1 fails validation.
(AGC)	 AA	67312-67365	GT	AGG
(GAT)	 AG	67443-68039	CC	GCC
Valid prediction for GlimmerHMM_glimmerT_7271-T1
Valid prediction for snap_scaffold_3-snap.2142-T1
Valid prediction for HiQ_model.g4738.t1
Valid prediction for GlimmerHMM_glimmerT_7280-T1
Valid prediction for snap_scaffold_3-snap.2158-T1
Valid prediction for GlimmerHMM_glimmerT_7279-T1
Couldn't classify 99925, 100228
Sorry, prediction pasa_asmbl_39115.p1 fails validation.
(AGC)	 CC	99925-100228	GT	TAG
(AAT)	 AG	100818-100945	GT	AGG
(CAT)	 AG	101372-101413	AT	GAA
-recovered pasa_asmbl_39115.p1, terminal, 101372, 101413
-recovered pasa_asmbl_39115.p1, internal, 100818, 100945
Valid prediction for HiQ_model.g4740.t1
Valid prediction for CodingQuarry_transcript_46267-T1
Valid prediction for HiQ_model.g4746.t1
Valid prediction for GlimmerHMM_glimmerT_7277-T1
Valid prediction for snap_scaffold_3-snap.2151-T1
Valid prediction for Augustus_model.g4742.t1
Valid prediction for HiQ_model.g4745.t1
Valid prediction for snap_scaffold_3-snap.2150-T1
Valid prediction for snap_scaffold_3-snap.2144-T1
Valid prediction for CodingQuarry_transcript_46270-T1
Couldn't classify 104101, 104223
Couldn't classify 105068, 105111
Sorry, prediction pasa_asmbl_39112.p1 fails validation.
(AGC)	 AC	104101-104223	GT	CCG
(GTG)	 AG	104651-104921	GT	AGG
(GCA)	 AG	105068-105111	CA	AAC
-recovered pasa_asmbl_39112.p1, internal, 104651, 104921
Valid prediction for snap_scaffold_3-snap.2149-T1
Valid prediction for GlimmerHMM_glimmerT_7290-T1
Valid prediction for snap_scaffold_3-snap.2140-T1
Valid prediction for GlimmerHMM_glimmerT_7274-T1
Valid prediction for snap_scaffold_3-snap.2154-T1
Valid prediction for snap_scaffold_3-snap.2164-T1
Valid prediction for Augustus_model.g4730.t1
Valid prediction for GlimmerHMM_glimmerT_7291-T1
Couldn't classify 68664, 69563
Sorry, prediction pasa_asmbl_39700.p1 fails validation.
(CCT)	 GC	68664-69563	AC	AGA
Valid prediction for CodingQuarry_transcript_46266-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17075, rend_intergenic: 11332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21965, rend_intergenic: 20797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34510, rend_intergenic: 22219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40895, rend_intergenic: 34676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46913, rend_intergenic: 44036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57235, rend_intergenic: 47051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62148, rend_intergenic: 59151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91359, rend_intergenic: 84810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122455, rend_intergenic: 119947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125698, rend_intergenic: 123497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144694, rend_intergenic: 139440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147541, rend_intergenic: 144894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154730, rend_intergenic: 149338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179018
-exon list size: 369


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 17075, rend_intergenic: 11332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21965, rend_intergenic: 20797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34510, rend_intergenic: 22219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40895, rend_intergenic: 34676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46913, rend_intergenic: 44036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57235, rend_intergenic: 47051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62148, rend_intergenic: 59151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91359, rend_intergenic: 84810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122455, rend_intergenic: 119947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125698, rend_intergenic: 123497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144694, rend_intergenic: 139440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147541, rend_intergenic: 144894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154730, rend_intergenic: 149338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support