-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_18813657-19002241

-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 pasa_asmbl_42112.p1
Valid prediction for snap_scaffold_4-snap.3889-T1
Valid prediction for GlimmerHMM_glimmerT_11179-T1
Valid prediction for Augustus_model.g7328.t1
Valid prediction for GlimmerHMM_glimmerT_11171-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3864-T1
Valid prediction for snap_scaffold_4-snap.3868-T1
Valid prediction for Augustus_model.g7339.t1
Valid prediction for GlimmerHMM_glimmerT_11180-T1
Valid prediction for snap_scaffold_4-snap.3882-T1
Valid prediction for GlimmerHMM_glimmerT_11181-T1
Valid prediction for Augustus_model.g7342.t1
Valid prediction for snap_scaffold_4-snap.3897-T1
Couldn't classify 175270, 175393
Couldn't classify 176974, 177167
Sorry, prediction pasa_asmbl_42256.p1 fails validation.
(TGG)	 AA	175270-175393	GT	AGG
(AGC)	 AG	176974-177167	GC	GGG
-recovered pasa_asmbl_42256.p1, internal, 176974, 177167
Valid prediction for snap_scaffold_4-snap.3894-T1
Valid prediction for snap_scaffold_4-snap.3859-T1
Valid prediction for snap_scaffold_4-snap.3881-T1
Valid prediction for Augustus_model.g7338.t1
Valid prediction for GlimmerHMM_glimmerT_11165-T1
Valid prediction for Augustus_model.g7336.t1
Valid prediction for HiQ_model.g7343.t1
Valid prediction for snap_scaffold_4-snap.3880-T1
Valid prediction for HiQ_model.g7335.t1
Valid prediction for snap_scaffold_4-snap.3891-T1
Valid prediction for GlimmerHMM_glimmerT_11173-T1
Valid prediction for snap_scaffold_4-snap.3895-T1
Valid prediction for GlimmerHMM_glimmerT_11174-T1
Valid prediction for GlimmerHMM_glimmerT_11169-T1
Valid prediction for snap_scaffold_4-snap.3858-T1
Valid prediction for snap_scaffold_4-snap.3866-T1
Valid prediction for CodingQuarry_transcript_49383-T1
Valid prediction for Augustus_model.g7341.t1
Valid prediction for snap_scaffold_4-snap.3878-T1
Valid prediction for Augustus_model.g7333.t1
Valid prediction for GlimmerHMM_glimmerT_11184-T1
Valid prediction for HiQ_model.g7327.t1
Valid prediction for GlimmerHMM_glimmerT_11167-T1
Valid prediction for snap_scaffold_4-snap.3887-T1
Valid prediction for snap_scaffold_4-snap.3876-T1
Valid prediction for snap_scaffold_4-snap.3875-T1
Valid prediction for Augustus_model.g7340.t1
Couldn't classify 180803, 180947
Sorry, prediction pasa_asmbl_42116.p1 fails validation.
(ACT)	 AG	180803-180947	GT	AGG
(CAC)	 AG	181168-181208	GT	AGG
(TGT)	 AG	181530-181590	GT	AGG
(ACC)	 AG	182239-182344	GT	AGG
(ACA)	 AG	182493-182763	AG	GAA
-recovered pasa_asmbl_42116.p1, terminal, 182493, 182763
-recovered pasa_asmbl_42116.p1, internal, 180803, 180947
-recovered pasa_asmbl_42116.p1, internal, 181168, 181208
-recovered pasa_asmbl_42116.p1, internal, 181530, 181590
-recovered pasa_asmbl_42116.p1, internal, 182239, 182344
Valid prediction for snap_scaffold_4-snap.3885-T1
Valid prediction for snap_scaffold_4-snap.3869-T1
Valid prediction for snap_scaffold_4-snap.3872-T1
Valid prediction for snap_scaffold_4-snap.3861-T1
Valid prediction for GlimmerHMM_glimmerT_11166-T1
Valid prediction for GlimmerHMM_glimmerT_11182-T1
Valid prediction for GlimmerHMM_glimmerT_11177-T1
Valid prediction for snap_scaffold_4-snap.3892-T1
Valid prediction for CodingQuarry_transcript_49378-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 CodingQuarry_transcript_49381-T1
Valid prediction for snap_scaffold_4-snap.3865-T1
Valid prediction for Augustus_model.g7329.t1
Valid prediction for snap_scaffold_4-snap.3873-T1
Valid prediction for snap_scaffold_4-snap.3867-T1
Valid prediction for Augustus_model.g7330.t1
Valid prediction for CodingQuarry_transcript_49380-T1
Valid prediction for GlimmerHMM_glimmerT_11176-T1
Valid prediction for GlimmerHMM_glimmerT_11178-T1
Valid prediction for snap_scaffold_4-snap.3896-T1
Valid prediction for CodingQuarry_transcript_49382-T1
Valid prediction for snap_scaffold_4-snap.3893-T1
Valid prediction for Augustus_model.g7331.t1
Valid prediction for Augustus_model.g7332.t1
Valid prediction for snap_scaffold_4-snap.3871-T1
Valid prediction for snap_scaffold_4-snap.3860-T1
Valid prediction for GlimmerHMM_glimmerT_11172-T1
Valid prediction for snap_scaffold_4-snap.3898-T1
Valid prediction for Augustus_model.g7334.t1
Valid prediction for GlimmerHMM_glimmerT_11168-T1
Valid prediction for snap_scaffold_4-snap.3883-T1
Valid prediction for pasa_asmbl_43392.p1
Valid prediction for GlimmerHMM_glimmerT_11170-T1
Valid prediction for snap_scaffold_4-snap.3888-T1
Valid prediction for snap_scaffold_4-snap.3884-T1
Valid prediction for snap_scaffold_4-snap.3862-T1
Couldn't classify 127055, 127186
Couldn't classify 127248, 127409
Sorry, prediction CodingQuarry_transcript_49379-T1 fails validation.
(ATG)	 AA	123672-124127	GT	CGG
(CTG)	 AG	124976-125099	GT	AGG
(AGG)	 AG	125911-126153	GT	AGG
(CTC)	 AG	127055-127186	CC	CCC
(TTC)	 CC	127248-127409	GT	AGG
(CTG)	 AG	128924-128943	GT	GAG
-recovered CodingQuarry_transcript_49379-T1, initial, 123672, 124127
-recovered CodingQuarry_transcript_49379-T1, terminal, 128924, 128943
-recovered CodingQuarry_transcript_49379-T1, internal, 124976, 125099
-recovered CodingQuarry_transcript_49379-T1, internal, 125911, 126153
-recovered CodingQuarry_transcript_49379-T1, internal, 128924, 128943
Valid prediction for snap_scaffold_4-snap.3870-T1
Valid prediction for snap_scaffold_4-snap.3879-T1
Valid prediction for HiQ_model.g7337.t1
Valid prediction for snap_scaffold_4-snap.3874-T1
Valid prediction for snap_scaffold_4-snap.3877-T1
Valid prediction for snap_scaffold_4-snap.3886-T1
Valid prediction for snap_scaffold_4-snap.3890-T1
Valid prediction for GlimmerHMM_glimmerT_11175-T1
Valid prediction for snap_scaffold_4-snap.3863-T1
Valid prediction for GlimmerHMM_glimmerT_11183-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7352, rend_intergenic: 4345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14389, rend_intergenic: 7785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19718, rend_intergenic: 15734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24322, rend_intergenic: 20792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30907, rend_intergenic: 24414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34505, rend_intergenic: 31596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64518, rend_intergenic: 51809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72919, rend_intergenic: 66956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77218, rend_intergenic: 73070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89022, rend_intergenic: 77288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96279, rend_intergenic: 93743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103161, rend_intergenic: 100969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112228, rend_intergenic: 103247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118646, rend_intergenic: 115615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127853, rend_intergenic: 119629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131139, rend_intergenic: 127987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137736, rend_intergenic: 134860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142398, rend_intergenic: 139296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146945, rend_intergenic: 146307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171794, rend_intergenic: 147253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174546, rend_intergenic: 172095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182763, rend_intergenic: 175709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188585
-exon list size: 350


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
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8.5    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 7352, rend_intergenic: 4345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14389, rend_intergenic: 7785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19718, rend_intergenic: 15734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24322, rend_intergenic: 20792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30907, rend_intergenic: 24414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34505, rend_intergenic: 31596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64518, rend_intergenic: 51809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72919, rend_intergenic: 66956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77218, rend_intergenic: 73070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89022, rend_intergenic: 77288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96279, rend_intergenic: 93743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103161, rend_intergenic: 100969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112228, rend_intergenic: 103247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118646, rend_intergenic: 115615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127853, rend_intergenic: 119629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131139, rend_intergenic: 127987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137736, rend_intergenic: 134860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142398, rend_intergenic: 139296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146945, rend_intergenic: 146307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171794, rend_intergenic: 147253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174546, rend_intergenic: 172095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182763, rend_intergenic: 175709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support