-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_12184631-12337632

-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_23026-T1
Valid prediction for snap_scaffold_9-snap.2415-T1
Valid prediction for Augustus_model.g15354.t1
Valid prediction for GlimmerHMM_glimmerT_23008-T1
Valid prediction for GlimmerHMM_glimmerT_23023-T1
Valid prediction for snap_scaffold_9-snap.2421-T1
Valid prediction for snap_scaffold_9-snap.2412-T1
Valid prediction for GlimmerHMM_glimmerT_23010-T1
Valid prediction for Augustus_model.g15357.t1
Valid prediction for HiQ_model.g15352.t1
Valid prediction for snap_scaffold_9-snap.2425-T1
Valid prediction for snap_scaffold_9-snap.2404-T1
Valid prediction for snap_scaffold_9-snap.2423-T1
Valid prediction for CodingQuarry_transcript_62365-T1
Valid prediction for snap_scaffold_9-snap.2398-T1
Valid prediction for snap_scaffold_9-snap.2402-T1
Valid prediction for GlimmerHMM_glimmerT_23028-T1
Valid prediction for GlimmerHMM_glimmerT_23011-T1
Valid prediction for snap_scaffold_9-snap.2417-T1
Valid prediction for GlimmerHMM_glimmerT_23019-T1
Valid prediction for Augustus_model.g15346.t1
Valid prediction for pasa_asmbl_54425.p2
Valid prediction for Augustus_model.g15358.t1
Couldn't classify 115506, 115868
Sorry, prediction pasa_asmbl_54426.p1 fails validation.
(GCG)	 GA	115506-115868	CA	CAC
Valid prediction for GlimmerHMM_glimmerT_23027-T1
Valid prediction for GlimmerHMM_glimmerT_23014-T1
Valid prediction for Augustus_model.g15349.t1
Valid prediction for Augustus_model.g15356.t1
Valid prediction for snap_scaffold_9-snap.2414-T1
Valid prediction for GlimmerHMM_glimmerT_23021-T1
Valid prediction for Augustus_model.g15350.t1
Valid prediction for Augustus_model.g15348.t1
Valid prediction for GlimmerHMM_glimmerT_23025-T1
Valid prediction for snap_scaffold_9-snap.2419-T1
Valid prediction for pasa_asmbl_54422.p1
Valid prediction for GlimmerHMM_glimmerT_23017-T1
Valid prediction for snap_scaffold_9-snap.2405-T1
Valid prediction for snap_scaffold_9-snap.2410-T1
Valid prediction for Augustus_model.g15359.t1
Couldn't classify 120719, 120910
Sorry, prediction pasa_asmbl_54430.p1 fails validation.
(CAA)	 AG	120719-120910	GT	GTG
(GTG)	 AG	121161-121332	GT	AGG
(GTA)	 AG	121446-121548	GT	AAG
(GAA)	 AG	121704-121848	TA	GAT
-recovered pasa_asmbl_54430.p1, terminal, 121704, 121848
-recovered pasa_asmbl_54430.p1, internal, 120719, 120910
-recovered pasa_asmbl_54430.p1, internal, 121161, 121332
-recovered pasa_asmbl_54430.p1, internal, 121446, 121548

-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_9-snap.2400-T1
Valid prediction for snap_scaffold_9-snap.2416-T1
Valid prediction for snap_scaffold_9-snap.2399-T1
Valid prediction for GlimmerHMM_glimmerT_23016-T1
Valid prediction for snap_scaffold_9-snap.2407-T1
Valid prediction for GlimmerHMM_glimmerT_23024-T1
Valid prediction for snap_scaffold_9-snap.2420-T1
Valid prediction for snap_scaffold_9-snap.2409-T1
Valid prediction for GlimmerHMM_glimmerT_23012-T1
Valid prediction for snap_scaffold_9-snap.2422-T1
Valid prediction for GlimmerHMM_glimmerT_23029-T1
Valid prediction for CodingQuarry_transcript_62364-T1
Valid prediction for snap_scaffold_9-snap.2424-T1
Valid prediction for GlimmerHMM_glimmerT_23013-T1
Valid prediction for CodingQuarry_transcript_62366-T1
Valid prediction for GlimmerHMM_glimmerT_23030-T1
Valid prediction for CodingQuarry_transcript_62367-T1
Valid prediction for Augustus_model.g15363.t1
Valid prediction for Augustus_model.g15361.t1
Valid prediction for snap_scaffold_9-snap.2418-T1
Valid prediction for Augustus_model.g15364.t1
Valid prediction for pasa_asmbl_55367.p1
Valid prediction for snap_scaffold_9-snap.2408-T1
Valid prediction for snap_scaffold_9-snap.2413-T1
Valid prediction for snap_scaffold_9-snap.2403-T1
Couldn't classify 401, 455
Sorry, prediction pasa_asmbl_55372.p1 fails validation.
(CAG)	 CT	401-455	GT	AGG
(GTA)	 AG	1415-1565	GT	AAG
(AAT)	 AG	1662-2295	AC	AAA
-recovered pasa_asmbl_55372.p1, terminal, 1662, 2295
-recovered pasa_asmbl_55372.p1, internal, 1415, 1565
Valid prediction for Augustus_model.g15362.t1
Valid prediction for GlimmerHMM_glimmerT_23015-T1
Valid prediction for GlimmerHMM_glimmerT_23031-T1
Valid prediction for GlimmerHMM_glimmerT_23018-T1
Valid prediction for Augustus_model.g15351.t1
Couldn't classify 116071, 116263
Sorry, prediction pasa_asmbl_55361.p1 fails validation.
(GAG)	 AG	116071-116263	GT	GGG
(TGT)	 AG	116360-116458	GT	CTG
(GTT)	 AG	116744-116976	GG	GAG
-recovered pasa_asmbl_55361.p1, terminal, 116744, 116976
-recovered pasa_asmbl_55361.p1, internal, 116071, 116263
-recovered pasa_asmbl_55361.p1, internal, 116360, 116458
Valid prediction for GlimmerHMM_glimmerT_23020-T1
Valid prediction for GlimmerHMM_glimmerT_23009-T1
Valid prediction for snap_scaffold_9-snap.2401-T1
Couldn't classify 115064, 115081
Sorry, prediction pasa_asmbl_55363.p1 fails validation.
(ATG)	 AA	112673-112765	GT	AAG
(GTG)	 AG	113430-113711	GT	AGG
(GTT)	 AG	113864-114086	GT	CGG
(AGA)	 AG	114191-114408	GT	AGG
(GCG)	 AG	114582-114688	GC	AAG
(TGT)	 AG	114841-114949	GT	AGG
(AGG)	 AG	115064-115081	AG	GCA
-recovered pasa_asmbl_55363.p1, initial, 112673, 112765
-recovered pasa_asmbl_55363.p1, internal, 113430, 113711
-recovered pasa_asmbl_55363.p1, internal, 113864, 114086
-recovered pasa_asmbl_55363.p1, internal, 114191, 114408
-recovered pasa_asmbl_55363.p1, internal, 114582, 114688
-recovered pasa_asmbl_55363.p1, internal, 114841, 114949
Valid prediction for HiQ_model.g15353.t1
Valid prediction for snap_scaffold_9-snap.2406-T1
Valid prediction for Augustus_model.g15355.t1
Valid prediction for pasa_asmbl_55365.p1
Valid prediction for Augustus_model.g15347.t1
Couldn't classify 7378, 7432
Sorry, prediction pasa_asmbl_55371.p1 fails validation.
(CAG)	 CT	7378-7432	GT	AGG
(GTA)	 AG	8760-8907	GT	AAG
(CGA)	 AG	8999-9650	TT	GAT
-recovered pasa_asmbl_55371.p1, terminal, 8999, 9650
-recovered pasa_asmbl_55371.p1, internal, 8760, 8907
Valid prediction for pasa_asmbl_55369.p1
Valid prediction for CodingQuarry_transcript_62369-T1
Valid prediction for HiQ_model.g15360.t1
Valid prediction for GlimmerHMM_glimmerT_23022-T1
Valid prediction for snap_scaffold_9-snap.2411-T1
Couldn't classify 74774, 74803
Couldn't classify 75533, 75663
Sorry, prediction pasa_asmbl_55364.p1 fails validation.
(CCT)	 TG	74774-74803	GT	AGG
(GTG)	 AG	74954-75167	GT	TGG
(GTG)	 AG	75533-75663	GC	TGG
-recovered pasa_asmbl_55364.p1, internal, 74954, 75167
-recovered pasa_asmbl_55364.p1, internal, 75533, 75663

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28678, rend_intergenic: 2510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33341, rend_intergenic: 30629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39876, rend_intergenic: 34859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72633, rend_intergenic: 46815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86446, rend_intergenic: 82695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95442, rend_intergenic: 90499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108204, rend_intergenic: 106589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113362, rend_intergenic: 112359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121976, rend_intergenic: 119610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123979, rend_intergenic: 123074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129776, rend_intergenic: 124124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137608, rend_intergenic: 133735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144881, rend_intergenic: 139978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153002
-exon list size: 375


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
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7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.5    
13.8    
14.1    
14.3    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.2    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.8    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 28678, rend_intergenic: 2510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33341, rend_intergenic: 30629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39876, rend_intergenic: 34859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72633, rend_intergenic: 46815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86446, rend_intergenic: 82695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95442, rend_intergenic: 90499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108204, rend_intergenic: 106589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113362, rend_intergenic: 112359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121976, rend_intergenic: 119610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123979, rend_intergenic: 123074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129776, rend_intergenic: 124124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137608, rend_intergenic: 133735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144881, rend_intergenic: 139978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support