-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_15856011-16019848

-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 HiQ_model.g5234.t1
Valid prediction for Augustus_model.g5249.t1
Valid prediction for GlimmerHMM_glimmerT_7950-T1
Valid prediction for Augustus_model.g5245.t1
Valid prediction for GlimmerHMM_glimmerT_7937-T1
Valid prediction for snap_scaffold_3-snap.3028-T1
Valid prediction for GlimmerHMM_glimmerT_7933-T1
Valid prediction for GlimmerHMM_glimmerT_7954-T1
Valid prediction for snap_scaffold_3-snap.3025-T1
Valid prediction for GlimmerHMM_glimmerT_7934-T1
Valid prediction for GlimmerHMM_glimmerT_7938-T1
Valid prediction for Augustus_model.g5253.t1
Valid prediction for snap_scaffold_3-snap.3053-T1
Valid prediction for GlimmerHMM_glimmerT_7948-T1
Valid prediction for snap_scaffold_3-snap.3032-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3045-T1
Valid prediction for snap_scaffold_3-snap.3023-T1
Valid prediction for GlimmerHMM_glimmerT_7936-T1
Valid prediction for GlimmerHMM_glimmerT_7957-T1
Valid prediction for snap_scaffold_3-snap.3041-T1
Valid prediction for GlimmerHMM_glimmerT_7951-T1
Valid prediction for Augustus_model.g5248.t1
Valid prediction for Augustus_model.g5235.t1
Valid prediction for Augustus_model.g5244.t1
Couldn't classify 4145, 4318
Sorry, prediction pasa_asmbl_40585.p1 fails validation.
(CAC)	 CG	4145-4318	GT	GGG
(GAT)	 AG	4412-4530	GT	AGG
(CTC)	 AG	4617-4695	GT	AGG
(GTG)	 AG	4998-5093	GT	AGG
(GGT)	 AG	5547-5642	GT	AGG
(AGA)	 AG	5921-6022	GT	ATG
(GGG)	 AG	6130-6227	GT	AAG
(AGC)	 AG	6313-6417	GT	AGG
(GTG)	 AG	6498-6728	GT	AGG
(GTC)	 AG	7285-7378	GT	AGG
(AGT)	 AG	7609-7710	GT	AGG
(AGG)	 AG	7845-7927	GT	AAG
(AAG)	 AG	8102-8240	GT	AGG
(TTT)	 AG	8332-8388	GT	ATG
(GAT)	 AG	8588-8688	GT	AGG
(CGT)	 AG	8903-9014	GT	AGG
(GGT)	 AG	9481-9615	GT	TGG
(GAA)	 AG	9716-9766	GT	TGG
(GTT)	 AG	9872-9937	GT	CTG
(GCC)	 AG	10508-10600	GT	AGG
(TTG)	 AG	10678-10728	GT	CAG
(CCA)	 AG	10848-10891	GT	AGG
(TGA)	 AG	11130-11258	GT	AGG
(GAT)	 AG	11344-11437	GT	GGG
(GAT)	 AG	11734-11889	AT	GAA
add_exon() Sorry, pasa_asmbl_40585.p1 11130-11258-terminal-1 is invalid.
-recovered pasa_asmbl_40585.p1, terminal, 11130, 11258
-recovered pasa_asmbl_40585.p1, terminal, 11734, 11889
-recovered pasa_asmbl_40585.p1, internal, 4412, 4530
-recovered pasa_asmbl_40585.p1, internal, 4617, 4695
-recovered pasa_asmbl_40585.p1, internal, 4998, 5093
-recovered pasa_asmbl_40585.p1, internal, 5547, 5642
-recovered pasa_asmbl_40585.p1, internal, 5921, 6022
-recovered pasa_asmbl_40585.p1, internal, 6130, 6227
-recovered pasa_asmbl_40585.p1, internal, 6313, 6417
-recovered pasa_asmbl_40585.p1, internal, 6498, 6728
-recovered pasa_asmbl_40585.p1, internal, 7285, 7378
-recovered pasa_asmbl_40585.p1, internal, 7609, 7710
-recovered pasa_asmbl_40585.p1, internal, 7845, 7927
-recovered pasa_asmbl_40585.p1, internal, 8102, 8240
-recovered pasa_asmbl_40585.p1, internal, 8332, 8388
-recovered pasa_asmbl_40585.p1, internal, 8588, 8688
-recovered pasa_asmbl_40585.p1, internal, 8903, 9014
-recovered pasa_asmbl_40585.p1, internal, 9481, 9615
-recovered pasa_asmbl_40585.p1, internal, 9716, 9766
-recovered pasa_asmbl_40585.p1, internal, 9872, 9937
-recovered pasa_asmbl_40585.p1, internal, 10508, 10600
-recovered pasa_asmbl_40585.p1, internal, 10678, 10728
-recovered pasa_asmbl_40585.p1, internal, 10848, 10891
-recovered pasa_asmbl_40585.p1, internal, 11130, 11258
-recovered pasa_asmbl_40585.p1, internal, 11344, 11437
Valid prediction for GlimmerHMM_glimmerT_7945-T1
Valid prediction for snap_scaffold_3-snap.3054-T1
Valid prediction for Augustus_model.g5247.t1
Valid prediction for snap_scaffold_3-snap.3029-T1
Valid prediction for snap_scaffold_3-snap.3051-T1
Valid prediction for Augustus_model.g5242.t1
Valid prediction for Augustus_model.g5246.t1
Valid prediction for snap_scaffold_3-snap.3047-T1
Valid prediction for GlimmerHMM_glimmerT_7953-T1
Valid prediction for snap_scaffold_3-snap.3050-T1
Valid prediction for snap_scaffold_3-snap.3031-T1
Valid prediction for GlimmerHMM_glimmerT_7952-T1
Valid prediction for Augustus_model.g5243.t1
Valid prediction for Augustus_model.g5237.t1
Valid prediction for Augustus_model.g5250.t1
Couldn't classify 11104, 11258
Sorry, prediction pasa_asmbl_40586.p1 fails validation.
(CCT)	 CA	11104-11258	GT	AGG
(GAT)	 AG	11344-11437	GT	GGG
(GAT)	 AG	11734-11889	AT	GAA
-recovered pasa_asmbl_40586.p1, terminal, 11734, 11889
-recovered pasa_asmbl_40586.p1, internal, 11344, 11437
Valid prediction for snap_scaffold_3-snap.3052-T1
Valid prediction for snap_scaffold_3-snap.3048-T1
Valid prediction for Augustus_model.g5236.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_3-snap.3037-T1
Valid prediction for GlimmerHMM_glimmerT_7958-T1
Valid prediction for snap_scaffold_3-snap.3057-T1
Valid prediction for snap_scaffold_3-snap.3036-T1
Valid prediction for HiQ_model.g5252.t1
Valid prediction for snap_scaffold_3-snap.3024-T1
Valid prediction for GlimmerHMM_glimmerT_7942-T1
Valid prediction for snap_scaffold_3-snap.3046-T1
Valid prediction for snap_scaffold_3-snap.3042-T1
Valid prediction for snap_scaffold_3-snap.3039-T1
Valid prediction for GlimmerHMM_glimmerT_7956-T1
Valid prediction for GlimmerHMM_glimmerT_7955-T1
Valid prediction for GlimmerHMM_glimmerT_7935-T1
Valid prediction for Augustus_model.g5254.t1
Valid prediction for GlimmerHMM_glimmerT_7939-T1
Valid prediction for snap_scaffold_3-snap.3026-T1
Valid prediction for snap_scaffold_3-snap.3056-T1
Couldn't classify 88174, 88347
Sorry, prediction pasa_asmbl_39455.p1 fails validation.
(AGG)	 GC	88174-88347	GT	ATG
(ATC)	 AG	90245-90412	GT	AGG
(ATC)	 AG	90717-90781	GT	AGG
(GAC)	 AG	92316-92413	GT	AGG
(GGG)	 AG	93946-94775	AA	AAA
-recovered pasa_asmbl_39455.p1, terminal, 93946, 94775
-recovered pasa_asmbl_39455.p1, internal, 90245, 90412
-recovered pasa_asmbl_39455.p1, internal, 90717, 90781
-recovered pasa_asmbl_39455.p1, internal, 92316, 92413
Valid prediction for Augustus_model.g5251.t1
Valid prediction for snap_scaffold_3-snap.3030-T1
Valid prediction for snap_scaffold_3-snap.3034-T1
Valid prediction for GlimmerHMM_glimmerT_7941-T1
Valid prediction for Augustus_model.g5240.t1
Valid prediction for snap_scaffold_3-snap.3043-T1
Valid prediction for snap_scaffold_3-snap.3027-T1
Valid prediction for CodingQuarry_transcript_46394-T1
Valid prediction for snap_scaffold_3-snap.3035-T1
Couldn't classify 82700, 82899
Couldn't classify 84830, 84932
Sorry, prediction pasa_asmbl_39779.p1 fails validation.
(GAT)	 CA	82700-82899	GT	AGG
(GCG)	 AG	84830-84932	TC	GGT
Valid prediction for Augustus_model.g5238.t1
Valid prediction for GlimmerHMM_glimmerT_7947-T1
Valid prediction for snap_scaffold_3-snap.3055-T1
Valid prediction for snap_scaffold_3-snap.3049-T1
Valid prediction for Augustus_model.g5239.t1
Valid prediction for GlimmerHMM_glimmerT_7946-T1
Couldn't classify 70338, 70417
Couldn't classify 72693, 72958
Sorry, prediction pasa_asmbl_39463.p1 fails validation.
(AAG)	 TG	70338-70417	GT	AAG
(GTC)	 AG	70999-71117	GT	CAG
(GCT)	 AG	72693-72958	AG	CCA
-recovered pasa_asmbl_39463.p1, internal, 70999, 71117
Valid prediction for Augustus_model.g5241.t1
Valid prediction for snap_scaffold_3-snap.3038-T1
Valid prediction for snap_scaffold_3-snap.3033-T1
Valid prediction for GlimmerHMM_glimmerT_7949-T1
Valid prediction for GlimmerHMM_glimmerT_7943-T1
Valid prediction for snap_scaffold_3-snap.3040-T1
Valid prediction for CodingQuarry_transcript_46393-T1
Valid prediction for GlimmerHMM_glimmerT_7944-T1
Valid prediction for snap_scaffold_3-snap.3058-T1
Valid prediction for GlimmerHMM_glimmerT_7940-T1
Valid prediction for snap_scaffold_3-snap.3044-T1
Valid prediction for pasa_asmbl_39465.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11889, rend_intergenic: 4049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25292, rend_intergenic: 20878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31115, rend_intergenic: 27662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98600, rend_intergenic: 95216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117029, rend_intergenic: 113216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120478, rend_intergenic: 118157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163838
-exon list size: 312


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.5    
2.9    
3.2    
3.5    
3.8    
4.1    
4.5    
4.8    
5.1    
5.4    
5.7    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
8.0    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
15.0    
15.3    
15.6    
15.9    
16.2    
16.6    
16.9    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.3    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.6    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.4    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.7    
29.0    
29.3    
29.6    
29.9    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.5    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.8    
41.1    
41.4    
41.7    
42.0    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.3    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.8    
47.1    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.9    
53.2    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.7    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
58.0    
58.3    
58.6    
58.9    
59.2    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.5    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.1    
70.4    
70.7    
71.0    
71.3    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.6    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.4    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.7    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.8    
84.1    
84.4    
84.7    
85.0    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.0    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.3    
94.6    
94.9    
95.2    
95.5    
95.9    
96.2    
96.5    
96.8    
97.1    
97.5    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 11889, rend_intergenic: 4049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25292, rend_intergenic: 20878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31115, rend_intergenic: 27662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98600, rend_intergenic: 95216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117029, rend_intergenic: 113216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120478, rend_intergenic: 118157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support