-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_3510042-3730769

-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 CodingQuarry_transcript_59611-T1
Valid prediction for snap_scaffold_8-snap.683-T1
Valid prediction for snap_scaffold_8-snap.673-T1
Valid prediction for Augustus_model.g12980.t1
Valid prediction for Augustus_model.g12972.t1
Valid prediction for snap_scaffold_8-snap.702-T1
Valid prediction for Augustus_model.g12983.t1
Valid prediction for Augustus_model.g12969.t1
Valid prediction for GlimmerHMM_glimmerT_19515-T1
Valid prediction for snap_scaffold_8-snap.678-T1
Couldn't classify 179341, 179388
Couldn't classify 182846, 182995
Sorry, prediction pasa_asmbl_52795.p1 fails validation.
(CTG)	 AG	179341-179388	GT	AGG
(GTG)	 AG	179514-179637	GT	CTG
(CGG)	 AG	180287-180389	GT	AGG
(CTC)	 AG	181288-181426	GT	AGG
(TCC)	 AG	182846-182995	GG	TCG
-recovered pasa_asmbl_52795.p1, terminal, 180287, 180389
-recovered pasa_asmbl_52795.p1, internal, 179341, 179388
-recovered pasa_asmbl_52795.p1, internal, 179514, 179637
-recovered pasa_asmbl_52795.p1, internal, 180287, 180389
-recovered pasa_asmbl_52795.p1, internal, 181288, 181426
Valid prediction for snap_scaffold_8-snap.681-T1
Valid prediction for GlimmerHMM_glimmerT_19518-T1
Valid prediction for snap_scaffold_8-snap.677-T1
Valid prediction for snap_scaffold_8-snap.676-T1
Valid prediction for GlimmerHMM_glimmerT_19512-T1
Valid prediction for Augustus_model.g12977.t1
Valid prediction for snap_scaffold_8-snap.692-T1
Valid prediction for Augustus_model.g12976.t1
Valid prediction for GlimmerHMM_glimmerT_19527-T1
Valid prediction for snap_scaffold_8-snap.674-T1
Valid prediction for GlimmerHMM_glimmerT_19517-T1
Valid prediction for GlimmerHMM_glimmerT_19511-T1
Valid prediction for HiQ_model.g12973.t1
Valid prediction for snap_scaffold_8-snap.685-T1
Valid prediction for snap_scaffold_8-snap.675-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_19521-T1
Valid prediction for GlimmerHMM_glimmerT_19519-T1
Valid prediction for snap_scaffold_8-snap.688-T1
Valid prediction for GlimmerHMM_glimmerT_19524-T1
Valid prediction for GlimmerHMM_glimmerT_19522-T1
Valid prediction for snap_scaffold_8-snap.701-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g12971.t1
Valid prediction for HiQ_model.g12974.t1
Valid prediction for snap_scaffold_8-snap.668-T1
Valid prediction for GlimmerHMM_glimmerT_19513-T1
Valid prediction for Augustus_model.g12982.t1
Valid prediction for GlimmerHMM_glimmerT_19528-T1
Valid prediction for snap_scaffold_8-snap.693-T1
Couldn't classify 113895, 114041
Sorry, prediction pasa_asmbl_52792.p1 fails validation.
(TGG)	 TC	113895-114041	GT	ATG
(CCC)	 AG	114253-114363	GT	AGG
(CCG)	 AG	114676-114797	GT	AGG
(GGC)	 AG	115189-115238	GT	AGG
(GTG)	 AG	115638-115728	GT	TGG
(GTT)	 AG	115945-116042	GT	AAG
(CCA)	 AG	116508-116560	GT	TGG
(GCC)	 AG	117289-117388	GT	CGG
(CCA)	 AG	119314-119444	GT	AGG
(GAC)	 AG	119566-119641	GT	AGG
(GAG)	 AG	119963-120009	GT	GGG
(TAT)	 AG	120431-120532	GT	CTG
(GAC)	 AG	120638-120755	GT	AGG
(GTT)	 AG	121493-121569	GG	GAG
add_exon() Sorry, pasa_asmbl_52792.p1 115189-115238-terminal-2 is invalid.
-recovered pasa_asmbl_52792.p1, terminal, 115189, 115238
-recovered pasa_asmbl_52792.p1, terminal, 121493, 121569
-recovered pasa_asmbl_52792.p1, internal, 114253, 114363
-recovered pasa_asmbl_52792.p1, internal, 114676, 114797
-recovered pasa_asmbl_52792.p1, internal, 115189, 115238
-recovered pasa_asmbl_52792.p1, internal, 115638, 115728
-recovered pasa_asmbl_52792.p1, internal, 115945, 116042
-recovered pasa_asmbl_52792.p1, internal, 116508, 116560
-recovered pasa_asmbl_52792.p1, internal, 117289, 117388
-recovered pasa_asmbl_52792.p1, internal, 119314, 119444
-recovered pasa_asmbl_52792.p1, internal, 119566, 119641
-recovered pasa_asmbl_52792.p1, internal, 119963, 120009
-recovered pasa_asmbl_52792.p1, internal, 120431, 120532
-recovered pasa_asmbl_52792.p1, internal, 120638, 120755
Valid prediction for snap_scaffold_8-snap.686-T1
Valid prediction for Augustus_model.g12979.t1
Valid prediction for snap_scaffold_8-snap.669-T1
Valid prediction for snap_scaffold_8-snap.665-T1
Valid prediction for pasa_asmbl_52791.p1
Couldn't classify 93363, 93501
Sorry, prediction pasa_asmbl_52781.p1 fails validation.
(GGA)	 TA	93363-93501	GT	AGG
(GTC)	 AG	94598-95010	TC	AGT
-recovered pasa_asmbl_52781.p1, terminal, 94598, 95010
Valid prediction for GlimmerHMM_glimmerT_19505-T1
Valid prediction for snap_scaffold_8-snap.663-T1
Valid prediction for Augustus_model.g12970.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_8-snap.703-T1
Valid prediction for GlimmerHMM_glimmerT_19520-T1
Valid prediction for snap_scaffold_8-snap.691-T1
Valid prediction for snap_scaffold_8-snap.698-T1
Valid prediction for snap_scaffold_8-snap.664-T1
Valid prediction for snap_scaffold_8-snap.704-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.667-T1
Valid prediction for snap_scaffold_8-snap.679-T1
Valid prediction for GlimmerHMM_glimmerT_19506-T1
Valid prediction for GlimmerHMM_glimmerT_19508-T1
Valid prediction for Augustus_model.g12981.t1
Valid prediction for snap_scaffold_8-snap.671-T1
Valid prediction for GlimmerHMM_glimmerT_19507-T1
Valid prediction for pasa_asmbl_51737.p1
Valid prediction for GlimmerHMM_glimmerT_19526-T1
Valid prediction for GlimmerHMM_glimmerT_19516-T1
Valid prediction for snap_scaffold_8-snap.666-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.689-T1
Valid prediction for snap_scaffold_8-snap.700-T1
Valid prediction for Augustus_model.g12968.t1
Valid prediction for snap_scaffold_8-snap.699-T1
Valid prediction for snap_scaffold_8-snap.684-T1
Valid prediction for HiQ_model.g12966.t1
Valid prediction for GlimmerHMM_glimmerT_19509-T1
Valid prediction for snap_scaffold_8-snap.697-T1
Valid prediction for snap_scaffold_8-snap.695-T1
Valid prediction for GlimmerHMM_glimmerT_19504-T1
Valid prediction for snap_scaffold_8-snap.696-T1
Valid prediction for GlimmerHMM_glimmerT_19514-T1
Valid prediction for GlimmerHMM_glimmerT_19523-T1
Valid prediction for Augustus_model.g12975.t1
Valid prediction for GlimmerHMM_glimmerT_19510-T1
Valid prediction for snap_scaffold_8-snap.670-T1
Valid prediction for snap_scaffold_8-snap.672-T1
Valid prediction for GlimmerHMM_glimmerT_19525-T1
Valid prediction for snap_scaffold_8-snap.694-T1
Valid prediction for Augustus_model.g12967.t1
Valid prediction for snap_scaffold_8-snap.682-T1
Valid prediction for Augustus_model.g12978.t1
Valid prediction for snap_scaffold_8-snap.680-T1
Valid prediction for snap_scaffold_8-snap.705-T1
Valid prediction for snap_scaffold_8-snap.687-T1
Valid prediction for snap_scaffold_8-snap.690-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9439, rend_intergenic: 7050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19020, rend_intergenic: 10180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30357, rend_intergenic: 29340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37506, rend_intergenic: 33375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47065, rend_intergenic: 44436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95010, rend_intergenic: 84319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110831, rend_intergenic: 108003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112925, rend_intergenic: 111208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125322, rend_intergenic: 118984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136444, rend_intergenic: 128539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147419, rend_intergenic: 146600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189352, rend_intergenic: 153412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215807, rend_intergenic: 201200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220728
-exon list size: 342


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 9439, rend_intergenic: 7050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19020, rend_intergenic: 10180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30357, rend_intergenic: 29340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37506, rend_intergenic: 33375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47065, rend_intergenic: 44436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95010, rend_intergenic: 84319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110831, rend_intergenic: 108003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112925, rend_intergenic: 111208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125322, rend_intergenic: 118984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136444, rend_intergenic: 128539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147419, rend_intergenic: 146600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189352, rend_intergenic: 153412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215807, rend_intergenic: 201200  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