-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_6149968-6377611

-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 Augustus_model.g25662.t1
Valid prediction for pasa_asmbl_16298.p1
Valid prediction for CodingQuarry_transcript_19995-T1
Valid prediction for snap_scaffold_16-snap.1191-T1
Valid prediction for snap_scaffold_16-snap.1197-T1
Valid prediction for snap_scaffold_16-snap.1190-T1
Couldn't classify 74141, 74185
Sorry, prediction pasa_asmbl_16302.p1 fails validation.
(CTG)	 GT	74141-74185	GT	AGG
(GGT)	 AG	74314-74448	GT	ATG
(GTA)	 AG	74785-75004	GT	AGG
(ACA)	 AG	75198-75315	GT	GGG
(CCA)	 AG	75765-75818	GT	CAG
(CTC)	 AG	78817-78905	GT	TGG
(GTC)	 AG	79196-79347	AG	AAA
-recovered pasa_asmbl_16302.p1, terminal, 79196, 79347
-recovered pasa_asmbl_16302.p1, internal, 74314, 74448
-recovered pasa_asmbl_16302.p1, internal, 74785, 75004
-recovered pasa_asmbl_16302.p1, internal, 75198, 75315
-recovered pasa_asmbl_16302.p1, internal, 75765, 75818
-recovered pasa_asmbl_16302.p1, internal, 78817, 78905
Valid prediction for GlimmerHMM_glimmerT_38455-T1
Valid prediction for Augustus_model.g25673.t1
Valid prediction for GlimmerHMM_glimmerT_38465-T1
Valid prediction for Augustus_model.g25675.t1
Valid prediction for snap_scaffold_16-snap.1212-T1
Valid prediction for snap_scaffold_16-snap.1198-T1
Couldn't classify 73713, 73810
Sorry, prediction pasa_asmbl_16301.p1 fails validation.
(ATG)	 CC	67526-67609	GT	AGG
(GTG)	 AG	69619-69739	GT	AGG
(ATA)	 AG	71111-71196	GT	AGG
(GCG)	 AG	71491-71562	GT	TGG
(CCC)	 AG	72236-72325	GT	AGG
(GAA)	 AG	72422-72488	GT	GGG
(GTT)	 AG	73185-73225	GT	AGG
(GTT)	 AG	73341-73379	GT	AGG
(GTT)	 AG	73496-73565	GT	AGG
(GCA)	 AG	73713-73810	GA	AGG
-recovered pasa_asmbl_16301.p1, initial, 67526, 67609
-recovered pasa_asmbl_16301.p1, internal, 69619, 69739
-recovered pasa_asmbl_16301.p1, internal, 71111, 71196
-recovered pasa_asmbl_16301.p1, internal, 71491, 71562
-recovered pasa_asmbl_16301.p1, internal, 72236, 72325
-recovered pasa_asmbl_16301.p1, internal, 72422, 72488
-recovered pasa_asmbl_16301.p1, internal, 73185, 73225
-recovered pasa_asmbl_16301.p1, internal, 73341, 73379
-recovered pasa_asmbl_16301.p1, internal, 73496, 73565
Valid prediction for snap_scaffold_16-snap.1203-T1
Valid prediction for snap_scaffold_16-snap.1183-T1
Valid prediction for snap_scaffold_16-snap.1196-T1
Valid prediction for snap_scaffold_16-snap.1186-T1
Valid prediction for GlimmerHMM_glimmerT_38438-T1
Valid prediction for snap_scaffold_16-snap.1208-T1
Valid prediction for snap_scaffold_16-snap.1200-T1
Valid prediction for snap_scaffold_16-snap.1214-T1
Valid prediction for GlimmerHMM_glimmerT_38466-T1
Valid prediction for GlimmerHMM_glimmerT_38467-T1
Valid prediction for snap_scaffold_16-snap.1211-T1
Valid prediction for GlimmerHMM_glimmerT_38447-T1
Valid prediction for GlimmerHMM_glimmerT_38442-T1
Valid prediction for GlimmerHMM_glimmerT_38439-T1
Valid prediction for snap_scaffold_16-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_38452-T1
Valid prediction for GlimmerHMM_glimmerT_38450-T1
Valid prediction for snap_scaffold_16-snap.1204-T1
Valid prediction for GlimmerHMM_glimmerT_38443-T1
Valid prediction for snap_scaffold_16-snap.1206-T1
Couldn't classify 86662, 87012
Sorry, prediction pasa_asmbl_17157.p1 fails validation.
(CCA)	 CC	86662-87012	CA	AAC
Valid prediction for CodingQuarry_transcript_19991-T1
Valid prediction for GlimmerHMM_glimmerT_38463-T1
Valid prediction for Augustus_model.g25674.t1
Valid prediction for Augustus_model.g25665.t1
Valid prediction for snap_scaffold_16-snap.1195-T1
Couldn't classify 34912, 34956
Sorry, prediction pasa_asmbl_16825.p1 fails validation.
(ATG)	 TG	34327-34421	GT	GGG
(GAA)	 AG	34589-34751	GT	CGG
(ACT)	 AG	34912-34956	AA	GGA
-recovered pasa_asmbl_16825.p1, initial, 34327, 34421
-recovered pasa_asmbl_16825.p1, internal, 34589, 34751
Valid prediction for CodingQuarry_transcript_19992-T1
Valid prediction for HiQ_model.g25666.t1
Valid prediction for pasa_asmbl_16733.p1
Valid prediction for Augustus_model.g25664.t1
Valid prediction for Augustus_model.g25669.t1
Valid prediction for snap_scaffold_16-snap.1220-T1
Valid prediction for GlimmerHMM_glimmerT_38454-T1
Valid prediction for Augustus_model.g25678.t1
Valid prediction for snap_scaffold_16-snap.1194-T1
Valid prediction for snap_scaffold_16-snap.1189-T1
Valid prediction for snap_scaffold_16-snap.1187-T1
Valid prediction for GlimmerHMM_glimmerT_38440-T1
Valid prediction for snap_scaffold_16-snap.1205-T1
Valid prediction for HiQ_model.g25671.t1
Valid prediction for snap_scaffold_16-snap.1181-T1
Valid prediction for pasa_asmbl_16293.p1
Valid prediction for GlimmerHMM_glimmerT_38448-T1
Couldn't classify 15430, 15506
Sorry, prediction pasa_asmbl_16286.p1 fails validation.
(GGG)	 CG	15430-15506	GT	AGG
(GTA)	 AG	15742-15902	GT	AGG
(GGG)	 AG	16024-16121	GT	GGG
(GAC)	 AG	16305-16460	GA	GAG
-recovered pasa_asmbl_16286.p1, terminal, 16305, 16460
-recovered pasa_asmbl_16286.p1, internal, 15742, 15902
-recovered pasa_asmbl_16286.p1, internal, 16024, 16121

-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_16-snap.1193-T1
Valid prediction for GlimmerHMM_glimmerT_38461-T1
Valid prediction for CodingQuarry_transcript_19994-T1
Valid prediction for Augustus_model.g25672.t1
Valid prediction for snap_scaffold_16-snap.1219-T1
Valid prediction for snap_scaffold_16-snap.1202-T1
Valid prediction for snap_scaffold_16-snap.1184-T1
Valid prediction for snap_scaffold_16-snap.1216-T1
Couldn't classify 145691, 145816
Couldn't classify 145848, 145919
Sorry, prediction CodingQuarry_transcript_19996-T1 fails validation.
(ATG)	 GG	145691-145816	CT	GCC
(CTG)	 GC	145848-145919	TT	AGT
Valid prediction for snap_scaffold_16-snap.1199-T1
Valid prediction for snap_scaffold_16-snap.1222-T1
Valid prediction for GlimmerHMM_glimmerT_38458-T1
Valid prediction for snap_scaffold_16-snap.1221-T1
Valid prediction for snap_scaffold_16-snap.1182-T1
Valid prediction for HiQ_model.g25668.t1
Valid prediction for Augustus_model.g25663.t1
Valid prediction for GlimmerHMM_glimmerT_38444-T1
Valid prediction for snap_scaffold_16-snap.1207-T1
Valid prediction for GlimmerHMM_glimmerT_38446-T1
Valid prediction for HiQ_model.g25667.t1
Valid prediction for HiQ_model.g25670.t1
Valid prediction for snap_scaffold_16-snap.1210-T1
Valid prediction for CodingQuarry_transcript_19993-T1
Valid prediction for GlimmerHMM_glimmerT_38451-T1
Valid prediction for snap_scaffold_16-snap.1213-T1
Valid prediction for snap_scaffold_16-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_38449-T1
Valid prediction for GlimmerHMM_glimmerT_38460-T1
Valid prediction for snap_scaffold_16-snap.1217-T1
Valid prediction for pasa_asmbl_17148.p1
Valid prediction for GlimmerHMM_glimmerT_38464-T1
Valid prediction for Augustus_model.g25677.t1
Valid prediction for snap_scaffold_16-snap.1201-T1
Valid prediction for GlimmerHMM_glimmerT_38445-T1
Valid prediction for pasa_asmbl_17150.p1
Valid prediction for snap_scaffold_16-snap.1192-T1
Valid prediction for GlimmerHMM_glimmerT_38462-T1
Valid prediction for pasa_asmbl_17154.p1
Valid prediction for GlimmerHMM_glimmerT_38459-T1
Valid prediction for snap_scaffold_16-snap.1209-T1
Valid prediction for GlimmerHMM_glimmerT_38453-T1
Valid prediction for snap_scaffold_16-snap.1215-T1
Valid prediction for Augustus_model.g25676.t1
Valid prediction for snap_scaffold_16-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_38441-T1
Valid prediction for GlimmerHMM_glimmerT_38456-T1
Valid prediction for GlimmerHMM_glimmerT_38457-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7389, rend_intergenic: 2787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13018, rend_intergenic: 7709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36238, rend_intergenic: 32025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62489, rend_intergenic: 55849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70615, rend_intergenic: 68085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79347, rend_intergenic: 73747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86638, rend_intergenic: 84646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130779, rend_intergenic: 122873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152714, rend_intergenic: 147182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179697, rend_intergenic: 177206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227644
-exon list size: 400


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.5    
3.7    
4.0    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.2    
14.4    
14.7    
14.9    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.7    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.4    
64.7    
64.9    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 7389, rend_intergenic: 2787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13018, rend_intergenic: 7709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36238, rend_intergenic: 32025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62489, rend_intergenic: 55849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70615, rend_intergenic: 68085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79347, rend_intergenic: 73747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86638, rend_intergenic: 84646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130779, rend_intergenic: 122873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152714, rend_intergenic: 147182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179697, rend_intergenic: 177206  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

-building DP trellis

-building trellis in range 193516 - 227644
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 194696 - 227644
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 195119 - 227644
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 195119 - 205180
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 205249 - 227644
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 208106 - 227644
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 214949 - 227644
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 214949 - 225738
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support