-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_4050244-4262560

-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_29788-T1
Couldn't classify 164747, 164753
Sorry, prediction pasa_asmbl_8548.p1 fails validation.
(ATG)	 AA	163400-163480	GT	CGG
(TGT)	 AG	163606-164381	GT	AGG
(GTC)	 AG	164747-164753	AA	CCA
-recovered pasa_asmbl_8548.p1, initial, 163400, 163480
-recovered pasa_asmbl_8548.p1, internal, 163606, 164381
Valid prediction for GlimmerHMM_glimmerT_29787-T1
Valid prediction for HiQ_model.g19825.t1
Valid prediction for GeneMark_model.51477_t
Valid prediction for GeneMark_model.51469_t
Valid prediction for GeneMark_model.51467_t
Valid prediction for Augustus_model.g19830.t1
Valid prediction for GeneMark_model.51446_t
Valid prediction for snap_scaffold_12-snap.863-T1
Valid prediction for snap_scaffold_12-snap.846-T1
Couldn't classify 164757, 164814
Sorry, prediction pasa_asmbl_8549.p1 fails validation.
(GTC)	 AT	164757-164814	GT	GAG
(CAA)	 AG	165332-165544	GT	ATG
(CGT)	 AG	165713-166245	CG	GAC
-recovered pasa_asmbl_8549.p1, terminal, 165713, 166245
-recovered pasa_asmbl_8549.p1, internal, 165332, 165544
Valid prediction for Augustus_model.g19828.t1
Valid prediction for GlimmerHMM_glimmerT_29777-T1
Valid prediction for GlimmerHMM_glimmerT_29785-T1
Valid prediction for GeneMark_model.51488_t
Valid prediction for GeneMark_model.51455_t
Valid prediction for CodingQuarry_transcript_10146-T1
Valid prediction for GlimmerHMM_glimmerT_29781-T1
Valid prediction for snap_scaffold_12-snap.854-T1
Valid prediction for HiQ_model.g19827.t1
Valid prediction for GlimmerHMM_glimmerT_29792-T1
Valid prediction for GeneMark_model.51453_t
Valid prediction for GeneMark_model.51459_t
Valid prediction for snap_scaffold_12-snap.840-T1
Valid prediction for GeneMark_model.51479_t
Valid prediction for GeneMark_model.51472_t
Valid prediction for GlimmerHMM_glimmerT_29790-T1
Valid prediction for GeneMark_model.51481_t
Valid prediction for GeneMark_model.51461_t
Valid prediction for Augustus_model.g19829.t1
Valid prediction for snap_scaffold_12-snap.857-T1
Valid prediction for snap_scaffold_12-snap.853-T1
Valid prediction for Augustus_model.g19821.t1
Valid prediction for GeneMark_model.51483_t
Valid prediction for snap_scaffold_12-snap.836-T1
Valid prediction for GeneMark_model.51452_t
Valid prediction for GeneMark_model.51470_t
Valid prediction for Augustus_model.g19819.t1
Valid prediction for Augustus_model.g19833.t1
Valid prediction for GlimmerHMM_glimmerT_29795-T1
Valid prediction for snap_scaffold_12-snap.838-T1
Valid prediction for snap_scaffold_12-snap.850-T1
Valid prediction for GlimmerHMM_glimmerT_29779-T1
Valid prediction for GeneMark_model.51445_t
Valid prediction for Augustus_model.g19823.t1
Valid prediction for snap_scaffold_12-snap.845-T1
Valid prediction for GeneMark_model.51441_t
Valid prediction for GlimmerHMM_glimmerT_29791-T1
Valid prediction for GlimmerHMM_glimmerT_29796-T1
Valid prediction for GeneMark_model.51465_t
Valid prediction for GeneMark_model.51454_t
Valid prediction for snap_scaffold_12-snap.864-T1
Couldn't classify 141554, 141571
Sorry, prediction pasa_asmbl_8544.p1 fails validation.
(TTC)	 GC	141554-141571	GT	AGG
(GGT)	 AG	141706-141820	GT	AGG
(AGG)	 AG	142023-142154	GT	AGG
(GCA)	 AG	142315-142398	GT	CAG
(GCC)	 AG	142671-142882	GT	AGG
(GCG)	 AG	143083-143348	GT	AGG
(ACG)	 AG	143686-143854	GT	TGG
(GCC)	 AG	144876-144985	GT	AGG
(GGC)	 AG	145653-145878	AA	GAA
-recovered pasa_asmbl_8544.p1, terminal, 145653, 145878
-recovered pasa_asmbl_8544.p1, internal, 141706, 141820
-recovered pasa_asmbl_8544.p1, internal, 142023, 142154
-recovered pasa_asmbl_8544.p1, internal, 142315, 142398
-recovered pasa_asmbl_8544.p1, internal, 142671, 142882
-recovered pasa_asmbl_8544.p1, internal, 143083, 143348
-recovered pasa_asmbl_8544.p1, internal, 143686, 143854
-recovered pasa_asmbl_8544.p1, internal, 144876, 144985
Valid prediction for Augustus_model.g19822.t1
Valid prediction for snap_scaffold_12-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_29782-T1
Valid prediction for snap_scaffold_12-snap.843-T1
Valid prediction for GeneMark_model.51464_t
Valid prediction for GeneMark_model.51486_t
Valid prediction for snap_scaffold_12-snap.848-T1
Valid prediction for snap_scaffold_12-snap.844-T1
Valid prediction for GlimmerHMM_glimmerT_29786-T1
Valid prediction for GeneMark_model.51463_t
Valid prediction for snap_scaffold_12-snap.849-T1
Valid prediction for GeneMark_model.51450_t
Valid prediction for Augustus_model.g19832.t1
Valid prediction for GeneMark_model.51476_t
Valid prediction for GlimmerHMM_glimmerT_29793-T1
Valid prediction for Augustus_model.g19826.t1
Valid prediction for snap_scaffold_12-snap.852-T1
Valid prediction for GeneMark_model.51443_t

-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_12-snap.860-T1
Valid prediction for GlimmerHMM_glimmerT_29776-T1
Valid prediction for snap_scaffold_12-snap.842-T1
Valid prediction for GeneMark_model.51444_t
Valid prediction for Augustus_model.g19820.t1
Valid prediction for GlimmerHMM_glimmerT_29778-T1
Valid prediction for GlimmerHMM_glimmerT_29784-T1
Valid prediction for GlimmerHMM_glimmerT_29794-T1
Valid prediction for GeneMark_model.51471_t
Valid prediction for GeneMark_model.51458_t
Valid prediction for GlimmerHMM_glimmerT_29775-T1
Valid prediction for GeneMark_model.51468_t
Valid prediction for snap_scaffold_12-snap.861-T1
Valid prediction for GeneMark_model.51442_t
Valid prediction for HiQ_model.g19824.t1
Valid prediction for snap_scaffold_12-snap.855-T1
Valid prediction for Augustus_model.g19831.t1
Valid prediction for GeneMark_model.51474_t
Valid prediction for GeneMark_model.51451_t
Valid prediction for GeneMark_model.51478_t
Valid prediction for snap_scaffold_12-snap.859-T1
Valid prediction for snap_scaffold_12-snap.834-T1
Valid prediction for GeneMark_model.51475_t
Valid prediction for GeneMark_model.51473_t
Valid prediction for snap_scaffold_12-snap.847-T1
Couldn't classify 58817, 58868
Sorry, prediction pasa_asmbl_7516.p1 fails validation.
(TCG)	 GG	58817-58868	GT	AGG
(CTA)	 AG	59375-59500	GT	AGG
(TGA)	 AG	59673-59804	GT	GTG
(TCA)	 AG	60058-60146	GT	AGG
(GTG)	 AG	60263-60325	GT	ATG
(TTG)	 AG	60442-60489	GT	AGG
(GCG)	 AG	60713-60827	GT	AGG
(TGG)	 AG	60956-61048	GT	AGG
(GAG)	 AG	61357-61457	GT	ACG
(CAA)	 AG	61641-61781	GG	GAG
-recovered pasa_asmbl_7516.p1, terminal, 61641, 61781
-recovered pasa_asmbl_7516.p1, internal, 59375, 59500
-recovered pasa_asmbl_7516.p1, internal, 59673, 59804
-recovered pasa_asmbl_7516.p1, internal, 60058, 60146
-recovered pasa_asmbl_7516.p1, internal, 60263, 60325
-recovered pasa_asmbl_7516.p1, internal, 60442, 60489
-recovered pasa_asmbl_7516.p1, internal, 60713, 60827
-recovered pasa_asmbl_7516.p1, internal, 60956, 61048
-recovered pasa_asmbl_7516.p1, internal, 61357, 61457
Valid prediction for snap_scaffold_12-snap.851-T1
Valid prediction for snap_scaffold_12-snap.833-T1
Valid prediction for snap_scaffold_12-snap.835-T1
Valid prediction for GeneMark_model.51456_t
Valid prediction for GeneMark_model.51484_t
Valid prediction for GeneMark_model.51485_t
Valid prediction for GeneMark_model.51457_t
Valid prediction for snap_scaffold_12-snap.858-T1
Valid prediction for GeneMark_model.51460_t
Valid prediction for GeneMark_model.51462_t
Valid prediction for GeneMark_model.51482_t
Valid prediction for GeneMark_model.51448_t
Valid prediction for GeneMark_model.51440_t
Valid prediction for GeneMark_model.51480_t
Valid prediction for snap_scaffold_12-snap.841-T1
Valid prediction for snap_scaffold_12-snap.839-T1
Valid prediction for snap_scaffold_12-snap.837-T1
Valid prediction for GeneMark_model.51449_t
Valid prediction for snap_scaffold_12-snap.862-T1
Valid prediction for snap_scaffold_12-snap.856-T1
Valid prediction for GlimmerHMM_glimmerT_29780-T1
Valid prediction for GeneMark_model.51447_t
Valid prediction for GeneMark_model.51466_t
Valid prediction for GeneMark_model.51487_t
Valid prediction for GlimmerHMM_glimmerT_29783-T1
Valid prediction for snap_scaffold_12-snap.831-T1
Valid prediction for GlimmerHMM_glimmerT_29789-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 112975, rend_intergenic: 111214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133309, rend_intergenic: 121015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152772, rend_intergenic: 150537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177908, rend_intergenic: 169719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191613, rend_intergenic: 180043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192685, rend_intergenic: 191632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204047, rend_intergenic: 193168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207201, rend_intergenic: 205394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212317
-exon list size: 590


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.2    
1.4    
1.5    
1.7    
1.9    
2.0    
2.2    
2.4    
2.5    
2.7    
2.9    
3.0    
3.2    
3.4    
3.5    
3.7    
3.9    
4.1    
4.2    
4.4    
4.6    
4.7    
4.9    
5.1    
5.2    
5.4    
5.6    
5.7    
5.9    
6.1    
6.2    
6.4    
6.6    
6.8    
6.9    
7.1    
7.3    
7.4    
7.6    
7.8    
7.9    
8.1    
8.3    
8.4    
8.6    
8.8    
9.0    
9.1    
9.3    
9.5    
9.6    
9.8    
10.0    
10.1    
10.3    
10.5    
10.6    
10.8    
11.0    
11.1    
11.3    
11.5    
11.7    
11.8    
12.0    
12.2    
12.3    
12.5    
12.7    
12.8    
13.0    
13.2    
13.3    
13.5    
13.7    
13.9    
14.0    
14.2    
14.4    
14.5    
14.7    
14.9    
15.0    
15.2    
15.4    
15.5    
15.7    
15.9    
16.0    
16.2    
16.4    
16.6    
16.7    
16.9    
17.1    
17.2    
17.4    
17.6    
17.7    
17.9    
18.1    
18.2    
18.4    
18.6    
18.8    
18.9    
19.1    
19.3    
19.4    
19.6    
19.8    
19.9    
20.1    
20.3    
20.4    
20.6    
20.8    
20.9    
21.1    
21.3    
21.5    
21.6    
21.8    
22.0    
22.1    
22.3    
22.5    
22.6    
22.8    
23.0    
23.1    
23.3    
23.5    
23.6    
23.8    
24.0    
24.2    
24.3    
24.5    
24.7    
24.8    
25.0    
25.2    
25.3    
25.5    
25.7    
25.8    
26.0    
26.2    
26.4    
26.5    
26.7    
26.9    
27.0    
27.2    
27.4    
27.5    
27.7    
27.9    
28.0    
28.2    
28.4    
28.5    
28.7    
28.9    
29.1    
29.2    
29.4    
29.6    
29.7    
29.9    
30.1    
30.2    
30.4    
30.6    
30.7    
30.9    
31.1    
31.2    
31.4    
31.6    
31.8    
31.9    
32.1    
32.3    
32.4    
32.6    
32.8    
32.9    
33.1    
33.3    
33.4    
33.6    
33.8    
34.0    
34.1    
34.3    
34.5    
34.6    
34.8    
35.0    
35.1    
35.3    
35.5    
35.6    
35.8    
36.0    
36.1    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.3    
37.5    
37.7    
37.8    
38.0    
38.2    
38.3    
38.5    
38.7    
38.9    
39.0    
39.2    
39.4    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.5    
40.7    
40.9    
41.0    
41.2    
41.4    
41.6    
41.7    
41.9    
42.1    
42.2    
42.4    
42.6    
42.7    
42.9    
43.1    
43.2    
43.4    
43.6    
43.8    
43.9    
44.1    
44.3    
44.4    
44.6    
44.8    
44.9    
45.1    
45.3    
45.4    
45.6    
45.8    
45.9    
46.1    
46.3    
46.5    
46.6    
46.8    
47.0    
47.1    
47.3    
47.5    
47.6    
47.8    
48.0    
48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.2    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.8    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.0    
52.2    
52.4    
52.5    
52.7    
52.9    
53.0    
53.2    
53.4    
53.5    
53.7    
53.9    
54.1    
54.2    
54.4    
54.6    
54.7    
54.9    
55.1    
55.2    
55.4    
55.6    
55.7    
55.9    
56.1    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.4    
57.6    
57.8    
57.9    
58.1    
58.3    
58.4    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.7    
61.8    
62.0    
62.2    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.9    
64.0    
64.2    
64.4    
64.5    
64.7    
64.9    
65.0    
65.2    
65.4    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.7    
67.9    
68.1    
68.2    
68.4    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 112975, rend_intergenic: 111214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133309, rend_intergenic: 121015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152772, rend_intergenic: 150537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177908, rend_intergenic: 169719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191613, rend_intergenic: 180043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192685, rend_intergenic: 191632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204047, rend_intergenic: 193168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207201, rend_intergenic: 205394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support