-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_4546500-4689840

-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_47548-T1
Valid prediction for snap_scaffold_21-snap.889-T1
Couldn't classify 45690, 46261
Sorry, prediction pasa_asmbl_28527.p1 fails validation.
(GTT)	 TA	45690-46261	GT	AGG
(CAG)	 AG	47413-47690	GT	AGG
(AAC)	 AG	48891-49102	GT	TGG
(TTT)	 AG	50332-50376	GT	GCG
(CTG)	 AG	51725-51820	GT	AGG
(ACC)	 AG	52031-52102	GT	GGG
(CTA)	 AG	52550-52579	GT	GGG
(AAA)	 AG	53325-53396	GT	AGG
(CAG)	 AG	53737-53878	GT	AGG
(GAC)	 AG	54170-54334	GT	AAG
(CGC)	 AG	54561-54789	GT	AGG
(GGA)	 AG	54911-56159	GC	GAG
-recovered pasa_asmbl_28527.p1, terminal, 54170, 54334
-recovered pasa_asmbl_28527.p1, terminal, 54911, 56159
-recovered pasa_asmbl_28527.p1, internal, 47413, 47690
-recovered pasa_asmbl_28527.p1, internal, 48891, 49102
-recovered pasa_asmbl_28527.p1, internal, 50332, 50376
-recovered pasa_asmbl_28527.p1, internal, 51725, 51820
-recovered pasa_asmbl_28527.p1, internal, 52031, 52102
-recovered pasa_asmbl_28527.p1, internal, 52550, 52579
-recovered pasa_asmbl_28527.p1, internal, 53325, 53396
-recovered pasa_asmbl_28527.p1, internal, 53737, 53878
-recovered pasa_asmbl_28527.p1, internal, 54170, 54334
-recovered pasa_asmbl_28527.p1, internal, 54561, 54789
-recovered pasa_asmbl_28527.p1, internal, 54911, 56159
Valid prediction for GlimmerHMM_glimmerT_47543-T1
Valid prediction for CodingQuarry_transcript_32499-T1
Valid prediction for snap_scaffold_21-snap.898-T1
Valid prediction for snap_scaffold_21-snap.890-T1
Valid prediction for Augustus_model.g31703.t1
Valid prediction for snap_scaffold_21-snap.900-T1
Valid prediction for snap_scaffold_21-snap.922-T1
Valid prediction for snap_scaffold_21-snap.906-T1
Valid prediction for Augustus_model.g31695.t1
Valid prediction for GlimmerHMM_glimmerT_47555-T1
Valid prediction for GlimmerHMM_glimmerT_47561-T1
Valid prediction for GlimmerHMM_glimmerT_47551-T1
Valid prediction for snap_scaffold_21-snap.895-T1
Valid prediction for GlimmerHMM_glimmerT_47562-T1
Valid prediction for GlimmerHMM_glimmerT_47546-T1
Valid prediction for Augustus_model.g31700.t1
Valid prediction for snap_scaffold_21-snap.911-T1
Valid prediction for CodingQuarry_transcript_32498-T1
Valid prediction for snap_scaffold_21-snap.893-T1
Valid prediction for GlimmerHMM_glimmerT_47572-T1
Valid prediction for snap_scaffold_21-snap.896-T1
Valid prediction for GlimmerHMM_glimmerT_47565-T1
Couldn't classify 54549, 54789
Sorry, prediction CodingQuarry_transcript_32497-T1 fails validation.
(ATG)	 AT	47594-47690	GT	AGG
(AAC)	 AG	48891-49123	GT	ATG
(TTT)	 AG	50332-50376	GT	GCG
(CTG)	 AG	51725-51820	GT	AGG
(ACC)	 AG	52031-52102	GT	GGG
(CTA)	 AG	52550-52579	GT	GGG
(AAA)	 AG	53325-53396	GT	AGG
(CAG)	 AG	53737-53878	GT	AGG
(GAC)	 AG	54170-54334	GT	AAG
(AAT)	 TG	54549-54789	GT	AGG
(GGA)	 AG	54911-56159	GC	GAG
-recovered CodingQuarry_transcript_32497-T1, initial, 47594, 47690
-recovered CodingQuarry_transcript_32497-T1, terminal, 54170, 54334
-recovered CodingQuarry_transcript_32497-T1, terminal, 54911, 56159
-recovered CodingQuarry_transcript_32497-T1, internal, 48891, 49123
-recovered CodingQuarry_transcript_32497-T1, internal, 50332, 50376
-recovered CodingQuarry_transcript_32497-T1, internal, 51725, 51820
-recovered CodingQuarry_transcript_32497-T1, internal, 52031, 52102
-recovered CodingQuarry_transcript_32497-T1, internal, 52550, 52579
-recovered CodingQuarry_transcript_32497-T1, internal, 53325, 53396
-recovered CodingQuarry_transcript_32497-T1, internal, 53737, 53878
-recovered CodingQuarry_transcript_32497-T1, internal, 54170, 54334
-recovered CodingQuarry_transcript_32497-T1, internal, 54911, 56159
Valid prediction for Augustus_model.g31690.t1
Valid prediction for snap_scaffold_21-snap.903-T1
Valid prediction for HiQ_model.g31694.t1
Valid prediction for snap_scaffold_21-snap.914-T1
Valid prediction for snap_scaffold_21-snap.907-T1
Valid prediction for snap_scaffold_21-snap.910-T1
Valid prediction for snap_scaffold_21-snap.897-T1
Couldn't classify 54549, 54789
Sorry, prediction CodingQuarry_transcript_32501-T1 fails validation.
(ATG)	 CC	53346-53396	GT	AGG
(CAG)	 AG	53740-53878	GT	AGG
(GAC)	 AG	54170-54334	GT	AAG
(AAT)	 TG	54549-54789	GT	AGG
(GGA)	 AG	54911-56159	GC	GAG
-recovered CodingQuarry_transcript_32501-T1, initial, 53346, 53396
-recovered CodingQuarry_transcript_32501-T1, terminal, 54170, 54334
-recovered CodingQuarry_transcript_32501-T1, terminal, 54911, 56159
-recovered CodingQuarry_transcript_32501-T1, internal, 53740, 53878
-recovered CodingQuarry_transcript_32501-T1, internal, 54170, 54334
-recovered CodingQuarry_transcript_32501-T1, internal, 54911, 56159
Couldn't classify 54549, 54789
Sorry, prediction CodingQuarry_transcript_32500-T1 fails validation.
(ATG)	 AT	47594-47690	GT	AGG
(AAC)	 AG	48891-49123	GT	ATG
(CTG)	 AG	51725-51820	GT	AGG
(ACC)	 AG	52031-52102	GT	GGG
(CTA)	 AG	52550-52579	GT	GGG
(AAA)	 AG	53325-53396	GT	AGG
(CAG)	 AG	53737-53878	GT	AGG
(GAC)	 AG	54170-54334	GT	AAG
(AAT)	 TG	54549-54789	GT	AGG
(GGA)	 AG	54911-56159	GC	GAG
-recovered CodingQuarry_transcript_32500-T1, initial, 47594, 47690
-recovered CodingQuarry_transcript_32500-T1, terminal, 54170, 54334
-recovered CodingQuarry_transcript_32500-T1, terminal, 54911, 56159
-recovered CodingQuarry_transcript_32500-T1, internal, 48891, 49123
-recovered CodingQuarry_transcript_32500-T1, internal, 51725, 51820
-recovered CodingQuarry_transcript_32500-T1, internal, 52031, 52102
-recovered CodingQuarry_transcript_32500-T1, internal, 52550, 52579
-recovered CodingQuarry_transcript_32500-T1, internal, 53325, 53396
-recovered CodingQuarry_transcript_32500-T1, internal, 53737, 53878
-recovered CodingQuarry_transcript_32500-T1, internal, 54170, 54334
-recovered CodingQuarry_transcript_32500-T1, internal, 54911, 56159
Valid prediction for snap_scaffold_21-snap.908-T1
Valid prediction for snap_scaffold_21-snap.918-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_47545-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 GlimmerHMM_glimmerT_47575-T1
Valid prediction for GlimmerHMM_glimmerT_47556-T1
Valid prediction for snap_scaffold_21-snap.894-T1
Valid prediction for Augustus_model.g31696.t1
Valid prediction for GlimmerHMM_glimmerT_47557-T1
Valid prediction for Augustus_model.g31689.t1
Valid prediction for GlimmerHMM_glimmerT_47559-T1
Valid prediction for GlimmerHMM_glimmerT_47567-T1
Valid prediction for snap_scaffold_21-snap.920-T1
Valid prediction for Augustus_model.g31692.t1
Valid prediction for pasa_asmbl_27576.p1
Valid prediction for HiQ_model.g31701.t1
Valid prediction for snap_scaffold_21-snap.888-T1
Valid prediction for GlimmerHMM_glimmerT_47560-T1
Valid prediction for Augustus_model.g31699.t1
Valid prediction for GlimmerHMM_glimmerT_47542-T1
Valid prediction for GlimmerHMM_glimmerT_47549-T1
Valid prediction for Augustus_model.g31705.t1
Valid prediction for GlimmerHMM_glimmerT_47574-T1
Valid prediction for Augustus_model.g31691.t1
Valid prediction for GlimmerHMM_glimmerT_47547-T1
Valid prediction for GlimmerHMM_glimmerT_47553-T1
Valid prediction for GlimmerHMM_glimmerT_47544-T1
Valid prediction for snap_scaffold_21-snap.916-T1
Valid prediction for HiQ_model.g31702.t1
Valid prediction for GlimmerHMM_glimmerT_47571-T1
Valid prediction for snap_scaffold_21-snap.913-T1
Valid prediction for snap_scaffold_21-snap.919-T1
Valid prediction for GlimmerHMM_glimmerT_47563-T1
Valid prediction for snap_scaffold_21-snap.912-T1
Valid prediction for snap_scaffold_21-snap.891-T1
Valid prediction for Augustus_model.g31697.t1
Valid prediction for snap_scaffold_21-snap.904-T1
Valid prediction for CodingQuarry_transcript_32502-T1
Valid prediction for snap_scaffold_21-snap.902-T1
Valid prediction for GlimmerHMM_glimmerT_47568-T1
Valid prediction for pasa_asmbl_27578.p1
Valid prediction for GlimmerHMM_glimmerT_47558-T1
Valid prediction for snap_scaffold_21-snap.921-T1
Valid prediction for snap_scaffold_21-snap.917-T1
Valid prediction for GlimmerHMM_glimmerT_47570-T1
Valid prediction for GlimmerHMM_glimmerT_47573-T1
Valid prediction for GlimmerHMM_glimmerT_47566-T1
Valid prediction for GlimmerHMM_glimmerT_47554-T1
Valid prediction for snap_scaffold_21-snap.909-T1
Valid prediction for snap_scaffold_21-snap.905-T1
Valid prediction for GlimmerHMM_glimmerT_47564-T1
Valid prediction for GlimmerHMM_glimmerT_47550-T1
Valid prediction for snap_scaffold_21-snap.915-T1
Valid prediction for snap_scaffold_21-snap.901-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g31698.t1
Valid prediction for snap_scaffold_21-snap.892-T1
Valid prediction for Augustus_model.g31704.t1
Valid prediction for GlimmerHMM_glimmerT_47569-T1
Valid prediction for snap_scaffold_21-snap.899-T1
Valid prediction for Augustus_model.g31693.t1
Valid prediction for snap_scaffold_21-snap.923-T1
Valid prediction for GlimmerHMM_glimmerT_47552-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6785, rend_intergenic: 2140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18621, rend_intergenic: 15393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22383, rend_intergenic: 18633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39884, rend_intergenic: 39115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48334, rend_intergenic: 41082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53246, rend_intergenic: 48763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68080, rend_intergenic: 62780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70893, rend_intergenic: 68148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78670, rend_intergenic: 70992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88423, rend_intergenic: 79007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137269, rend_intergenic: 136111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139944, rend_intergenic: 137442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 143341
-exon list size: 332


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 6785, rend_intergenic: 2140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18621, rend_intergenic: 15393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22383, rend_intergenic: 18633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39884, rend_intergenic: 39115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48334, rend_intergenic: 41082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53246, rend_intergenic: 48763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68080, rend_intergenic: 62780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70893, rend_intergenic: 68148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78670, rend_intergenic: 70992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88423, rend_intergenic: 79007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137269, rend_intergenic: 136111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139944, rend_intergenic: 137442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support