-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_4629383-4789699

-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 snap_scaffold_2-snap.1079-T1
Valid prediction for snap_scaffold_2-snap.1075-T1
Valid prediction for snap_scaffold_2-snap.1062-T1
Valid prediction for Augustus_model.g2483.t1
Valid prediction for snap_scaffold_2-snap.1083-T1
Valid prediction for snap_scaffold_2-snap.1070-T1
Valid prediction for Augustus_model.g2479.t1
Valid prediction for snap_scaffold_2-snap.1054-T1
Couldn't classify 156730, 156851
Couldn't classify 157650, 157786
Sorry, prediction CodingQuarry_transcript_28542-T1 fails validation.
(ATG)	 AC	155831-155951	GT	GGG
(AGG)	 AG	156175-156273	GT	CAG
(AGA)	 AG	156730-156851	AT	GGA
(AGC)	 AC	157650-157786	GT	AGG
(CTC)	 AG	157959-158041	GT	AGG
(GAG)	 AG	158577-158608	GC	GAG
-recovered CodingQuarry_transcript_28542-T1, initial, 155831, 155951
-recovered CodingQuarry_transcript_28542-T1, terminal, 158577, 158608
-recovered CodingQuarry_transcript_28542-T1, internal, 156175, 156273
-recovered CodingQuarry_transcript_28542-T1, internal, 157959, 158041
-recovered CodingQuarry_transcript_28542-T1, internal, 158577, 158608
Valid prediction for snap_scaffold_2-snap.1066-T1
Valid prediction for pasa_asmbl_24376.p1
Couldn't classify 156730, 156851
Couldn't classify 157650, 157786
Sorry, prediction CodingQuarry_transcript_28543-T1 fails validation.
(ATG)	 AC	155831-155951	GT	GGG
(AGG)	 AG	156175-156273	GT	CAG
(AGA)	 AG	156730-156851	AT	GGA
(AGC)	 AC	157650-157786	GT	AGG
(CTC)	 AG	157959-158041	GT	AGG
(AGC)	 AG	158572-158816	AG	AAA
-recovered CodingQuarry_transcript_28543-T1, initial, 155831, 155951
-recovered CodingQuarry_transcript_28543-T1, terminal, 158572, 158816
-recovered CodingQuarry_transcript_28543-T1, internal, 156175, 156273
-recovered CodingQuarry_transcript_28543-T1, internal, 157959, 158041
Couldn't classify 156730, 156851
Couldn't classify 157650, 157786
Sorry, prediction pasa_asmbl_24382.p1 fails validation.
(ATG)	 AC	155831-155951	GT	GGG
(AGG)	 AG	156175-156273	GT	CAG
(AGA)	 AG	156730-156851	AT	GGA
(AGC)	 AC	157650-157786	GT	AGG
(CTC)	 AG	157959-158041	GT	AGG
(AGC)	 AG	158572-158763	GT	AGG
(TCT)	 AG	159110-159114	AC	AAA
-recovered pasa_asmbl_24382.p1, initial, 155831, 155951
-recovered pasa_asmbl_24382.p1, terminal, 159110, 159114
-recovered pasa_asmbl_24382.p1, internal, 156175, 156273
-recovered pasa_asmbl_24382.p1, internal, 157959, 158041
-recovered pasa_asmbl_24382.p1, internal, 158572, 158763
Valid prediction for GlimmerHMM_glimmerT_3710-T1
Valid prediction for GlimmerHMM_glimmerT_3696-T1
Valid prediction for Augustus_model.g2489.t1
Valid prediction for snap_scaffold_2-snap.1060-T1
Valid prediction for snap_scaffold_2-snap.1068-T1
Valid prediction for Augustus_model.g2484.t1
Valid prediction for GlimmerHMM_glimmerT_3697-T1
Valid prediction for Augustus_model.g2480.t1
Valid prediction for HiQ_model.g2476.t1
Valid prediction for snap_scaffold_2-snap.1077-T1
Valid prediction for snap_scaffold_2-snap.1072-T1
Valid prediction for GlimmerHMM_glimmerT_3702-T1
Valid prediction for GlimmerHMM_glimmerT_3693-T1
Valid prediction for GlimmerHMM_glimmerT_3705-T1
Valid prediction for GlimmerHMM_glimmerT_3707-T1
Valid prediction for GlimmerHMM_glimmerT_3700-T1
Valid prediction for snap_scaffold_2-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_3688-T1
Couldn't classify 294, 458
Sorry, prediction pasa_asmbl_24375.p1 fails validation.
(CAT)	 AG	294-458	GT	GGG
(GCG)	 AG	1856-1996	GT	AGG
(ACG)	 AG	2200-2352	GT	TGG
(GTG)	 AG	2741-2854	CA	AAC
-recovered pasa_asmbl_24375.p1, terminal, 2741, 2854
-recovered pasa_asmbl_24375.p1, internal, 294, 458
-recovered pasa_asmbl_24375.p1, internal, 1856, 1996
-recovered pasa_asmbl_24375.p1, internal, 2200, 2352
Valid prediction for GlimmerHMM_glimmerT_3703-T1
Valid prediction for Augustus_model.g2470.t1
Valid prediction for GlimmerHMM_glimmerT_3691-T1
Valid prediction for snap_scaffold_2-snap.1056-T1
Valid prediction for snap_scaffold_2-snap.1052-T1
Valid prediction for CodingQuarry_transcript_28538-T1
Valid prediction for Augustus_model.g2472.t1
Valid prediction for Augustus_model.g2486.t1
Valid prediction for GlimmerHMM_glimmerT_3708-T1
Valid prediction for snap_scaffold_2-snap.1064-T1
Valid prediction for snap_scaffold_2-snap.1058-T1
Couldn't classify 156730, 156851
Couldn't classify 157650, 157786
Sorry, prediction CodingQuarry_transcript_28541-T1 fails validation.
(ATG)	 AC	155831-155951	GT	GGG
(AGG)	 AG	156175-156273	GT	CAG
(AGA)	 AG	156730-156851	AT	GGA
(AGC)	 AC	157650-157786	GT	AGG
(CTC)	 AG	157959-158041	GT	AGG
(AGC)	 AG	158572-158763	GT	AGG
(TCT)	 AG	159110-159114	AC	AAA
-recovered CodingQuarry_transcript_28541-T1, initial, 155831, 155951
-recovered CodingQuarry_transcript_28541-T1, terminal, 159110, 159114
-recovered CodingQuarry_transcript_28541-T1, internal, 156175, 156273
-recovered CodingQuarry_transcript_28541-T1, internal, 157959, 158041
-recovered CodingQuarry_transcript_28541-T1, internal, 158572, 158763
Valid prediction for GlimmerHMM_glimmerT_3714-T1
Valid prediction for GlimmerHMM_glimmerT_3701-T1
Valid prediction for snap_scaffold_2-snap.1081-T1
Valid prediction for snap_scaffold_2-snap.1051-T1
Valid prediction for GlimmerHMM_glimmerT_3711-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 Augustus_model.g2481.t1
Valid prediction for snap_scaffold_2-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_3695-T1
Valid prediction for GlimmerHMM_glimmerT_3690-T1
Valid prediction for GlimmerHMM_glimmerT_3689-T1
Valid prediction for snap_scaffold_2-snap.1065-T1
Valid prediction for pasa_asmbl_23093.p1
Valid prediction for GlimmerHMM_glimmerT_3704-T1
Valid prediction for snap_scaffold_2-snap.1085-T1
Valid prediction for pasa_asmbl_23098.p1
Valid prediction for GlimmerHMM_glimmerT_3692-T1
Valid prediction for CodingQuarry_transcript_28540-T1
Valid prediction for snap_scaffold_2-snap.1057-T1
Valid prediction for Augustus_model.g2477.t1
Valid prediction for Augustus_model.g2475.t1
Valid prediction for GlimmerHMM_glimmerT_3694-T1
Valid prediction for snap_scaffold_2-snap.1082-T1
Valid prediction for GlimmerHMM_glimmerT_3706-T1
Valid prediction for HiQ_model.g2485.t1
Valid prediction for snap_scaffold_2-snap.1076-T1
Couldn't classify 97393, 97428
Couldn't classify 101030, 101193
Sorry, prediction pasa_asmbl_23089.p1 fails validation.
(GAA)	 CT	97393-97428	GT	TGG
(GAT)	 AG	98628-98748	GT	GAG
(GTG)	 AG	100060-100257	GT	GAG
(TTA)	 AG	100769-100879	GT	AGG
(GTT)	 AG	101030-101193	CT	ACC
add_exon() Sorry, pasa_asmbl_23089.p1 98628-98748-terminal-3 is invalid.
-recovered pasa_asmbl_23089.p1, terminal, 98628, 98748
-recovered pasa_asmbl_23089.p1, internal, 98628, 98748
-recovered pasa_asmbl_23089.p1, internal, 100060, 100257
-recovered pasa_asmbl_23089.p1, internal, 100769, 100879
Valid prediction for GlimmerHMM_glimmerT_3713-T1
Valid prediction for snap_scaffold_2-snap.1053-T1
Valid prediction for GlimmerHMM_glimmerT_3712-T1
Valid prediction for snap_scaffold_2-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_3699-T1
Valid prediction for snap_scaffold_2-snap.1069-T1
Valid prediction for HiQ_model.g2488.t1
Valid prediction for snap_scaffold_2-snap.1080-T1
Valid prediction for Augustus_model.g2473.t1
Valid prediction for snap_scaffold_2-snap.1061-T1
Valid prediction for snap_scaffold_2-snap.1055-T1
Valid prediction for Augustus_model.g2471.t1
Valid prediction for HiQ_model.g2487.t1
Valid prediction for Augustus_model.g2474.t1
Valid prediction for CodingQuarry_transcript_28539-T1
Valid prediction for GlimmerHMM_glimmerT_3709-T1
Valid prediction for snap_scaffold_2-snap.1074-T1
Valid prediction for Augustus_model.g2478.t1
Valid prediction for snap_scaffold_2-snap.1078-T1
Valid prediction for snap_scaffold_2-snap.1063-T1
Valid prediction for snap_scaffold_2-snap.1067-T1
Valid prediction for Augustus_model.g2482.t1
Valid prediction for GlimmerHMM_glimmerT_3698-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16831, rend_intergenic: 9351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17488, rend_intergenic: 17276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21768, rend_intergenic: 17627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22275, rend_intergenic: 22258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28816, rend_intergenic: 22294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40192, rend_intergenic: 33005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55405, rend_intergenic: 47745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66852, rend_intergenic: 58909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89563, rend_intergenic: 87989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91443, rend_intergenic: 91157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103664, rend_intergenic: 97852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113043, rend_intergenic: 109073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125886, rend_intergenic: 123169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148759, rend_intergenic: 145784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151577, rend_intergenic: 148811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160317
-exon list size: 335


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    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.7    
27.0    
27.3    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.5    
31.8    
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    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
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    
68.2    
68.5    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.7    
73.0    
73.3    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
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 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 16831, rend_intergenic: 9351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17488, rend_intergenic: 17276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21768, rend_intergenic: 17627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22275, rend_intergenic: 22258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28816, rend_intergenic: 22294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40192, rend_intergenic: 33005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55405, rend_intergenic: 47745  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66852, rend_intergenic: 58909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89563, rend_intergenic: 87989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91443, rend_intergenic: 91157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103664, rend_intergenic: 97852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113043, rend_intergenic: 109073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125886, rend_intergenic: 123169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148759, rend_intergenic: 145784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151577, rend_intergenic: 148811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support