-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_8223910-8311070

-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.g33272.t1
Valid prediction for snap_scaffold_22-snap.1658-T1
Valid prediction for Augustus_model.g33275.t1
Valid prediction for Augustus_model.g33281.t1
Valid prediction for snap_scaffold_22-snap.1671-T1
Valid prediction for snap_scaffold_22-snap.1663-T1
Valid prediction for snap_scaffold_22-snap.1653-T1
Valid prediction for Augustus_model.g33279.t1
Valid prediction for GlimmerHMM_glimmerT_49875-T1
Valid prediction for snap_scaffold_22-snap.1665-T1
Valid prediction for GlimmerHMM_glimmerT_49874-T1
Valid prediction for snap_scaffold_22-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_49877-T1
Valid prediction for Augustus_model.g33278.t1
Valid prediction for GlimmerHMM_glimmerT_49884-T1
Valid prediction for snap_scaffold_22-snap.1662-T1
Valid prediction for GlimmerHMM_glimmerT_49878-T1
Valid prediction for snap_scaffold_22-snap.1668-T1
Valid prediction for snap_scaffold_22-snap.1655-T1
Valid prediction for snap_scaffold_22-snap.1669-T1
Valid prediction for snap_scaffold_22-snap.1661-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: -)Couldn't classify 54015, 54290
Sorry, prediction pasa_asmbl_29472.p1 fails validation.
(ATG)	 CA	53141-53308	GT	AGG
(GTG)	 AG	53588-53863	GT	AAG
(GGA)	 AG	54015-54290	CC	CCC
-recovered pasa_asmbl_29472.p1, initial, 53141, 53308
-recovered pasa_asmbl_29472.p1, internal, 53588, 53863
Valid prediction for Augustus_model.g33283.t1
Valid prediction for Augustus_model.g33282.t1
Valid prediction for GlimmerHMM_glimmerT_49882-T1
Couldn't classify 21729, 23285
Sorry, prediction pasa_asmbl_29475.p1 fails validation.
(ATG)	 TG	20952-21215	GT	AGG
(CTG)	 AG	21500-21634	GT	TCG
(GTG)	 AG	21729-23285	CC	CCC
-recovered pasa_asmbl_29475.p1, initial, 20952, 21215
-recovered pasa_asmbl_29475.p1, internal, 21500, 21634
Valid prediction for snap_scaffold_22-snap.1654-T1
Valid prediction for snap_scaffold_22-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_49876-T1
Valid prediction for snap_scaffold_22-snap.1667-T1
Valid prediction for GlimmerHMM_glimmerT_49873-T1
Couldn't classify 55036, 55383
Couldn't classify 57227, 57320
Sorry, prediction pasa_asmbl_29471.p1 fails validation.
(CCT)	 CC	55036-55383	GT	TGG
(GAC)	 AG	55566-55731	GT	AGG
(CGT)	 AG	55908-56049	GT	AGG
(TCT)	 AG	56398-56520	GT	AGG
(GTT)	 AG	56763-56854	GT	GGG
(ACC)	 AG	56934-56997	GT	AGG
(GTC)	 AG	57227-57320	CT	CCC
add_exon() Sorry, pasa_asmbl_29471.p1 55566-55731-terminal-3 is invalid.
-recovered pasa_asmbl_29471.p1, terminal, 55566, 55731
-recovered pasa_asmbl_29471.p1, internal, 55566, 55731
-recovered pasa_asmbl_29471.p1, internal, 55908, 56049
-recovered pasa_asmbl_29471.p1, internal, 56398, 56520
-recovered pasa_asmbl_29471.p1, internal, 56763, 56854
-recovered pasa_asmbl_29471.p1, internal, 56934, 56997
Valid prediction for snap_scaffold_22-snap.1656-T1
Valid prediction for pasa_asmbl_29469.p1
Valid prediction for snap_scaffold_22-snap.1673-T1
Valid prediction for GlimmerHMM_glimmerT_49889-T1
Valid prediction for snap_scaffold_22-snap.1670-T1
Valid prediction for HiQ_model.g33273.t1
Valid prediction for GlimmerHMM_glimmerT_49887-T1
Valid prediction for Augustus_model.g33276.t1
Valid prediction for CodingQuarry_transcript_34241-T1
Valid prediction for Augustus_model.g33280.t1
Valid prediction for Augustus_model.g33274.t1
Valid prediction for GlimmerHMM_glimmerT_49880-T1
Valid prediction for snap_scaffold_22-snap.1666-T1
Valid prediction for snap_scaffold_22-snap.1672-T1
Valid prediction for snap_scaffold_22-snap.1659-T1
Valid prediction for Augustus_model.g33277.t1
Valid prediction for snap_scaffold_22-snap.1657-T1
Valid prediction for snap_scaffold_22-snap.1652-T1
Valid prediction for GlimmerHMM_glimmerT_49888-T1
Valid prediction for GlimmerHMM_glimmerT_49879-T1
Valid prediction for GlimmerHMM_glimmerT_49881-T1
Valid prediction for pasa_asmbl_29466.p1
Valid prediction for CodingQuarry_transcript_34237-T1
Valid prediction for CodingQuarry_transcript_34240-T1
Valid prediction for CodingQuarry_transcript_34238-T1
Couldn't classify 23445, 23632
Sorry, prediction pasa_asmbl_29473.p1 fails validation.
(AGC)	 TC	23445-23632	GT	AGG
(TCA)	 AG	24011-24141	GT	AGG
(AAC)	 AG	24632-24728	GT	AGG
(GTT)	 AG	25356-25463	GT	AGG
(ACT)	 AG	26359-26460	GT	AGG
(CAT)	 AG	26825-27164	AC	GAA
-recovered pasa_asmbl_29473.p1, terminal, 26825, 27164
-recovered pasa_asmbl_29473.p1, internal, 24011, 24141
-recovered pasa_asmbl_29473.p1, internal, 24632, 24728
-recovered pasa_asmbl_29473.p1, internal, 25356, 25463
-recovered pasa_asmbl_29473.p1, internal, 26359, 26460
Valid prediction for CodingQuarry_transcript_34239-T1
Valid prediction for GlimmerHMM_glimmerT_49885-T1
Valid prediction for GlimmerHMM_glimmerT_49886-T1
Valid prediction for GlimmerHMM_glimmerT_49883-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12028, rend_intergenic: 7917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17627, rend_intergenic: 12327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34021, rend_intergenic: 27077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47780, rend_intergenic: 36966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49679, rend_intergenic: 47823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58976, rend_intergenic: 52921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66368, rend_intergenic: 59781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70536, rend_intergenic: 70356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76861, rend_intergenic: 71351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80033, rend_intergenic: 77146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 87161
-exon list size: 283


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.2    
4.6    
4.9    
5.3    
5.6    
6.0    
6.3    
6.7    
7.0    
7.4    
7.7    
8.1    
8.4    
8.8    
9.1    
9.5    
9.8    
10.2    
10.5    
10.9    
11.2    
11.6    
11.9    
12.3    
12.6    
13.0    
13.3    
13.7    
14.0    
14.4    
14.7    
15.1    
15.4    
15.8    
16.1    
16.5    
16.8    
17.2    
17.5    
17.9    
18.2    
18.6    
18.9    
19.3    
19.6    
20.0    
20.4    
20.7    
21.1    
21.4    
21.8    
22.1    
22.5    
22.8    
23.2    
23.5    
23.9    
24.2    
24.6    
24.9    
25.3    
25.6    
26.0    
26.3    
26.7    
27.0    
27.4    
27.7    
28.1    
28.4    
28.8    
29.1    
29.5    
29.8    
30.2    
30.5    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.1    
35.4    
35.8    
36.1    
36.5    
36.8    
37.2    
37.5    
37.9    
38.2    
38.6    
38.9    
39.3    
39.6    
40.0    
40.4    
40.7    
41.1    
41.4    
41.8    
42.1    
42.5    
42.8    
43.2    
43.5    
43.9    
44.2    
44.6    
44.9    
45.3    
45.6    
46.0    
46.3    
46.7    
47.0    
47.4    
47.7    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.3    
52.6    
53.0    
53.3    
53.7    
54.0    
54.4    
54.7    
55.1    
55.4    
55.8    
56.1    
56.5    
56.8    
57.2    
57.5    
57.9    
58.2    
58.6    
58.9    
59.3    
59.6    
60.0    
60.4    
60.7    
61.1    
61.4    
61.8    
62.1    
62.5    
62.8    
63.2    
63.5    
63.9    
64.2    
64.6    
64.9    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.5    
69.8    
70.2    
70.5    
70.9    
71.2    
71.6    
71.9    
72.3    
72.6    
73.0    
73.3    
73.7    
74.0    
74.4    
74.7    
75.1    
75.4    
75.8    
76.1    
76.5    
76.8    
77.2    
77.5    
77.9    
78.2    
78.6    
78.9    
79.3    
79.6    
80.0    
80.4    
80.7    
81.1    
81.4    
81.8    
82.1    
82.5    
82.8    
83.2    
83.5    
83.9    
84.2    
84.6    
84.9    
85.3    
85.6    
86.0    
86.3    
86.7    
87.0    
87.4    
87.7    
88.1    
88.4    
88.8    
89.1    
89.5    
89.8    
90.2    
90.5    
90.9    
91.2    
91.6    
91.9    
92.3    
92.6    
93.0    
93.3    
93.7    
94.0    
94.4    
94.7    
95.1    
95.4    
95.8    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 12028, rend_intergenic: 7917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17627, rend_intergenic: 12327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34021, rend_intergenic: 27077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47780, rend_intergenic: 36966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49679, rend_intergenic: 47823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58976, rend_intergenic: 52921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66368, rend_intergenic: 59781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70536, rend_intergenic: 70356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76861, rend_intergenic: 71351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80033, rend_intergenic: 77146  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