-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_5062754-5266121

-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.g19361.t1
Valid prediction for GlimmerHMM_glimmerT_29329-T1
Couldn't classify 17685, 17741
Sorry, prediction pasa_asmbl_7640.p1 fails validation.
(TCC)	 GC	17685-17741	GT	AGG
(GCC)	 AG	17859-17959	GT	AAG
(AAA)	 AG	18039-18146	GT	ATG
(GGC)	 AG	18566-18629	GT	AGG
(GTG)	 AG	19006-19080	GT	TTG
(CCC)	 AG	19489-19572	GT	AGG
(GAG)	 AG	19820-19988	GT	AGG
(CGA)	 AG	20145-20194	AG	AGA
-recovered pasa_asmbl_7640.p1, terminal, 20145, 20194
-recovered pasa_asmbl_7640.p1, internal, 17859, 17959
-recovered pasa_asmbl_7640.p1, internal, 18039, 18146
-recovered pasa_asmbl_7640.p1, internal, 18566, 18629
-recovered pasa_asmbl_7640.p1, internal, 19006, 19080
-recovered pasa_asmbl_7640.p1, internal, 19489, 19572
-recovered pasa_asmbl_7640.p1, internal, 19820, 19988
Valid prediction for GlimmerHMM_glimmerT_29337-T1
Valid prediction for snap_scaffold_12-snap.1049-T1
Valid prediction for GlimmerHMM_glimmerT_29336-T1
Valid prediction for snap_scaffold_12-snap.1035-T1
Valid prediction for snap_scaffold_12-snap.1043-T1
Valid prediction for Augustus_model.g19355.t1
Valid prediction for GlimmerHMM_glimmerT_29334-T1
Valid prediction for GlimmerHMM_glimmerT_29347-T1
Valid prediction for Augustus_model.g19356.t1
Valid prediction for GlimmerHMM_glimmerT_29343-T1
Valid prediction for snap_scaffold_12-snap.1063-T1
Valid prediction for Augustus_model.g19362.t1
Valid prediction for GlimmerHMM_glimmerT_29331-T1
Valid prediction for snap_scaffold_12-snap.1051-T1
Valid prediction for snap_scaffold_12-snap.1037-T1
Valid prediction for snap_scaffold_12-snap.1057-T1
Valid prediction for snap_scaffold_12-snap.1047-T1
Valid prediction for snap_scaffold_12-snap.1053-T1
Valid prediction for GlimmerHMM_glimmerT_29340-T1
Valid prediction for GlimmerHMM_glimmerT_29328-T1
Valid prediction for snap_scaffold_12-snap.1060-T1
Valid prediction for GlimmerHMM_glimmerT_29351-T1
Valid prediction for Augustus_model.g19352.t1
Valid prediction for snap_scaffold_12-snap.1045-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_29327-T1
Valid prediction for Augustus_model.g19360.t1
Valid prediction for HiQ_model.g19353.t1
Valid prediction for HiQ_model.g19354.t1
Valid prediction for GlimmerHMM_glimmerT_29342-T1
Valid prediction for GlimmerHMM_glimmerT_29333-T1
Couldn't classify 121711, 121909
Sorry, prediction pasa_asmbl_8488.p1 fails validation.
(CAG)	 CG	121711-121909	GT	AGG
(GTC)	 AG	122394-122560	GT	AGG
(GTG)	 AG	124182-124403	GG	AAG
-recovered pasa_asmbl_8488.p1, terminal, 124182, 124403
-recovered pasa_asmbl_8488.p1, internal, 122394, 122560
Valid prediction for Augustus_model.g19358.t1
Valid prediction for snap_scaffold_12-snap.1042-T1
Valid prediction for snap_scaffold_12-snap.1046-T1
Valid prediction for Augustus_model.g19350.t1
Valid prediction for snap_scaffold_12-snap.1050-T1
Valid prediction for snap_scaffold_12-snap.1044-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.1062-T1
Valid prediction for GlimmerHMM_glimmerT_29352-T1
Valid prediction for CodingQuarry_transcript_10217-T1
Valid prediction for snap_scaffold_12-snap.1041-T1
Valid prediction for pasa_asmbl_8480.p1
Valid prediction for GlimmerHMM_glimmerT_29338-T1
Valid prediction for GlimmerHMM_glimmerT_29330-T1
Valid prediction for GlimmerHMM_glimmerT_29335-T1
Valid prediction for Augustus_model.g19351.t1
Valid prediction for GlimmerHMM_glimmerT_29344-T1
Valid prediction for snap_scaffold_12-snap.1061-T1
Valid prediction for GlimmerHMM_glimmerT_29345-T1
Valid prediction for GlimmerHMM_glimmerT_29348-T1
Valid prediction for snap_scaffold_12-snap.1034-T1
Couldn't classify 120777, 120881
Sorry, prediction pasa_asmbl_9181.p1 fails validation.
(ATG)	 AC	114976-115395	GT	AGG
(CCT)	 AG	116563-116692	GT	CTG
(GTG)	 AG	116868-117015	GT	GCG
(GCC)	 AG	117432-117631	GT	GGG
(CGG)	 AG	117904-118034	GT	AGG
(CTA)	 AG	118794-118898	GT	AAG
(AGG)	 AG	119252-119365	GT	TTG
(GAG)	 AG	119744-119913	GT	AGG
(GAC)	 AG	120320-120467	GT	AGG
(CTT)	 AG	120777-120881	CA	ATC
-recovered pasa_asmbl_9181.p1, initial, 114976, 115395
-recovered pasa_asmbl_9181.p1, internal, 116563, 116692
-recovered pasa_asmbl_9181.p1, internal, 116868, 117015
-recovered pasa_asmbl_9181.p1, internal, 117432, 117631
-recovered pasa_asmbl_9181.p1, internal, 117904, 118034
-recovered pasa_asmbl_9181.p1, internal, 118794, 118898
-recovered pasa_asmbl_9181.p1, internal, 119252, 119365
-recovered pasa_asmbl_9181.p1, internal, 119744, 119913
-recovered pasa_asmbl_9181.p1, internal, 120320, 120467
Valid prediction for GlimmerHMM_glimmerT_29332-T1
Valid prediction for snap_scaffold_12-snap.1038-T1
Valid prediction for snap_scaffold_12-snap.1036-T1
Valid prediction for GlimmerHMM_glimmerT_29349-T1
Valid prediction for snap_scaffold_12-snap.1056-T1
Valid prediction for snap_scaffold_12-snap.1054-T1
Valid prediction for snap_scaffold_12-snap.1052-T1
Valid prediction for Augustus_model.g19359.t1
Valid prediction for GlimmerHMM_glimmerT_29326-T1
Valid prediction for snap_scaffold_12-snap.1064-T1
Valid prediction for snap_scaffold_12-snap.1048-T1
Couldn't classify 169917, 170123
Couldn't classify 173158, 173547
Sorry, prediction pasa_asmbl_8483.p1 fails validation.
(CTC)	 CT	169917-170123	GT	AGG
(ATA)	 AG	170714-170905	GT	TAG
(CTG)	 AG	172720-172842	GT	AGG
(AAC)	 AG	173158-173547	GC	GGG
-recovered pasa_asmbl_8483.p1, internal, 170714, 170905
-recovered pasa_asmbl_8483.p1, internal, 172720, 172842
-recovered pasa_asmbl_8483.p1, internal, 173158, 173547
Valid prediction for snap_scaffold_12-snap.1033-T1
Valid prediction for snap_scaffold_12-snap.1039-T1
Valid prediction for snap_scaffold_12-snap.1065-T1
Valid prediction for snap_scaffold_12-snap.1040-T1
Valid prediction for GlimmerHMM_glimmerT_29346-T1
Valid prediction for GlimmerHMM_glimmerT_29350-T1
Valid prediction for GlimmerHMM_glimmerT_29341-T1
Valid prediction for Augustus_model.g19357.t1
Valid prediction for snap_scaffold_12-snap.1059-T1
Valid prediction for pasa_asmbl_8477.p1
Valid prediction for GlimmerHMM_glimmerT_29339-T1
Valid prediction for snap_scaffold_12-snap.1058-T1
Valid prediction for snap_scaffold_12-snap.1055-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51917, rend_intergenic: 43905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116869, rend_intergenic: 112057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125630, rend_intergenic: 117815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127117, rend_intergenic: 126663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130350, rend_intergenic: 127127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136962, rend_intergenic: 132724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139135, rend_intergenic: 137979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145234, rend_intergenic: 140916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155282, rend_intergenic: 148885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163509, rend_intergenic: 155783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170848, rend_intergenic: 169287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184849, rend_intergenic: 183469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189241, rend_intergenic: 186200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191913, rend_intergenic: 190546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195746, rend_intergenic: 195614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203368
-exon list size: 293


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.0    
2.4    
2.7    
3.1    
3.4    
3.7    
4.1    
4.4    
4.7    
5.1    
5.4    
5.8    
6.1    
6.4    
6.8    
7.1    
7.5    
7.8    
8.1    
8.5    
8.8    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.2    
11.5    
11.9    
12.2    
12.5    
12.9    
13.2    
13.6    
13.9    
14.2    
14.6    
14.9    
15.3    
15.6    
15.9    
16.3    
16.6    
16.9    
17.3    
17.6    
18.0    
18.3    
18.6    
19.0    
19.3    
19.7    
20.0    
20.3    
20.7    
21.0    
21.4    
21.7    
22.0    
22.4    
22.7    
23.1    
23.4    
23.7    
24.1    
24.4    
24.7    
25.1    
25.4    
25.8    
26.1    
26.4    
26.8    
27.1    
27.5    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.2    
31.5    
31.9    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.3    
35.6    
35.9    
36.3    
36.6    
36.9    
37.3    
37.6    
38.0    
38.3    
38.6    
39.0    
39.3    
39.7    
40.0    
40.3    
40.7    
41.0    
41.4    
41.7    
42.0    
42.4    
42.7    
43.1    
43.4    
43.7    
44.1    
44.4    
44.7    
45.1    
45.4    
45.8    
46.1    
46.4    
46.8    
47.1    
47.5    
47.8    
48.1    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.9    
52.2    
52.5    
52.9    
53.2    
53.6    
53.9    
54.2    
54.6    
54.9    
55.3    
55.6    
55.9    
56.3    
56.6    
56.9    
57.3    
57.6    
58.0    
58.3    
58.6    
59.0    
59.3    
59.7    
60.0    
60.3    
60.7    
61.0    
61.4    
61.7    
62.0    
62.4    
62.7    
63.1    
63.4    
63.7    
64.1    
64.4    
64.7    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.1    
68.5    
68.8    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
72.5    
72.9    
73.2    
73.6    
73.9    
74.2    
74.6    
74.9    
75.3    
75.6    
75.9    
76.3    
76.6    
76.9    
77.3    
77.6    
78.0    
78.3    
78.6    
79.0    
79.3    
79.7    
80.0    
80.3    
80.7    
81.0    
81.4    
81.7    
82.0    
82.4    
82.7    
83.1    
83.4    
83.7    
84.1    
84.4    
84.7    
85.1    
85.4    
85.8    
86.1    
86.4    
86.8    
87.1    
87.5    
87.8    
88.1    
88.5    
88.8    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.2    
91.5    
91.9    
92.2    
92.5    
92.9    
93.2    
93.6    
93.9    
94.2    
94.6    
94.9    
95.3    
95.6    
95.9    
96.3    
96.6    
96.9    
97.3    
97.6    
98.0    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 51917, rend_intergenic: 43905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116869, rend_intergenic: 112057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125630, rend_intergenic: 117815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127117, rend_intergenic: 126663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130350, rend_intergenic: 127127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136962, rend_intergenic: 132724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139135, rend_intergenic: 137979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145234, rend_intergenic: 140916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155282, rend_intergenic: 148885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163509, rend_intergenic: 155783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170848, rend_intergenic: 169287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184849, rend_intergenic: 183469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189241, rend_intergenic: 186200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191913, rend_intergenic: 190546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195746, rend_intergenic: 195614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support