-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_5723156-5867137

-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_47757-T1
Valid prediction for snap_scaffold_21-snap.1167-T1
Valid prediction for GlimmerHMM_glimmerT_47736-T1
Valid prediction for CodingQuarry_transcript_32558-T1
Valid prediction for GlimmerHMM_glimmerT_47751-T1
Valid prediction for snap_scaffold_21-snap.1172-T1
Valid prediction for GlimmerHMM_glimmerT_47756-T1
Valid prediction for snap_scaffold_21-snap.1162-T1
Valid prediction for Augustus_model.g31859.t1
Valid prediction for snap_scaffold_21-snap.1147-T1
Valid prediction for CodingQuarry_transcript_32556-T1
Valid prediction for snap_scaffold_21-snap.1144-T1
Valid prediction for snap_scaffold_21-snap.1157-T1
Couldn't classify 6529, 6690
Couldn't classify 8044, 8189
Sorry, prediction pasa_asmbl_28587.p1 fails validation.
(CCA)	 CC	6529-6690	GT	AGG
(GAG)	 AG	7596-7782	GT	CGG
(GGA)	 AG	8044-8189	AG	GCA
-recovered pasa_asmbl_28587.p1, internal, 7596, 7782
Valid prediction for Augustus_model.g31857.t1
Valid prediction for HiQ_model.g31860.t1
Valid prediction for Augustus_model.g31843.t1
Valid prediction for Augustus_model.g31858.t1
Couldn't classify 84070, 84089
Sorry, prediction pasa_asmbl_28591.p1 fails validation.
(AAT)	 AG	84070-84089	GT	GAG
(GGT)	 AG	84406-84483	GT	CAG
(ACG)	 AG	84699-84776	GT	AGG
(TGT)	 AG	84932-85007	GT	TTG
(CGA)	 AG	85125-85238	GT	AGG
(ATT)	 AG	85332-85370	GT	AGG
(GGG)	 AG	85699-85818	GC	TGG
(GAG)	 AG	86007-86060	GT	TGG
(CTC)	 AG	86164-86250	GT	AGG
(GTT)	 AG	86335-86502	AG	GAA
-recovered pasa_asmbl_28591.p1, terminal, 84070, 84089
-recovered pasa_asmbl_28591.p1, terminal, 86335, 86502
-recovered pasa_asmbl_28591.p1, internal, 84070, 84089
-recovered pasa_asmbl_28591.p1, internal, 84406, 84483
-recovered pasa_asmbl_28591.p1, internal, 84699, 84776
-recovered pasa_asmbl_28591.p1, internal, 84932, 85007
-recovered pasa_asmbl_28591.p1, internal, 85125, 85238
-recovered pasa_asmbl_28591.p1, internal, 85332, 85370
-recovered pasa_asmbl_28591.p1, internal, 85699, 85818
-recovered pasa_asmbl_28591.p1, internal, 86007, 86060
-recovered pasa_asmbl_28591.p1, internal, 86164, 86250
Valid prediction for snap_scaffold_21-snap.1145-T1
Valid prediction for snap_scaffold_21-snap.1159-T1
Valid prediction for GlimmerHMM_glimmerT_47755-T1
Valid prediction for snap_scaffold_21-snap.1152-T1
Valid prediction for snap_scaffold_21-snap.1142-T1
Valid prediction for snap_scaffold_21-snap.1164-T1
Valid prediction for GlimmerHMM_glimmerT_47747-T1
Valid prediction for snap_scaffold_21-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_47739-T1
Valid prediction for Augustus_model.g31854.t1
Valid prediction for snap_scaffold_21-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_47758-T1
Couldn't classify 107182, 107194
Sorry, prediction pasa_asmbl_28592.p1 fails validation.
(ACC)	 AG	107182-107194	GT	GGG
(GGC)	 AG	107315-107392	GT	TGG
(TGA)	 AG	107491-107611	GT	AGG
(CTG)	 AG	107752-107890	GT	AGG
(GGA)	 AG	107990-108114	GT	AGG
(GTA)	 AG	108250-108637	TC	GAT
-recovered pasa_asmbl_28592.p1, terminal, 108250, 108637
-recovered pasa_asmbl_28592.p1, internal, 107182, 107194
-recovered pasa_asmbl_28592.p1, internal, 107315, 107392
-recovered pasa_asmbl_28592.p1, internal, 107491, 107611
-recovered pasa_asmbl_28592.p1, internal, 107752, 107890
-recovered pasa_asmbl_28592.p1, internal, 107990, 108114
Valid prediction for GlimmerHMM_glimmerT_47759-T1
Couldn't classify 8456, 8502
Sorry, prediction pasa_asmbl_28588.p1 fails validation.
(GAT)	 GG	8456-8502	GT	ATG
(ATT)	 AG	8665-9400	GC	GAG
-recovered pasa_asmbl_28588.p1, terminal, 8665, 9400
-recovered pasa_asmbl_28588.p1, internal, 8665, 9400
Valid prediction for snap_scaffold_21-snap.1156-T1
Valid prediction for Augustus_model.g31841.t1
Valid prediction for pasa_asmbl_28593.p1
Valid prediction for Augustus_model.g31842.t1
Valid prediction for snap_scaffold_21-snap.1169-T1
Valid prediction for pasa_asmbl_28964.p1
Valid prediction for GlimmerHMM_glimmerT_47740-T1
Valid prediction for GlimmerHMM_glimmerT_47745-T1
Valid prediction for HiQ_model.g31853.t1
Valid prediction for snap_scaffold_21-snap.1165-T1
Valid prediction for GlimmerHMM_glimmerT_47738-T1
Valid prediction for snap_scaffold_21-snap.1168-T1
Valid prediction for GlimmerHMM_glimmerT_47752-T1
Valid prediction for CodingQuarry_transcript_32559-T1
Valid prediction for GlimmerHMM_glimmerT_47753-T1
Valid prediction for HiQ_model.g31849.t1
Valid prediction for Augustus_model.g31840.t1
Valid prediction for Augustus_model.g31855.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_47760-T1
Valid prediction for snap_scaffold_21-snap.1153-T1
Valid prediction for snap_scaffold_21-snap.1154-T1
Valid prediction for snap_scaffold_21-snap.1173-T1
Valid prediction for snap_scaffold_21-snap.1150-T1
Valid prediction for snap_scaffold_21-snap.1163-T1
Valid prediction for Augustus_model.g31845.t1
Valid prediction for CodingQuarry_transcript_32552-T1
Couldn't classify 105698, 106092
Couldn't classify 106254, 106329
Sorry, prediction pasa_asmbl_27690.p1 fails validation.
(GAG)	 GT	105698-106092	GT	AGG
(GTA)	 AG	106254-106329	CT	AGC
Valid prediction for Augustus_model.g31852.t1
Valid prediction for GlimmerHMM_glimmerT_47737-T1
Valid prediction for pasa_asmbl_27704.p1
Valid prediction for snap_scaffold_21-snap.1149-T1
Valid prediction for snap_scaffold_21-snap.1158-T1
Valid prediction for CodingQuarry_transcript_32554-T1
Valid prediction for snap_scaffold_21-snap.1151-T1
Valid prediction for GlimmerHMM_glimmerT_47750-T1
Valid prediction for Augustus_model.g31844.t1
Valid prediction for Augustus_model.g31856.t1
Valid prediction for GlimmerHMM_glimmerT_47754-T1
Valid prediction for snap_scaffold_21-snap.1143-T1
Valid prediction for GlimmerHMM_glimmerT_47749-T1
Valid prediction for HiQ_model.g31846.t1
Valid prediction for GlimmerHMM_glimmerT_47748-T1
Valid prediction for HiQ_model.g31861.t1
Valid prediction for pasa_asmbl_27691.p1
Valid prediction for pasa_asmbl_27701.p1
Valid prediction for snap_scaffold_21-snap.1166-T1
Valid prediction for snap_scaffold_21-snap.1170-T1
Valid prediction for snap_scaffold_21-snap.1155-T1
Valid prediction for Augustus_model.g31850.t1
Valid prediction for Augustus_model.g31847.t1
Valid prediction for CodingQuarry_transcript_32553-T1
Couldn't classify 84589, 84909
Sorry, prediction pasa_asmbl_28194.p1 fails validation.
(GGG)	 GG	84589-84909	GT	TGG
Valid prediction for Augustus_model.g31851.t1
Valid prediction for CodingQuarry_transcript_32560-T1
Valid prediction for snap_scaffold_21-snap.1161-T1
Valid prediction for GlimmerHMM_glimmerT_47744-T1
Valid prediction for HiQ_model.g31848.t1
Valid prediction for GlimmerHMM_glimmerT_47743-T1
Valid prediction for GlimmerHMM_glimmerT_47741-T1
Valid prediction for snap_scaffold_21-snap.1160-T1
Couldn't classify 83660, 84525
Sorry, prediction pasa_asmbl_27700.p1 fails validation.
(ATG)	 GA	74885-74887	GT	TGG
(GAT)	 AG	76921-77022	GT	AGG
(GGC)	 AG	78065-78188	GT	AGG
(GCA)	 AG	79843-80013	GT	AGG
(GGT)	 AG	82898-83023	GT	AGG
(ATG)	 AG	83660-84525	AG	ACA
-recovered pasa_asmbl_27700.p1, initial, 74885, 74887
-recovered pasa_asmbl_27700.p1, internal, 76921, 77022
-recovered pasa_asmbl_27700.p1, internal, 78065, 78188
-recovered pasa_asmbl_27700.p1, internal, 79843, 80013
-recovered pasa_asmbl_27700.p1, internal, 82898, 83023
Valid prediction for Augustus_model.g31862.t1
Valid prediction for CodingQuarry_transcript_32551-T1
Valid prediction for GlimmerHMM_glimmerT_47746-T1
Valid prediction for GlimmerHMM_glimmerT_47742-T1
Couldn't classify 6556, 6694
Sorry, prediction pasa_asmbl_27705.p1 fails validation.
(CCC)	 CT	6556-6694	GT	AGG
(TTA)	 AG	6807-6863	GT	GGG
(TCA)	 AG	6976-7041	GT	GTG
(ACT)	 AG	7158-7678	AC	GAA
-recovered pasa_asmbl_27705.p1, terminal, 7158, 7678
-recovered pasa_asmbl_27705.p1, internal, 6807, 6863
-recovered pasa_asmbl_27705.p1, internal, 6976, 7041
Valid prediction for CodingQuarry_transcript_32555-T1
Valid prediction for snap_scaffold_21-snap.1171-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 56745, rend_intergenic: 51041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60055, rend_intergenic: 57143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98369, rend_intergenic: 94810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120251, rend_intergenic: 115343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140516, rend_intergenic: 139968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142456, rend_intergenic: 140658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 143982
-exon list size: 351


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 56745, rend_intergenic: 51041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60055, rend_intergenic: 57143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98369, rend_intergenic: 94810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120251, rend_intergenic: 115343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140516, rend_intergenic: 139968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142456, rend_intergenic: 140658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support