-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_15178960-15361520

-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_4-snap.3066-T1
Valid prediction for HiQ_model.g7021.t1
Valid prediction for snap_scaffold_4-snap.3049-T1
Valid prediction for snap_scaffold_4-snap.3078-T1
Valid prediction for snap_scaffold_4-snap.3041-T1
Valid prediction for Augustus_model.g7018.t1
Valid prediction for snap_scaffold_4-snap.3037-T1
Valid prediction for HiQ_model.g7023.t1
Valid prediction for snap_scaffold_4-snap.3044-T1
Valid prediction for snap_scaffold_4-snap.3040-T1
Valid prediction for snap_scaffold_4-snap.3057-T1
Valid prediction for snap_scaffold_4-snap.3060-T1
Valid prediction for snap_scaffold_4-snap.3070-T1
Valid prediction for CodingQuarry_transcript_49251-T1
Valid prediction for GlimmerHMM_glimmerT_10676-T1
Valid prediction for GlimmerHMM_glimmerT_10686-T1
Valid prediction for GlimmerHMM_glimmerT_10702-T1
Valid prediction for GlimmerHMM_glimmerT_10675-T1
Valid prediction for snap_scaffold_4-snap.3074-T1
Valid prediction for GlimmerHMM_glimmerT_10683-T1
Valid prediction for GlimmerHMM_glimmerT_10696-T1
Valid prediction for snap_scaffold_4-snap.3059-T1
Valid prediction for GlimmerHMM_glimmerT_10691-T1
Valid prediction for CodingQuarry_transcript_49252-T1
Valid prediction for GlimmerHMM_glimmerT_10682-T1
Valid prediction for GlimmerHMM_glimmerT_10704-T1
Valid prediction for snap_scaffold_4-snap.3058-T1
Couldn't classify 169924, 170049
Sorry, prediction pasa_asmbl_41944.p1 fails validation.
(GTG)	 CA	169924-170049	GT	TTG
(GAT)	 AG	170422-170641	GT	CTG
(TCG)	 AG	172306-172379	GT	AGG
(GTG)	 AG	172518-172614	GT	GAG
(AGA)	 AG	172884-173066	GT	CTG
(ATC)	 AG	173277-173398	GT	ACG
(GAT)	 AG	173937-174081	GT	CTG
(GGA)	 AG	174708-174823	GC	AGG
(GAC)	 AG	175097-175241	GT	AGG
(GGG)	 AG	175508-175632	GT	AGG
(TCG)	 AG	175851-175992	GT	AGG
(CTG)	 AG	176400-176512	AC	AGA
-recovered pasa_asmbl_41944.p1, terminal, 176400, 176512
-recovered pasa_asmbl_41944.p1, internal, 170422, 170641
-recovered pasa_asmbl_41944.p1, internal, 172306, 172379
-recovered pasa_asmbl_41944.p1, internal, 172518, 172614
-recovered pasa_asmbl_41944.p1, internal, 172884, 173066
-recovered pasa_asmbl_41944.p1, internal, 173277, 173398
-recovered pasa_asmbl_41944.p1, internal, 173937, 174081
-recovered pasa_asmbl_41944.p1, internal, 174708, 174823
-recovered pasa_asmbl_41944.p1, internal, 175097, 175241
-recovered pasa_asmbl_41944.p1, internal, 175508, 175632
-recovered pasa_asmbl_41944.p1, internal, 175851, 175992
Valid prediction for snap_scaffold_4-snap.3082-T1
Valid prediction for pasa_asmbl_41939.p1
Valid prediction for GlimmerHMM_glimmerT_10701-T1
Valid prediction for Augustus_model.g7022.t1
Valid prediction for GlimmerHMM_glimmerT_10688-T1
Valid prediction for Augustus_model.g7014.t1
Valid prediction for snap_scaffold_4-snap.3053-T1
Valid prediction for snap_scaffold_4-snap.3064-T1
Valid prediction for GlimmerHMM_glimmerT_10677-T1
Valid prediction for snap_scaffold_4-snap.3052-T1
Valid prediction for snap_scaffold_4-snap.3075-T1
Valid prediction for GlimmerHMM_glimmerT_10678-T1
Valid prediction for GlimmerHMM_glimmerT_10698-T1
Valid prediction for snap_scaffold_4-snap.3063-T1
Valid prediction for snap_scaffold_4-snap.3043-T1
Valid prediction for GlimmerHMM_glimmerT_10703-T1
Valid prediction for snap_scaffold_4-snap.3069-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 snap_scaffold_4-snap.3038-T1
Valid prediction for snap_scaffold_4-snap.3042-T1
Valid prediction for GlimmerHMM_glimmerT_10694-T1
Valid prediction for snap_scaffold_4-snap.3051-T1
Valid prediction for snap_scaffold_4-snap.3067-T1
Valid prediction for snap_scaffold_4-snap.3050-T1
Valid prediction for Augustus_model.g7017.t1
Valid prediction for GlimmerHMM_glimmerT_10681-T1
Valid prediction for snap_scaffold_4-snap.3046-T1
Valid prediction for GlimmerHMM_glimmerT_10693-T1
Valid prediction for snap_scaffold_4-snap.3055-T1
Valid prediction for Augustus_model.g7016.t1
Valid prediction for GlimmerHMM_glimmerT_10689-T1
Valid prediction for snap_scaffold_4-snap.3083-T1
Valid prediction for snap_scaffold_4-snap.3079-T1
Valid prediction for snap_scaffold_4-snap.3071-T1
Valid prediction for snap_scaffold_4-snap.3054-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10685-T1
Valid prediction for GlimmerHMM_glimmerT_10679-T1
Valid prediction for GlimmerHMM_glimmerT_10697-T1
Valid prediction for GlimmerHMM_glimmerT_10687-T1
Valid prediction for snap_scaffold_4-snap.3062-T1
Valid prediction for snap_scaffold_4-snap.3056-T1
Valid prediction for snap_scaffold_4-snap.3045-T1
Valid prediction for snap_scaffold_4-snap.3073-T1
Valid prediction for snap_scaffold_4-snap.3039-T1
Valid prediction for snap_scaffold_4-snap.3048-T1
Valid prediction for GlimmerHMM_glimmerT_10680-T1
Valid prediction for GlimmerHMM_glimmerT_10700-T1
Valid prediction for GlimmerHMM_glimmerT_10699-T1
Valid prediction for snap_scaffold_4-snap.3081-T1
Valid prediction for snap_scaffold_4-snap.3072-T1
Valid prediction for GlimmerHMM_glimmerT_10684-T1
Valid prediction for GlimmerHMM_glimmerT_10692-T1
Valid prediction for Augustus_model.g7015.t1
Valid prediction for snap_scaffold_4-snap.3076-T1
Valid prediction for Augustus_model.g7020.t1
Valid prediction for GlimmerHMM_glimmerT_10690-T1
Valid prediction for snap_scaffold_4-snap.3065-T1
Valid prediction for snap_scaffold_4-snap.3077-T1
Valid prediction for Augustus_model.g7019.t1
Valid prediction for snap_scaffold_4-snap.3068-T1
Valid prediction for snap_scaffold_4-snap.3061-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10695-T1
Valid prediction for snap_scaffold_4-snap.3047-T1
Valid prediction for snap_scaffold_4-snap.3036-T1
Valid prediction for snap_scaffold_4-snap.3080-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3349, rend_intergenic: 1555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16214, rend_intergenic: 12847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31455, rend_intergenic: 25677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46136, rend_intergenic: 34922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52380, rend_intergenic: 46143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57996, rend_intergenic: 52574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68588, rend_intergenic: 58133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79517, rend_intergenic: 68654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95651, rend_intergenic: 90317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100188, rend_intergenic: 96903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106315, rend_intergenic: 104520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129284, rend_intergenic: 120287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133826, rend_intergenic: 130153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143329, rend_intergenic: 135646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148498, rend_intergenic: 143728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172685, rend_intergenic: 150231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174025, rend_intergenic: 172892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178643, rend_intergenic: 175802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182561
-exon list size: 333


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    
10.1    
10.4    
10.7    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.8    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
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    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.6    
37.9    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
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    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.1    
62.4    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
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    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.1    
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 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 3349, rend_intergenic: 1555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16214, rend_intergenic: 12847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31455, rend_intergenic: 25677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46136, rend_intergenic: 34922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52380, rend_intergenic: 46143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57996, rend_intergenic: 52574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68588, rend_intergenic: 58133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79517, rend_intergenic: 68654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95651, rend_intergenic: 90317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100188, rend_intergenic: 96903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106315, rend_intergenic: 104520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129284, rend_intergenic: 120287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133826, rend_intergenic: 130153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143329, rend_intergenic: 135646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148498, rend_intergenic: 143728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172685, rend_intergenic: 150231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174025, rend_intergenic: 172892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178643, rend_intergenic: 175802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support