-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_5503543-5629951

-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_20-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_46005-T1
Valid prediction for GlimmerHMM_glimmerT_46013-T1
Valid prediction for GlimmerHMM_glimmerT_46000-T1
Valid prediction for snap_scaffold_20-snap.1196-T1
Valid prediction for Augustus_model.g30541.t1
Valid prediction for snap_scaffold_20-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_45998-T1
Valid prediction for snap_scaffold_20-snap.1177-T1
Valid prediction for GlimmerHMM_glimmerT_46008-T1
Valid prediction for snap_scaffold_20-snap.1200-T1
Valid prediction for HiQ_model.g30540.t1
Couldn't classify 34561, 34626
Couldn't classify 37588, 37596
Sorry, prediction pasa_asmbl_26622.p1 fails validation.
(CTC)	 AC	34561-34626	GT	GGG
(GTG)	 AG	34790-35041	GT	AGG
(GTG)	 AG	35264-35389	GT	AGG
(AAG)	 AG	35579-35773	GT	TCG
(ATT)	 AG	35976-36146	GT	CGG
(GCC)	 AG	36282-36495	GT	AGG
(ATG)	 AG	36852-37004	GT	GGG
(GCG)	 AG	37249-37361	GT	CAG
(GTT)	 AG	37588-37596	GG	AGG
add_exon() Sorry, pasa_asmbl_26622.p1 36852-37004-initial-1 is invalid.
-recovered pasa_asmbl_26622.p1, initial, 36852, 37004
-recovered pasa_asmbl_26622.p1, internal, 34790, 35041
-recovered pasa_asmbl_26622.p1, internal, 35264, 35389
-recovered pasa_asmbl_26622.p1, internal, 35579, 35773
-recovered pasa_asmbl_26622.p1, internal, 35976, 36146
-recovered pasa_asmbl_26622.p1, internal, 36282, 36495
-recovered pasa_asmbl_26622.p1, internal, 36852, 37004
-recovered pasa_asmbl_26622.p1, internal, 37249, 37361
Valid prediction for snap_scaffold_20-snap.1192-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.1182-T1
Valid prediction for snap_scaffold_20-snap.1178-T1
Valid prediction for GlimmerHMM_glimmerT_46003-T1
Couldn't classify 38011, 38096
Sorry, prediction pasa_asmbl_26624.p1 fails validation.
(CTG)	 GC	38011-38096	GT	AGG
(GTA)	 AG	38191-38253	GT	AGG
(TAA)	 AG	38355-38457	GT	AGG
(TAC)	 AG	38566-38655	GT	AAG
(CAA)	 AG	38756-38858	GT	TGG
(ACG)	 AG	38983-39157	GT	AGG
(GTG)	 AG	39348-39404	GT	AGG
(GTT)	 AG	39561-39683	GT	AGG
(GTT)	 AG	39917-40036	GT	AGG
(CGT)	 AG	40165-40327	GT	AGG
(GAG)	 AG	40569-40715	GT	AGG
(CAG)	 AG	40927-41070	GT	AGG
(AGG)	 AG	41202-41452	GT	AGG
(AGA)	 AG	41613-41781	GT	AGG
(GAA)	 AG	41905-42058	GT	GAG
(ACG)	 AG	42319-42484	GT	CGG
(GGC)	 AG	42806-42977	AA	AGA
-recovered pasa_asmbl_26624.p1, terminal, 42806, 42977
-recovered pasa_asmbl_26624.p1, internal, 38191, 38253
-recovered pasa_asmbl_26624.p1, internal, 38355, 38457
-recovered pasa_asmbl_26624.p1, internal, 38566, 38655
-recovered pasa_asmbl_26624.p1, internal, 38756, 38858
-recovered pasa_asmbl_26624.p1, internal, 38983, 39157
-recovered pasa_asmbl_26624.p1, internal, 39348, 39404
-recovered pasa_asmbl_26624.p1, internal, 39561, 39683
-recovered pasa_asmbl_26624.p1, internal, 39917, 40036
-recovered pasa_asmbl_26624.p1, internal, 40165, 40327
-recovered pasa_asmbl_26624.p1, internal, 40569, 40715
-recovered pasa_asmbl_26624.p1, internal, 40927, 41070
-recovered pasa_asmbl_26624.p1, internal, 41202, 41452
-recovered pasa_asmbl_26624.p1, internal, 41613, 41781
-recovered pasa_asmbl_26624.p1, internal, 41905, 42058
-recovered pasa_asmbl_26624.p1, internal, 42319, 42484
Valid prediction for Augustus_model.g30534.t1
Valid prediction for GlimmerHMM_glimmerT_46011-T1
Valid prediction for GlimmerHMM_glimmerT_46001-T1
Valid prediction for CodingQuarry_transcript_30510-T1
Valid prediction for snap_scaffold_20-snap.1191-T1
Valid prediction for Augustus_model.g30538.t1
Valid prediction for snap_scaffold_20-snap.1181-T1
Valid prediction for Augustus_model.g30535.t1
Couldn't classify 32123, 32239
Sorry, prediction pasa_asmbl_26621.p1 fails validation.
(ATG)	 CA	31720-31965	GT	AAG
(AAT)	 AG	32123-32239	GC	ACG
-recovered pasa_asmbl_26621.p1, initial, 31720, 31965
-recovered pasa_asmbl_26621.p1, internal, 32123, 32239
Valid prediction for snap_scaffold_20-snap.1180-T1
Valid prediction for GlimmerHMM_glimmerT_46016-T1
Valid prediction for pasa_asmbl_26626.p1
Valid prediction for GlimmerHMM_glimmerT_45996-T1
Valid prediction for snap_scaffold_20-snap.1197-T1
Valid prediction for snap_scaffold_20-snap.1175-T1
Valid prediction for snap_scaffold_20-snap.1190-T1
Valid prediction for GlimmerHMM_glimmerT_46007-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_46017-T1
Valid prediction for snap_scaffold_20-snap.1186-T1
Valid prediction for snap_scaffold_20-snap.1199-T1
Valid prediction for GlimmerHMM_glimmerT_46015-T1
Valid prediction for snap_scaffold_20-snap.1184-T1
Valid prediction for GlimmerHMM_glimmerT_46014-T1
Valid prediction for CodingQuarry_transcript_30506-T1
Valid prediction for snap_scaffold_20-snap.1201-T1
Valid prediction for pasa_asmbl_25775.p1
Valid prediction for CodingQuarry_transcript_30507-T1
Valid prediction for CodingQuarry_transcript_30511-T1
Valid prediction for Augustus_model.g30533.t1
Valid prediction for CodingQuarry_transcript_30508-T1
Valid prediction for GlimmerHMM_glimmerT_46002-T1
Valid prediction for Augustus_model.g30544.t1
Valid prediction for Augustus_model.g30545.t1
Valid prediction for snap_scaffold_20-snap.1179-T1
Valid prediction for GlimmerHMM_glimmerT_46012-T1
Valid prediction for Augustus_model.g30546.t1
Valid prediction for GlimmerHMM_glimmerT_46006-T1
Valid prediction for GlimmerHMM_glimmerT_46009-T1
Valid prediction for snap_scaffold_20-snap.1202-T1
Valid prediction for snap_scaffold_20-snap.1193-T1
Valid prediction for snap_scaffold_20-snap.1203-T1
Valid prediction for HiQ_model.g30542.t1
Valid prediction for snap_scaffold_20-snap.1189-T1
Valid prediction for snap_scaffold_20-snap.1176-T1
Valid prediction for Augustus_model.g30548.t1
Valid prediction for GlimmerHMM_glimmerT_45997-T1
Valid prediction for GlimmerHMM_glimmerT_46004-T1
Valid prediction for snap_scaffold_20-snap.1195-T1
Valid prediction for HiQ_model.g30536.t1
Valid prediction for GlimmerHMM_glimmerT_46018-T1
Valid prediction for GlimmerHMM_glimmerT_45999-T1
Valid prediction for snap_scaffold_20-snap.1198-T1
Valid prediction for Augustus_model.g30547.t1
Valid prediction for pasa_asmbl_25769.p1
Valid prediction for snap_scaffold_20-snap.1183-T1
Valid prediction for Augustus_model.g30537.t1
Valid prediction for GlimmerHMM_glimmerT_46010-T1
Valid prediction for snap_scaffold_20-snap.1194-T1
Valid prediction for CodingQuarry_transcript_30509-T1
Valid prediction for snap_scaffold_20-snap.1204-T1
Valid prediction for Augustus_model.g30543.t1
Valid prediction for Augustus_model.g30539.t1
Valid prediction for snap_scaffold_20-snap.1187-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9430, rend_intergenic: 3666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23159, rend_intergenic: 20335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46089, rend_intergenic: 44433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51675, rend_intergenic: 50096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62725, rend_intergenic: 58798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91684, rend_intergenic: 79239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111013, rend_intergenic: 103913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 126409
-exon list size: 331


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    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.1    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
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    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
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    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.9    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
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 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 9430, rend_intergenic: 3666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23159, rend_intergenic: 20335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46089, rend_intergenic: 44433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51675, rend_intergenic: 50096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62725, rend_intergenic: 58798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91684, rend_intergenic: 79239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111013, rend_intergenic: 103913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support