-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_692953-882425

-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_13-snap.149-T1
Valid prediction for Augustus_model.g20602.t1
Valid prediction for GlimmerHMM_glimmerT_31021-T1
Valid prediction for snap_scaffold_13-snap.138-T1
Valid prediction for GlimmerHMM_glimmerT_31018-T1
Valid prediction for snap_scaffold_13-snap.137-T1
Valid prediction for Augustus_model.g20588.t1
Valid prediction for snap_scaffold_13-snap.134-T1
Valid prediction for snap_scaffold_13-snap.167-T1
Valid prediction for snap_scaffold_13-snap.135-T1
Couldn't classify 45695, 45903
Sorry, prediction pasa_asmbl_10514.p1 fails validation.
(ACC)	 AG	45695-45903	GT	AGG
(TAA)	 AG	46076-46227	GT	TGG
(TGC)	 AG	47467-47645	GT	AGG
(GAT)	 AG	49695-49836	GT	TGG
(GTT)	 AG	50012-50079	GG	GAG
-recovered pasa_asmbl_10514.p1, terminal, 50012, 50079
-recovered pasa_asmbl_10514.p1, internal, 45695, 45903
-recovered pasa_asmbl_10514.p1, internal, 46076, 46227
-recovered pasa_asmbl_10514.p1, internal, 47467, 47645
-recovered pasa_asmbl_10514.p1, internal, 49695, 49836
Couldn't classify 21345, 21384
Couldn't classify 23607, 23779
Sorry, prediction pasa_asmbl_10504.p1 fails validation.
(GGA)	 GG	21345-21384	GT	AGG
(AAG)	 AG	21490-21522	GT	CAG
(TTC)	 AG	21624-21800	GT	AGG
(ATG)	 AG	22090-22307	GC	AGG
(AAA)	 AG	22848-23034	GT	GGG
(TTC)	 AG	23218-23436	GT	AGG
(ACG)	 AG	23607-23779	GT	AGG
add_exon() Sorry, pasa_asmbl_10504.p1 22090-22307-initial-1 is invalid.
-recovered pasa_asmbl_10504.p1, initial, 22090, 22307
-recovered pasa_asmbl_10504.p1, internal, 21490, 21522
-recovered pasa_asmbl_10504.p1, internal, 21624, 21800
-recovered pasa_asmbl_10504.p1, internal, 22090, 22307
-recovered pasa_asmbl_10504.p1, internal, 22848, 23034
-recovered pasa_asmbl_10504.p1, internal, 23218, 23436
-recovered pasa_asmbl_10504.p1, internal, 23607, 23779
Valid prediction for Augustus_model.g20579.t1
Valid prediction for Augustus_model.g20582.t1
Valid prediction for snap_scaffold_13-snap.133-T1
Valid prediction for Augustus_model.g20591.t1
Valid prediction for Augustus_model.g20598.t1
Couldn't classify 161717, 162406
Sorry, prediction pasa_asmbl_9374.p1 fails validation.
(TCT)	 TC	161717-162406	TC	TCT
Valid prediction for Augustus_model.g20601.t1
Valid prediction for GlimmerHMM_glimmerT_31009-T1
Valid prediction for GlimmerHMM_glimmerT_31028-T1
Valid prediction for GlimmerHMM_glimmerT_31019-T1
Valid prediction for snap_scaffold_13-snap.142-T1
Valid prediction for CodingQuarry_transcript_12852-T1
Valid prediction for Augustus_model.g20596.t1
Valid prediction for Augustus_model.g20585.t1
Valid prediction for Augustus_model.g20581.t1
Valid prediction for snap_scaffold_13-snap.139-T1
Valid prediction for snap_scaffold_13-snap.141-T1
Valid prediction for Augustus_model.g20603.t1
Valid prediction for GlimmerHMM_glimmerT_31011-T1
Valid prediction for GlimmerHMM_glimmerT_31014-T1
Valid prediction for GlimmerHMM_glimmerT_31025-T1
Valid prediction for snap_scaffold_13-snap.151-T1
Valid prediction for Augustus_model.g20583.t1
Valid prediction for snap_scaffold_13-snap.147-T1
Valid prediction for snap_scaffold_13-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_31024-T1
Valid prediction for Augustus_model.g20589.t1
Couldn't classify 39278, 39379
Couldn't classify 41197, 41418
Sorry, prediction pasa_asmbl_10506.p1 fails validation.
(GCA)	 CA	39278-39379	GT	AGG
(TTG)	 AG	39579-39719	GT	AGG
(GAG)	 AG	39878-40036	GT	AGG
(GAA)	 AG	40130-40351	GT	AGG
(CTT)	 AG	40897-41025	GT	AGG
(CAG)	 AG	41197-41418	AC	GGA
-recovered pasa_asmbl_10506.p1, internal, 39579, 39719
-recovered pasa_asmbl_10506.p1, internal, 39878, 40036
-recovered pasa_asmbl_10506.p1, internal, 40130, 40351
-recovered pasa_asmbl_10506.p1, internal, 40897, 41025
Valid prediction for snap_scaffold_13-snap.152-T1
Valid prediction for snap_scaffold_13-snap.161-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31029-T1
Valid prediction for snap_scaffold_13-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_31016-T1
Valid prediction for snap_scaffold_13-snap.171-T1
Valid prediction for HiQ_model.g20578.t1
Valid prediction for snap_scaffold_13-snap.140-T1
Valid prediction for snap_scaffold_13-snap.169-T1
Valid prediction for Augustus_model.g20599.t1
Valid prediction for snap_scaffold_13-snap.170-T1
Valid prediction for snap_scaffold_13-snap.144-T1
Valid prediction for snap_scaffold_13-snap.160-T1
Couldn't classify 33596, 33755
Couldn't classify 35452, 35599
Sorry, prediction pasa_asmbl_10505.p1 fails validation.
(CAG)	 TT	33596-33755	GT	GGG
(GGC)	 AG	34104-34270	GT	AGG
(GGT)	 AG	34496-34590	GT	AGG
(GCA)	 AG	35248-35376	GT	AGG
(AAC)	 AG	35452-35599	GG	TGG
-recovered pasa_asmbl_10505.p1, internal, 34104, 34270
-recovered pasa_asmbl_10505.p1, internal, 34496, 34590
-recovered pasa_asmbl_10505.p1, internal, 35248, 35376
Valid prediction for GlimmerHMM_glimmerT_31004-T1
Valid prediction for GlimmerHMM_glimmerT_31008-T1
Valid prediction for CodingQuarry_transcript_12853-T1
Valid prediction for GlimmerHMM_glimmerT_31017-T1
Valid prediction for snap_scaffold_13-snap.163-T1
Valid prediction for GlimmerHMM_glimmerT_31006-T1
Valid prediction for snap_scaffold_13-snap.155-T1
Valid prediction for snap_scaffold_13-snap.172-T1
Valid prediction for Augustus_model.g20592.t1
Valid prediction for Augustus_model.g20593.t1
Valid prediction for snap_scaffold_13-snap.157-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_13-snap.148-T1
Valid prediction for HiQ_model.g20587.t1
Valid prediction for Augustus_model.g20577.t1
Valid prediction for GlimmerHMM_glimmerT_31015-T1
Valid prediction for snap_scaffold_13-snap.146-T1
Valid prediction for Augustus_model.g20594.t1
Valid prediction for snap_scaffold_13-snap.132-T1
Valid prediction for Augustus_model.g20597.t1
Valid prediction for CodingQuarry_transcript_12855-T1
Valid prediction for GlimmerHMM_glimmerT_31013-T1
Valid prediction for Augustus_model.g20586.t1
Valid prediction for snap_scaffold_13-snap.159-T1
Valid prediction for GlimmerHMM_glimmerT_31022-T1
Valid prediction for snap_scaffold_13-snap.165-T1
Valid prediction for snap_scaffold_13-snap.162-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31007-T1
Valid prediction for Augustus_model.g20595.t1
Valid prediction for Augustus_model.g20580.t1
Valid prediction for snap_scaffold_13-snap.156-T1
Valid prediction for snap_scaffold_13-snap.130-T1
Valid prediction for snap_scaffold_13-snap.166-T1
Valid prediction for GlimmerHMM_glimmerT_31027-T1
Valid prediction for pasa_asmbl_9372.p1
Valid prediction for snap_scaffold_13-snap.168-T1
Valid prediction for Augustus_model.g20590.t1
Valid prediction for snap_scaffold_13-snap.136-T1
Valid prediction for CodingQuarry_transcript_12854-T1
Valid prediction for GlimmerHMM_glimmerT_31012-T1
Valid prediction for Augustus_model.g20600.t1
Valid prediction for snap_scaffold_13-snap.164-T1
Valid prediction for snap_scaffold_13-snap.131-T1
Valid prediction for snap_scaffold_13-snap.143-T1
Valid prediction for GlimmerHMM_glimmerT_31026-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_31010-T1
Valid prediction for snap_scaffold_13-snap.150-T1
Valid prediction for GlimmerHMM_glimmerT_31005-T1
Valid prediction for GlimmerHMM_glimmerT_31023-T1
Valid prediction for Augustus_model.g20584.t1
Valid prediction for snap_scaffold_13-snap.145-T1
Valid prediction for GlimmerHMM_glimmerT_31003-T1
Valid prediction for snap_scaffold_13-snap.154-T1
Valid prediction for GlimmerHMM_glimmerT_31020-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 147674, rend_intergenic: 145208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171326, rend_intergenic: 167980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189473
-exon list size: 309


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.5    
3.9    
4.2    
4.5    
4.8    
5.1    
5.5    
5.8    
6.1    
6.4    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
10.0    
10.3    
10.6    
10.9    
11.3    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.8    
14.1    
14.5    
14.8    
15.1    
15.4    
15.8    
16.1    
16.4    
16.7    
17.0    
17.4    
17.7    
18.0    
18.3    
18.6    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.5    
21.9    
22.2    
22.5    
22.8    
23.2    
23.5    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.0    
26.4    
26.7    
27.0    
27.3    
27.7    
28.0    
28.3    
28.6    
28.9    
29.3    
29.6    
29.9    
30.2    
30.5    
30.9    
31.2    
31.5    
31.8    
32.2    
32.5    
32.8    
33.1    
33.4    
33.8    
34.1    
34.4    
34.7    
35.0    
35.4    
35.7    
36.0    
36.3    
36.7    
37.0    
37.3    
37.6    
37.9    
38.3    
38.6    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.8    
41.2    
41.5    
41.8    
42.1    
42.4    
42.8    
43.1    
43.4    
43.7    
44.1    
44.4    
44.7    
45.0    
45.3    
45.7    
46.0    
46.3    
46.6    
46.9    
47.3    
47.6    
47.9    
48.2    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.8    
52.1    
52.4    
52.7    
53.1    
53.4    
53.7    
54.0    
54.3    
54.7    
55.0    
55.3    
55.6    
55.9    
56.3    
56.6    
56.9    
57.2    
57.6    
57.9    
58.2    
58.5    
58.8    
59.2    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.4    
61.7    
62.1    
62.4    
62.7    
63.0    
63.3    
63.7    
64.0    
64.3    
64.6    
65.0    
65.3    
65.6    
65.9    
66.2    
66.6    
66.9    
67.2    
67.5    
67.8    
68.2    
68.5    
68.8    
69.1    
69.5    
69.8    
70.1    
70.4    
70.7    
71.1    
71.4    
71.7    
72.0    
72.3    
72.7    
73.0    
73.3    
73.6    
74.0    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.5    
76.8    
77.2    
77.5    
77.8    
78.1    
78.5    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.4    
81.7    
82.0    
82.3    
82.6    
83.0    
83.3    
83.6    
83.9    
84.2    
84.6    
84.9    
85.2    
85.5    
85.9    
86.2    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.7    
89.1    
89.4    
89.7    
90.0    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.6    
93.9    
94.2    
94.5    
94.9    
95.2    
95.5    
95.8    
96.1    
96.5    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 147674, rend_intergenic: 145208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171326, rend_intergenic: 167980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11294
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10665
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 10451