-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_541998-785997

-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_37730-T1
Valid prediction for Augustus_model.g25134.t1
Valid prediction for snap_scaffold_16-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_37736-T1
Valid prediction for GlimmerHMM_glimmerT_37716-T1
Valid prediction for Augustus_model.g25131.t1
Valid prediction for snap_scaffold_16-snap.104-T1
Valid prediction for snap_scaffold_16-snap.108-T1
Couldn't classify 153322, 154137
Sorry, prediction pasa_asmbl_16039.p1 fails validation.
(ATG)	 GT	153322-154137	AA	CAA
Valid prediction for snap_scaffold_16-snap.115-T1
Valid prediction for snap_scaffold_16-snap.129-T1
Valid prediction for GlimmerHMM_glimmerT_37718-T1
Valid prediction for Augustus_model.g25130.t1
Couldn't classify 120634, 120741
Couldn't classify 121761, 121906
Sorry, prediction CodingQuarry_transcript_19884-T1 fails validation.
(ATG)	 AG	120486-120536	GT	ATG
(GGC)	 AG	120634-120741	AT	CCA
(AGA)	 AC	121761-121906	GT	GGG
(AGA)	 AG	122016-122101	GT	TGG
(TTG)	 AG	122187-122296	GT	CGG
(TTT)	 AG	122374-122467	GT	ATG
(CTG)	 AG	122786-122976	GT	AGG
(GTA)	 AG	123102-123227	AC	AAA
-recovered CodingQuarry_transcript_19884-T1, initial, 120486, 120536
-recovered CodingQuarry_transcript_19884-T1, terminal, 123102, 123227
-recovered CodingQuarry_transcript_19884-T1, internal, 120486, 120536
-recovered CodingQuarry_transcript_19884-T1, internal, 122016, 122101
-recovered CodingQuarry_transcript_19884-T1, internal, 122187, 122296
-recovered CodingQuarry_transcript_19884-T1, internal, 122374, 122467
-recovered CodingQuarry_transcript_19884-T1, internal, 122786, 122976
Valid prediction for snap_scaffold_16-snap.122-T1
Valid prediction for snap_scaffold_16-snap.99-T1
Valid prediction for Augustus_model.g25125.t1
Valid prediction for Augustus_model.g25133.t1
Valid prediction for Augustus_model.g25143.t1
Valid prediction for GlimmerHMM_glimmerT_37710-T1
Valid prediction for snap_scaffold_16-snap.112-T1
Valid prediction for GlimmerHMM_glimmerT_37722-T1
Valid prediction for snap_scaffold_16-snap.103-T1
Couldn't classify 133227, 133355
Sorry, prediction pasa_asmbl_16036.p1 fails validation.
(ATG)	 AC	131486-131591	GT	CTG
(CAA)	 AG	133027-133094	GT	TGG
(GAA)	 AG	133227-133355	GA	GGG
-recovered pasa_asmbl_16036.p1, initial, 131486, 131591
-recovered pasa_asmbl_16036.p1, internal, 133027, 133094
Valid prediction for HiQ_model.g25142.t1
Valid prediction for snap_scaffold_16-snap.127-T1
Valid prediction for GlimmerHMM_glimmerT_37727-T1
Valid prediction for GlimmerHMM_glimmerT_37724-T1
Valid prediction for pasa_asmbl_16042.p1
Valid prediction for GlimmerHMM_glimmerT_37731-T1
Valid prediction for HiQ_model.g25148.t1
Valid prediction for snap_scaffold_16-snap.110-T1
Valid prediction for pasa_asmbl_16045.p1
Valid prediction for GlimmerHMM_glimmerT_37723-T1
Valid prediction for snap_scaffold_16-snap.98-T1
Valid prediction for snap_scaffold_16-snap.111-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g25144.t1
Valid prediction for Augustus_model.g25147.t1
Valid prediction for GlimmerHMM_glimmerT_37712-T1
Valid prediction for snap_scaffold_16-snap.97-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_37732-T1
Valid prediction for CodingQuarry_transcript_19887-T1
Valid prediction for Augustus_model.g25136.t1
Valid prediction for Augustus_model.g25140.t1
Valid prediction for snap_scaffold_16-snap.114-T1
Couldn't classify 120634, 120741
Couldn't classify 121761, 121906
Sorry, prediction pasa_asmbl_16031.p1 fails validation.
(ATG)	 AG	120486-120536	GT	ATG
(GGC)	 AG	120634-120741	AT	CCA
(AGA)	 AC	121761-121906	GT	GGG
(AGA)	 AG	122016-122101	GT	TGG
(TTG)	 AG	122187-122296	GT	CGG
(TTT)	 AG	122374-122467	GT	ATG
(CTG)	 AG	122786-122976	GT	AGG
(GTA)	 AG	123102-123227	AC	AAA
-recovered pasa_asmbl_16031.p1, initial, 120486, 120536
-recovered pasa_asmbl_16031.p1, terminal, 123102, 123227
-recovered pasa_asmbl_16031.p1, internal, 120486, 120536
-recovered pasa_asmbl_16031.p1, internal, 122016, 122101
-recovered pasa_asmbl_16031.p1, internal, 122187, 122296
-recovered pasa_asmbl_16031.p1, internal, 122374, 122467
-recovered pasa_asmbl_16031.p1, internal, 122786, 122976
Valid prediction for snap_scaffold_16-snap.120-T1
Couldn't classify 146013, 146210
Couldn't classify 151333, 151366
Sorry, prediction pasa_asmbl_16038.p1 fails validation.
(CAG)	 TA	146013-146210	GT	AGG
(GCT)	 AG	146390-146599	GT	AGG
(GCC)	 AG	149488-149659	GT	AGG
(TTG)	 AG	151075-151219	GT	ACG
(TCA)	 AG	151333-151366	AA	GCA
add_exon() Sorry, pasa_asmbl_16038.p1 149488-149659-terminal-3 is invalid.
-recovered pasa_asmbl_16038.p1, terminal, 149488, 149659
-recovered pasa_asmbl_16038.p1, internal, 146390, 146599
-recovered pasa_asmbl_16038.p1, internal, 149488, 149659
-recovered pasa_asmbl_16038.p1, internal, 151075, 151219
Couldn't classify 109256, 109507
Couldn't classify 115215, 115377
Sorry, prediction pasa_asmbl_16030.p1 fails validation.
(CGG)	 CG	109256-109507	GT	AGG
(GGT)	 AG	110245-110346	GT	AGG
(GAA)	 AG	110452-110554	GT	AGG
(GTG)	 AG	110692-110833	GT	AAG
(GAC)	 AG	113180-113268	GT	AGG
(CCC)	 AG	114483-114559	GT	AGG
(ATG)	 AG	114657-114802	GT	GGG
(CTA)	 AG	114885-115034	GT	AGG
(AGA)	 AG	115215-115377	GT	AGG
-recovered pasa_asmbl_16030.p1, initial, 114657, 114802
add_exon() Sorry, pasa_asmbl_16030.p1 114885-115034-terminal-1 is invalid.
-recovered pasa_asmbl_16030.p1, terminal, 114885, 115034
-recovered pasa_asmbl_16030.p1, internal, 110245, 110346
-recovered pasa_asmbl_16030.p1, internal, 110452, 110554
-recovered pasa_asmbl_16030.p1, internal, 110692, 110833
-recovered pasa_asmbl_16030.p1, internal, 113180, 113268
-recovered pasa_asmbl_16030.p1, internal, 114483, 114559
-recovered pasa_asmbl_16030.p1, internal, 114657, 114802
-recovered pasa_asmbl_16030.p1, internal, 114885, 115034
-recovered pasa_asmbl_16030.p1, internal, 115215, 115377
Valid prediction for Augustus_model.g25126.t1
Valid prediction for snap_scaffold_16-snap.124-T1
Valid prediction for CodingQuarry_transcript_19886-T1
Valid prediction for GlimmerHMM_glimmerT_37720-T1
Valid prediction for snap_scaffold_16-snap.119-T1
Valid prediction for snap_scaffold_16-snap.107-T1
Valid prediction for snap_scaffold_16-snap.123-T1
Valid prediction for snap_scaffold_16-snap.113-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_16-snap.133-T1
Valid prediction for HiQ_model.g25150.t1
Valid prediction for Augustus_model.g25127.t1
Valid prediction for Augustus_model.g25138.t1
Valid prediction for snap_scaffold_16-snap.106-T1
Valid prediction for GlimmerHMM_glimmerT_37713-T1
Valid prediction for GlimmerHMM_glimmerT_37721-T1
Valid prediction for snap_scaffold_16-snap.131-T1
Valid prediction for Augustus_model.g25153.t1
Valid prediction for GlimmerHMM_glimmerT_37711-T1
Valid prediction for GlimmerHMM_glimmerT_37726-T1
Valid prediction for snap_scaffold_16-snap.109-T1
Valid prediction for Augustus_model.g25135.t1
Valid prediction for Augustus_model.g25145.t1
Valid prediction for GlimmerHMM_glimmerT_37715-T1
Valid prediction for GlimmerHMM_glimmerT_37725-T1
Valid prediction for snap_scaffold_16-snap.102-T1
Valid prediction for GlimmerHMM_glimmerT_37714-T1
Valid prediction for Augustus_model.g25141.t1
Valid prediction for snap_scaffold_16-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_37719-T1
Valid prediction for snap_scaffold_16-snap.118-T1
Valid prediction for Augustus_model.g25146.t1
Valid prediction for GlimmerHMM_glimmerT_37738-T1
Valid prediction for CodingQuarry_transcript_19890-T1
Valid prediction for Augustus_model.g25129.t1
Valid prediction for GlimmerHMM_glimmerT_37734-T1
Valid prediction for GlimmerHMM_glimmerT_37717-T1
Valid prediction for snap_scaffold_16-snap.105-T1
Valid prediction for snap_scaffold_16-snap.132-T1
Valid prediction for HiQ_model.g25151.t1
Valid prediction for snap_scaffold_16-snap.100-T1
Valid prediction for snap_scaffold_16-snap.116-T1
Valid prediction for GlimmerHMM_glimmerT_37728-T1
Valid prediction for snap_scaffold_16-snap.125-T1
Valid prediction for pasa_asmbl_16902.p1
Valid prediction for Augustus_model.g25152.t1
Valid prediction for Augustus_model.g25149.t1
Couldn't classify 60068, 60215
Couldn't classify 61189, 61241
Sorry, prediction pasa_asmbl_16894.p1 fails validation.
(TGT)	 AG	60068-60215	GT	TGG
(CCC)	 AG	60553-60668	GT	AGG
(AAT)	 AG	60799-60943	GT	TGG
(GAG)	 AG	61189-61241	AA	CCA
-recovered pasa_asmbl_16894.p1, internal, 60068, 60215
-recovered pasa_asmbl_16894.p1, internal, 60553, 60668
-recovered pasa_asmbl_16894.p1, internal, 60799, 60943
Valid prediction for snap_scaffold_16-snap.126-T1
Valid prediction for Augustus_model.g25132.t1
Valid prediction for GlimmerHMM_glimmerT_37740-T1
Valid prediction for GlimmerHMM_glimmerT_37737-T1
Valid prediction for snap_scaffold_16-snap.121-T1
Valid prediction for snap_scaffold_16-snap.130-T1
Valid prediction for Augustus_model.g25139.t1
Valid prediction for snap_scaffold_16-snap.101-T1
Valid prediction for Augustus_model.g25128.t1
Valid prediction for GlimmerHMM_glimmerT_37735-T1
Valid prediction for GlimmerHMM_glimmerT_37739-T1
Valid prediction for Augustus_model.g25137.t1
Valid prediction for GlimmerHMM_glimmerT_37729-T1
Valid prediction for GlimmerHMM_glimmerT_37733-T1
Couldn't classify 37190, 37193
Sorry, prediction CodingQuarry_transcript_19889-T1 fails validation.
(ATG)	 GT	34498-34550	GT	GGG
(AGT)	 AG	34675-34820	GT	TAG
(TTC)	 AG	35382-35550	GT	AGG
(GCA)	 AG	36851-37006	GT	ATG
(TTG)	 GG	37190-37193	AG	GAA
-recovered CodingQuarry_transcript_19889-T1, initial, 34498, 34550
-recovered CodingQuarry_transcript_19889-T1, internal, 34675, 34820
-recovered CodingQuarry_transcript_19889-T1, internal, 35382, 35550
-recovered CodingQuarry_transcript_19889-T1, internal, 36851, 37006
Valid prediction for CodingQuarry_transcript_19888-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43211, rend_intergenic: 38903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244000
-exon list size: 332


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    
25.1    
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    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
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    
75.1    
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 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 43211, rend_intergenic: 38903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 215940 - 244000
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-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 215940 - 242193
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 215940 - 228021
-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

-building DP trellis

-building trellis in range 228080 - 242193
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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