-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_3803492-4084376

-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 CodingQuarry_transcript_35550-T1
Valid prediction for GlimmerHMM_glimmerT_52093-T1
Valid prediction for GeneMark_model.90433_t
Valid prediction for snap_scaffold_23-snap.759-T1
Valid prediction for GlimmerHMM_glimmerT_52074-T1
Valid prediction for GeneMark_model.90439_t
Valid prediction for snap_scaffold_23-snap.760-T1
Valid prediction for snap_scaffold_23-snap.776-T1
Valid prediction for GlimmerHMM_glimmerT_52088-T1
Valid prediction for GeneMark_model.90445_t
Valid prediction for GlimmerHMM_glimmerT_52087-T1
Valid prediction for snap_scaffold_23-snap.753-T1
Valid prediction for snap_scaffold_23-snap.764-T1
Valid prediction for snap_scaffold_23-snap.757-T1
Valid prediction for Augustus_model.g35007.t1
Couldn't classify 269989, 270100
Sorry, prediction pasa_asmbl_30777.p1 fails validation.
(ATG)	 AC	265821-265879	GT	GGG
(TGA)	 AG	266211-266277	GT	TGG
(GAC)	 AG	266401-266546	GT	GCG
(AAC)	 AG	266726-266814	GT	CAG
(ACT)	 AG	266912-267006	GT	AGG
(GAC)	 AG	267229-267324	GT	TGG
(AGT)	 AG	267504-267599	GT	AGG
(GAT)	 AG	267743-267818	GT	CGG
(GTG)	 AG	268309-268326	GT	AGG
(GTG)	 AG	269768-269867	GT	AGG
(CGA)	 AG	269989-270100	GA	CCG
-recovered pasa_asmbl_30777.p1, initial, 265821, 265879
-recovered pasa_asmbl_30777.p1, internal, 266211, 266277
-recovered pasa_asmbl_30777.p1, internal, 266401, 266546
-recovered pasa_asmbl_30777.p1, internal, 266726, 266814
-recovered pasa_asmbl_30777.p1, internal, 266912, 267006
-recovered pasa_asmbl_30777.p1, internal, 267229, 267324
-recovered pasa_asmbl_30777.p1, internal, 267504, 267599
-recovered pasa_asmbl_30777.p1, internal, 267743, 267818
-recovered pasa_asmbl_30777.p1, internal, 268309, 268326
-recovered pasa_asmbl_30777.p1, internal, 269768, 269867
Valid prediction for Augustus_model.g35008.t1
Valid prediction for snap_scaffold_23-snap.775-T1
Valid prediction for snap_scaffold_23-snap.754-T1
Valid prediction for Augustus_model.g35006.t1
Valid prediction for GeneMark_model.90435_t
Couldn't classify 226423, 226550
Couldn't classify 227301, 227341
Sorry, prediction pasa_asmbl_31220.p1 fails validation.
(GGT)	 AA	226423-226550	GT	AAG
(CAT)	 AG	226773-226924	GT	AGG
(GCA)	 AG	227301-227341	AT	GCA
add_exon() Sorry, pasa_asmbl_31220.p1 226773-226924-terminal-2 is invalid.
-recovered pasa_asmbl_31220.p1, terminal, 226773, 226924
-recovered pasa_asmbl_31220.p1, internal, 226773, 226924
Valid prediction for GlimmerHMM_glimmerT_52075-T1
Valid prediction for GeneMark_model.90417_t
Valid prediction for GeneMark_model.90446_t
Valid prediction for GeneMark_model.90423_t
Couldn't classify 229446, 229544
Sorry, prediction pasa_asmbl_30775.p2 fails validation.
(GGT)	 GA	229446-229544	GT	AAG
(TTG)	 AG	229654-229746	GT	ATG
(TAC)	 AG	229983-230088	GT	AGG
(GTA)	 AG	230192-230283	GT	AGG
(ATA)	 AG	230394-230423	AG	GAA
-recovered pasa_asmbl_30775.p2, terminal, 230394, 230423
-recovered pasa_asmbl_30775.p2, internal, 229654, 229746
-recovered pasa_asmbl_30775.p2, internal, 229983, 230088
-recovered pasa_asmbl_30775.p2, internal, 230192, 230283
Valid prediction for GeneMark_model.90420_t
Valid prediction for GlimmerHMM_glimmerT_52091-T1
Valid prediction for GlimmerHMM_glimmerT_52080-T1
Valid prediction for GlimmerHMM_glimmerT_52077-T1
Valid prediction for GlimmerHMM_glimmerT_52097-T1
Valid prediction for snap_scaffold_23-snap.752-T1
Valid prediction for Augustus_model.g35009.t1
Valid prediction for GeneMark_model.90425_t
Valid prediction for Augustus_model.g35005.t1
Valid prediction for GeneMark_model.90428_t
Valid prediction for snap_scaffold_23-snap.767-T1
Valid prediction for snap_scaffold_23-snap.779-T1
Valid prediction for snap_scaffold_23-snap.768-T1
Valid prediction for Augustus_model.g35013.t1
Valid prediction for GeneMark_model.90434_t
Valid prediction for GlimmerHMM_glimmerT_52076-T1
Valid prediction for GeneMark_model.90422_t
Valid prediction for Augustus_model.g35003.t1
Valid prediction for snap_scaffold_23-snap.761-T1
Couldn't classify 270170, 270206
Sorry, prediction pasa_asmbl_30778.p1 fails validation.
(CTG)	 GT	270170-270206	GT	AGG
(CCC)	 AG	270329-270496	GT	GGG
(GTA)	 AG	270869-271062	GT	AGG
(GCA)	 AG	271275-271367	GT	GGG
(ATG)	 AG	271532-271630	GT	CAG
(GTC)	 AG	271744-271803	GT	CGG
(ATG)	 AG	272572-272679	TA	AAT
-recovered pasa_asmbl_30778.p1, initial, 271532, 271630
-recovered pasa_asmbl_30778.p1, terminal, 272572, 272679
-recovered pasa_asmbl_30778.p1, internal, 270329, 270496
-recovered pasa_asmbl_30778.p1, internal, 270869, 271062
-recovered pasa_asmbl_30778.p1, internal, 271275, 271367
-recovered pasa_asmbl_30778.p1, internal, 271532, 271630
-recovered pasa_asmbl_30778.p1, internal, 271744, 271803
Valid prediction for HiQ_model.g35017.t1
Valid prediction for snap_scaffold_23-snap.750-T1
Valid prediction for GeneMark_model.90441_t
Valid prediction for snap_scaffold_23-snap.762-T1
Valid prediction for GlimmerHMM_glimmerT_52084-T1
Valid prediction for GlimmerHMM_glimmerT_52083-T1
Valid prediction for Augustus_model.g35012.t1
Valid prediction for Augustus_model.g35004.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_52085-T1
Valid prediction for snap_scaffold_23-snap.774-T1
Couldn't classify 95977, 96171
Sorry, prediction pasa_asmbl_31541.p1 fails validation.
(GGT)	 CA	95977-96171	GT	AGG
(CAA)	 AG	97061-97331	GT	AGG
(GAA)	 AG	97556-97755	AT	AAA
-recovered pasa_asmbl_31541.p1, terminal, 97556, 97755
-recovered pasa_asmbl_31541.p1, internal, 97061, 97331
Valid prediction for GeneMark_model.90419_t
Valid prediction for GeneMark_model.90431_t
Valid prediction for GeneMark_model.90438_t
Valid prediction for GeneMark_model.90436_t
Valid prediction for GeneMark_model.90424_t
Valid prediction for GlimmerHMM_glimmerT_52081-T1
Valid prediction for snap_scaffold_23-snap.756-T1
Valid prediction for GeneMark_model.90440_t
Valid prediction for snap_scaffold_23-snap.770-T1
Valid prediction for GlimmerHMM_glimmerT_52098-T1
Valid prediction for GlimmerHMM_glimmerT_52095-T1
Valid prediction for snap_scaffold_23-snap.777-T1
Valid prediction for CodingQuarry_transcript_35551-T1
Valid prediction for snap_scaffold_23-snap.773-T1
Valid prediction for snap_scaffold_23-snap.778-T1
Couldn't classify 27645, 27912
Sorry, prediction pasa_asmbl_31544.p1 fails validation.
(GCC)	 CA	27645-27912	GT	ACG
(TGC)	 AG	28029-28079	GT	CAG
(TCG)	 AG	28316-28387	GT	ACG
(ATG)	 AG	28489-28557	GT	AGG
(AGG)	 AG	28821-28880	GT	CTG
(TGG)	 AG	29032-29091	GT	GGG
(CTG)	 AG	29775-29852	GT	AAG
(AAT)	 AG	30626-30735	GT	AGG
(GGC)	 AG	30825-30964	GT	CAG
(CGA)	 AG	31203-31287	GT	GGG
(TTG)	 AG	31399-31543	GT	TGG
(GTA)	 AG	31913-31992	GT	AGG
(ATG)	 AG	32103-32226	GT	TGG
(GTG)	 AG	32570-32766	GT	TGG
(GGT)	 AG	32908-33081	GT	CTG
(GTA)	 AG	33206-33337	GT	GGG
(GCC)	 AG	33606-33858	GT	AAG
(GCA)	 AG	33975-34114	GT	AGG
(GTG)	 AG	34239-34338	GT	TGG
(CTG)	 AG	34473-35041	AG	AAA
-recovered pasa_asmbl_31544.p1, initial, 28489, 28557
-recovered pasa_asmbl_31544.p1, initial, 32103, 32226
-recovered pasa_asmbl_31544.p1, terminal, 34473, 35041
-recovered pasa_asmbl_31544.p1, internal, 28029, 28079
-recovered pasa_asmbl_31544.p1, internal, 28316, 28387
-recovered pasa_asmbl_31544.p1, internal, 28489, 28557
-recovered pasa_asmbl_31544.p1, internal, 28821, 28880
-recovered pasa_asmbl_31544.p1, internal, 29032, 29091
-recovered pasa_asmbl_31544.p1, internal, 29775, 29852
-recovered pasa_asmbl_31544.p1, internal, 30626, 30735
-recovered pasa_asmbl_31544.p1, internal, 30825, 30964
-recovered pasa_asmbl_31544.p1, internal, 31203, 31287
-recovered pasa_asmbl_31544.p1, internal, 31399, 31543
-recovered pasa_asmbl_31544.p1, internal, 31913, 31992
-recovered pasa_asmbl_31544.p1, internal, 32103, 32226
-recovered pasa_asmbl_31544.p1, internal, 32570, 32766
-recovered pasa_asmbl_31544.p1, internal, 32908, 33081
-recovered pasa_asmbl_31544.p1, internal, 33206, 33337
-recovered pasa_asmbl_31544.p1, internal, 33606, 33858
-recovered pasa_asmbl_31544.p1, internal, 33975, 34114
-recovered pasa_asmbl_31544.p1, internal, 34239, 34338
Valid prediction for GeneMark_model.90432_t
Valid prediction for snap_scaffold_23-snap.755-T1
Valid prediction for GeneMark_model.90443_t
Valid prediction for snap_scaffold_23-snap.765-T1
Valid prediction for pasa_asmbl_31543.p1
Couldn't classify 29838, 29853
Sorry, prediction CodingQuarry_transcript_35552-T1 fails validation.
(ATG)	 CT	29838-29853	TA	AGT
(AAT)	 AG	30626-30735	GT	AGG
(GGC)	 AG	30825-30964	GT	CAG
(CGA)	 AG	31203-31287	GT	GGG
(TTG)	 AG	31399-31543	GT	TGG
(GTA)	 AG	31913-31992	GT	AGG
(ATG)	 AG	32103-32226	GT	TGG
(GTG)	 AG	32570-32766	GT	TGG
(GGT)	 AG	32908-33081	GT	CTG
(GTA)	 AG	33206-33337	GT	GGG
(GCC)	 AG	33606-33858	GT	AAG
(GCA)	 AG	33975-34114	GT	AGG
(GTG)	 AG	34239-34338	GT	TGG
(CTG)	 AG	34473-35041	AG	AAA
-recovered CodingQuarry_transcript_35552-T1, initial, 32103, 32226
-recovered CodingQuarry_transcript_35552-T1, terminal, 34473, 35041
-recovered CodingQuarry_transcript_35552-T1, internal, 30626, 30735
-recovered CodingQuarry_transcript_35552-T1, internal, 30825, 30964
-recovered CodingQuarry_transcript_35552-T1, internal, 31203, 31287
-recovered CodingQuarry_transcript_35552-T1, internal, 31399, 31543
-recovered CodingQuarry_transcript_35552-T1, internal, 31913, 31992
-recovered CodingQuarry_transcript_35552-T1, internal, 32103, 32226
-recovered CodingQuarry_transcript_35552-T1, internal, 32570, 32766
-recovered CodingQuarry_transcript_35552-T1, internal, 32908, 33081
-recovered CodingQuarry_transcript_35552-T1, internal, 33206, 33337
-recovered CodingQuarry_transcript_35552-T1, internal, 33606, 33858
-recovered CodingQuarry_transcript_35552-T1, internal, 33975, 34114
-recovered CodingQuarry_transcript_35552-T1, internal, 34239, 34338
Valid prediction for HiQ_model.g35015.t1
Valid prediction for snap_scaffold_23-snap.758-T1
Valid prediction for GeneMark_model.90442_t
Valid prediction for GeneMark_model.90415_t
Valid prediction for GeneMark_model.90418_t
Valid prediction for snap_scaffold_23-snap.771-T1
Valid prediction for GeneMark_model.90447_t
Valid prediction for GeneMark_model.90421_t
Valid prediction for Augustus_model.g35014.t1
Valid prediction for GeneMark_model.90426_t
Valid prediction for Augustus_model.g35011.t1
Valid prediction for snap_scaffold_23-snap.749-T1
Valid prediction for GlimmerHMM_glimmerT_52086-T1
Valid prediction for snap_scaffold_23-snap.763-T1
Valid prediction for GeneMark_model.90416_t
Valid prediction for GlimmerHMM_glimmerT_52092-T1
Valid prediction for GlimmerHMM_glimmerT_52079-T1
Valid prediction for GeneMark_model.90427_t
Valid prediction for snap_scaffold_23-snap.769-T1
Valid prediction for GlimmerHMM_glimmerT_52090-T1
Valid prediction for GlimmerHMM_glimmerT_52094-T1
Valid prediction for GeneMark_model.90444_t
Valid prediction for GlimmerHMM_glimmerT_52082-T1
Valid prediction for Augustus_model.g35010.t1
Valid prediction for GeneMark_model.90429_t
Valid prediction for snap_scaffold_23-snap.766-T1
Valid prediction for Augustus_model.g35018.t1
Valid prediction for GlimmerHMM_glimmerT_52096-T1
Valid prediction for snap_scaffold_23-snap.772-T1
Valid prediction for Augustus_model.g35016.t1
Valid prediction for GlimmerHMM_glimmerT_52078-T1
Valid prediction for GlimmerHMM_glimmerT_52089-T1
Valid prediction for snap_scaffold_23-snap.751-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 279247, rend_intergenic: 275802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 280885
-exon list size: 434


building trellis

0.2    
0.5    
0.7    
0.9    
1.1    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.4    
3.7    
3.9    
4.1    
4.4    
4.6    
4.8    
5.0    
5.3    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.3    
7.6    
7.8    
8.0    
8.3    
8.5    
8.7    
8.9    
9.2    
9.4    
9.6    
9.9    
10.1    
10.3    
10.6    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.2    
12.4    
12.6    
12.8    
13.1    
13.3    
13.5    
13.8    
14.0    
14.2    
14.4    
14.7    
14.9    
15.1    
15.4    
15.6    
15.8    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.7    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.2    
23.4    
23.6    
23.9    
24.1    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.8    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.4    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.7    
58.9    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.9    
74.1    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.3    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 279247, rend_intergenic: 275802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 22117
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 1 - 21971
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-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 1 - 11180
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 1 - 10971
-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 11188 - 21971
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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