-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_4367114-4531764

-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.925-T1
Valid prediction for Augustus_model.g30449.t1
Valid prediction for snap_scaffold_20-snap.940-T1
Couldn't classify 1541, 1687
Sorry, prediction pasa_asmbl_26580.p1 fails validation.
(CCT)	 AG	1541-1687	GT	AGG
(GCC)	 AG	2283-2414	GT	AGG
(AAG)	 AG	2552-2631	GT	CAG
(CTA)	 AG	2805-3549	GT	ACG
(GAA)	 AG	3741-3839	GT	AGG
(GCG)	 AG	3928-4570	GT	AGG
(TTT)	 AG	4654-4761	GT	AGG
(GGG)	 AG	5734-5855	GT	AGG
(AAG)	 AG	7568-7630	CC	GAC
add_exon() Sorry, pasa_asmbl_26580.p1 4654-4761-terminal-1 is invalid.
-recovered pasa_asmbl_26580.p1, terminal, 4654, 4761
-recovered pasa_asmbl_26580.p1, terminal, 7568, 7630
-recovered pasa_asmbl_26580.p1, internal, 1541, 1687
-recovered pasa_asmbl_26580.p1, internal, 2283, 2414
-recovered pasa_asmbl_26580.p1, internal, 2552, 2631
-recovered pasa_asmbl_26580.p1, internal, 2805, 3549
-recovered pasa_asmbl_26580.p1, internal, 3741, 3839
-recovered pasa_asmbl_26580.p1, internal, 3928, 4570
-recovered pasa_asmbl_26580.p1, internal, 4654, 4761
-recovered pasa_asmbl_26580.p1, internal, 5734, 5855
Valid prediction for snap_scaffold_20-snap.945-T1
Valid prediction for GlimmerHMM_glimmerT_45873-T1
Valid prediction for snap_scaffold_20-snap.926-T1
Valid prediction for snap_scaffold_20-snap.954-T1
Valid prediction for HiQ_model.g30445.t1
Valid prediction for GlimmerHMM_glimmerT_45870-T1
Valid prediction for GlimmerHMM_glimmerT_45869-T1
Valid prediction for snap_scaffold_20-snap.942-T1
Valid prediction for snap_scaffold_20-snap.918-T1
Valid prediction for snap_scaffold_20-snap.921-T1
Valid prediction for GlimmerHMM_glimmerT_45880-T1
Couldn't classify 26525, 27034
Sorry, prediction pasa_asmbl_26588.p2 fails validation.
(ATG)	 TC	26525-27034	TC	ACT
Valid prediction for snap_scaffold_20-snap.949-T1
Valid prediction for snap_scaffold_20-snap.939-T1
Valid prediction for Augustus_model.g30454.t1
Valid prediction for HiQ_model.g30444.t1
Valid prediction for pasa_asmbl_26585.p1
Valid prediction for GlimmerHMM_glimmerT_45886-T1
Valid prediction for snap_scaffold_20-snap.923-T1
Valid prediction for snap_scaffold_20-snap.946-T1
Valid prediction for GlimmerHMM_glimmerT_45866-T1
Valid prediction for snap_scaffold_20-snap.922-T1
Valid prediction for Augustus_model.g30447.t1
Valid prediction for GlimmerHMM_glimmerT_45867-T1
Valid prediction for GlimmerHMM_glimmerT_45872-T1
Valid prediction for snap_scaffold_20-snap.948-T1
Valid prediction for CodingQuarry_transcript_30494-T1
Valid prediction for snap_scaffold_20-snap.947-T1
Valid prediction for GlimmerHMM_glimmerT_45879-T1
Valid prediction for Augustus_model.g30448.t1
Valid prediction for snap_scaffold_20-snap.924-T1
Couldn't classify 28710, 28841
Couldn't classify 30594, 30718
Sorry, prediction pasa_asmbl_26589.p1 fails validation.
(GGT)	 CA	28710-28841	GT	AGG
(GGC)	 AG	29047-29235	GT	AGG
(GAC)	 AG	29492-29614	GT	AGG
(GTG)	 AG	30059-30196	GT	AGG
(AAA)	 AG	30318-30435	GT	CGG
(GTA)	 AG	30594-30718	CT	ACC
-recovered pasa_asmbl_26589.p1, internal, 29047, 29235
-recovered pasa_asmbl_26589.p1, internal, 29492, 29614
-recovered pasa_asmbl_26589.p1, internal, 30059, 30196
-recovered pasa_asmbl_26589.p1, internal, 30318, 30435

-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_45875-T1
Valid prediction for snap_scaffold_20-snap.938-T1
Valid prediction for GlimmerHMM_glimmerT_45874-T1
Valid prediction for Augustus_model.g30451.t1
Valid prediction for GlimmerHMM_glimmerT_45882-T1
Valid prediction for Augustus_model.g30450.t1
Valid prediction for GlimmerHMM_glimmerT_45871-T1
Couldn't classify 34999, 35131
Couldn't classify 36020, 36193
Sorry, prediction pasa_asmbl_26323.p1 fails validation.
(GTG)	 GT	34999-35131	GT	CTG
(GCA)	 AG	35537-35637	GT	GGG
(TCT)	 AG	36020-36193	CC	TAC
-recovered pasa_asmbl_26323.p1, internal, 35537, 35637
Valid prediction for snap_scaffold_20-snap.929-T1
Valid prediction for snap_scaffold_20-snap.928-T1
Couldn't classify 20129, 20155
Sorry, prediction pasa_asmbl_25746.p2 fails validation.
(AGA)	 GT	20129-20155	GT	AGG
(ATG)	 AG	20716-20846	GT	AAG
(GCT)	 AG	21072-21168	GT	AGG
(TTC)	 AG	21436-21507	GT	CAG
(AAC)	 AG	21640-21702	GT	AGG
(TTG)	 AG	21848-21979	TC	AAT
-recovered pasa_asmbl_25746.p2, initial, 20716, 20846
-recovered pasa_asmbl_25746.p2, terminal, 21848, 21979
-recovered pasa_asmbl_25746.p2, internal, 20716, 20846
-recovered pasa_asmbl_25746.p2, internal, 21072, 21168
-recovered pasa_asmbl_25746.p2, internal, 21436, 21507
-recovered pasa_asmbl_25746.p2, internal, 21640, 21702
Valid prediction for snap_scaffold_20-snap.920-T1
Valid prediction for GlimmerHMM_glimmerT_45884-T1
Valid prediction for Augustus_model.g30457.t1
Valid prediction for snap_scaffold_20-snap.932-T1
Couldn't classify 47386, 47512
Sorry, prediction pasa_asmbl_25737.p1 fails validation.
(CCT)	 CC	47386-47512	GT	AGG
(GGT)	 AG	49981-50097	GC	AGG
(CGG)	 AG	51961-52109	GT	AGG
(GTC)	 AG	52452-52604	GT	ACG
(GAT)	 AG	53055-53171	GT	ACG
(ACG)	 AG	53390-53477	GT	CGG
(AGG)	 AG	53709-53872	GT	CGG
(GAT)	 AG	53989-54054	CA	GAC
-recovered pasa_asmbl_25737.p1, terminal, 53989, 54054
-recovered pasa_asmbl_25737.p1, internal, 49981, 50097
-recovered pasa_asmbl_25737.p1, internal, 51961, 52109
-recovered pasa_asmbl_25737.p1, internal, 52452, 52604
-recovered pasa_asmbl_25737.p1, internal, 53055, 53171
-recovered pasa_asmbl_25737.p1, internal, 53390, 53477
-recovered pasa_asmbl_25737.p1, internal, 53709, 53872
Valid prediction for snap_scaffold_20-snap.951-T1
Valid prediction for snap_scaffold_20-snap.927-T1
Valid prediction for snap_scaffold_20-snap.935-T1
Valid prediction for GlimmerHMM_glimmerT_45876-T1
Valid prediction for GlimmerHMM_glimmerT_45878-T1
Valid prediction for snap_scaffold_20-snap.950-T1
Valid prediction for snap_scaffold_20-snap.944-T1
Couldn't classify 40943, 41093
Couldn't classify 44030, 44104
Sorry, prediction pasa_asmbl_26333.p1 fails validation.
(GGT)	 AA	40943-41093	GT	AGG
(GAC)	 AG	41214-41277	GT	AGG
(TAT)	 AG	41493-41661	GT	AGG
(CTG)	 AG	41963-42145	GT	TGG
(AGG)	 AG	42402-42520	GT	AGG
(AGG)	 AG	43000-43156	GT	AGG
(GCA)	 AG	43716-43832	GT	AGG
(GAC)	 AG	44030-44104	TG	AGT
-recovered pasa_asmbl_26333.p1, internal, 41214, 41277
-recovered pasa_asmbl_26333.p1, internal, 41493, 41661
-recovered pasa_asmbl_26333.p1, internal, 41963, 42145
-recovered pasa_asmbl_26333.p1, internal, 42402, 42520
-recovered pasa_asmbl_26333.p1, internal, 43000, 43156
-recovered pasa_asmbl_26333.p1, internal, 43716, 43832
Valid prediction for snap_scaffold_20-snap.919-T1
Valid prediction for snap_scaffold_20-snap.941-T1
Valid prediction for snap_scaffold_20-snap.955-T1
Valid prediction for snap_scaffold_20-snap.933-T1
Valid prediction for snap_scaffold_20-snap.917-T1
Valid prediction for Augustus_model.g30446.t1
Valid prediction for snap_scaffold_20-snap.937-T1
Valid prediction for snap_scaffold_20-snap.952-T1
Valid prediction for Augustus_model.g30453.t1
Valid prediction for GlimmerHMM_glimmerT_45868-T1
Valid prediction for snap_scaffold_20-snap.953-T1
Valid prediction for GlimmerHMM_glimmerT_45885-T1
Valid prediction for snap_scaffold_20-snap.936-T1
Valid prediction for GlimmerHMM_glimmerT_45881-T1
Valid prediction for HiQ_model.g30456.t1
Valid prediction for snap_scaffold_20-snap.943-T1
Valid prediction for snap_scaffold_20-snap.931-T1
Valid prediction for GlimmerHMM_glimmerT_45883-T1
Valid prediction for Augustus_model.g30452.t1
Valid prediction for CodingQuarry_transcript_30495-T1
Valid prediction for snap_scaffold_20-snap.934-T1
Valid prediction for GlimmerHMM_glimmerT_45877-T1
Valid prediction for Augustus_model.g30455.t1
Valid prediction for CodingQuarry_transcript_30496-T1
Valid prediction for snap_scaffold_20-snap.930-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19433, rend_intergenic: 12508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114052, rend_intergenic: 110112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137746, rend_intergenic: 115968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157983, rend_intergenic: 154272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164651
-exon list size: 324


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.1    
6.4    
6.7    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.1    
10.4    
10.7    
11.0    
11.3    
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    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
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    
25.2    
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    
29.8    
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    
34.4    
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    
38.7    
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    
43.3    
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    
47.9    
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    
52.5    
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    
57.1    
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    
61.7    
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    
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    
70.2    
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    
75.2    
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    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
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    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
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: 19433, rend_intergenic: 12508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114052, rend_intergenic: 110112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137746, rend_intergenic: 115968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157983, rend_intergenic: 154272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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