-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_12044571-12284940

-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_6-snap.2567-T1
Valid prediction for snap_scaffold_6-snap.2563-T1
Valid prediction for snap_scaffold_6-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_15973-T1
Valid prediction for GeneMark_model.26786_t
Valid prediction for GlimmerHMM_glimmerT_15947-T1
Valid prediction for GlimmerHMM_glimmerT_15959-T1
Valid prediction for GlimmerHMM_glimmerT_15971-T1
Valid prediction for GlimmerHMM_glimmerT_15943-T1
Valid prediction for HiQ_model.g10715.t1
Valid prediction for GlimmerHMM_glimmerT_15957-T1
Valid prediction for GlimmerHMM_glimmerT_15968-T1
Valid prediction for snap_scaffold_6-snap.2546-T1
Valid prediction for GlimmerHMM_glimmerT_15963-T1
Valid prediction for pasa_asmbl_47313.p1
Valid prediction for GlimmerHMM_glimmerT_15976-T1
Valid prediction for snap_scaffold_6-snap.2543-T1
Valid prediction for Augustus_model.g10726.t1
Valid prediction for Augustus_model.g10724.t1
Valid prediction for HiQ_model.g10725.t1
Valid prediction for GlimmerHMM_glimmerT_15984-T1
Couldn't classify 197226, 197396
Sorry, prediction pasa_asmbl_47325.p1 fails validation.
(ATG)	 CC	196217-196220	GT	GGG
(GTT)	 AG	196761-196909	GT	AGG
(GTT)	 AG	196981-197118	GT	AGG
(CAT)	 AG	197226-197396	AT	TGA
-recovered pasa_asmbl_47325.p1, initial, 196217, 196220
-recovered pasa_asmbl_47325.p1, internal, 196761, 196909
-recovered pasa_asmbl_47325.p1, internal, 196981, 197118
Valid prediction for snap_scaffold_6-snap.2571-T1
Valid prediction for GlimmerHMM_glimmerT_15966-T1
Valid prediction for snap_scaffold_6-snap.2544-T1
Valid prediction for snap_scaffold_6-snap.2569-T1
Valid prediction for Augustus_model.g10719.t1
Valid prediction for HiQ_model.g10723.t1
Valid prediction for snap_scaffold_6-snap.2560-T1
Valid prediction for snap_scaffold_6-snap.2559-T1
Valid prediction for GlimmerHMM_glimmerT_15955-T1
Valid prediction for Augustus_model.g10721.t1
Valid prediction for GeneMark_model.26799_t
Valid prediction for CodingQuarry_transcript_55099-T1
Valid prediction for GlimmerHMM_glimmerT_15950-T1
Valid prediction for Augustus_model.g10718.t1
Valid prediction for GeneMark_model.26781_t
Valid prediction for GeneMark_model.26796_t
Valid prediction for Augustus_model.g10713.t1
Valid prediction for snap_scaffold_6-snap.2566-T1
Valid prediction for GeneMark_model.26776_t
Valid prediction for Augustus_model.g10708.t1
Valid prediction for HiQ_model.g10707.t1
Valid prediction for Augustus_model.g10709.t1
Couldn't classify 204420, 204566
Sorry, prediction pasa_asmbl_47326.p1 fails validation.
(GCA)	 AG	204420-204566	GT	AGG
(GCA)	 AG	204649-204760	GT	AGG
(GTG)	 AG	205008-205129	AA	AAA
-recovered pasa_asmbl_47326.p1, terminal, 205008, 205129
-recovered pasa_asmbl_47326.p1, internal, 204420, 204566
-recovered pasa_asmbl_47326.p1, internal, 204649, 204760
Couldn't classify 181964, 182062
Couldn't classify 188698, 188760
Sorry, prediction pasa_asmbl_47324.p1 fails validation.
(GGG)	 TA	181964-182062	GT	AGG
(GAA)	 AG	182459-182488	GT	AGG
(AAT)	 AG	184687-184804	GT	TGG
(GAT)	 AG	186771-186820	GT	TGG
(AGT)	 AG	186928-187008	GT	CGG
(ATT)	 AG	187319-187411	GT	GGG
(AAC)	 AG	188698-188760	GT	AGG
-recovered pasa_asmbl_47324.p1, internal, 182459, 182488
-recovered pasa_asmbl_47324.p1, internal, 184687, 184804
-recovered pasa_asmbl_47324.p1, internal, 186771, 186820
-recovered pasa_asmbl_47324.p1, internal, 186928, 187008
-recovered pasa_asmbl_47324.p1, internal, 187319, 187411
-recovered pasa_asmbl_47324.p1, internal, 188698, 188760
Valid prediction for GlimmerHMM_glimmerT_15962-T1
Valid prediction for GeneMark_model.26788_t
Valid prediction for snap_scaffold_6-snap.2572-T1
Valid prediction for snap_scaffold_6-snap.2534-T1
Valid prediction for Augustus_model.g10696.t1
Valid prediction for snap_scaffold_6-snap.2537-T1
Couldn't classify 131829, 131872
Couldn't classify 141190, 141277
Sorry, prediction pasa_asmbl_47315.p1 fails validation.
(CGA)	 GG	131829-131872	GT	AGG
(GAG)	 AG	134485-134630	GT	AGG
(TCT)	 AG	135283-135505	GT	AGG
(GCC)	 AG	135774-135904	GT	AGG
(AAC)	 AG	136125-136165	GT	AGG
(GTT)	 AG	136954-137098	GT	AGG
(ATA)	 AG	139786-139857	GT	AGG
(GTG)	 AG	140122-140175	GT	AGG
(ATG)	 AG	140355-140429	GT	TGG
(TGT)	 AG	140652-140754	GT	AGG
(GCT)	 AG	141190-141277	GG	TGG
add_exon() Sorry, pasa_asmbl_47315.p1 140355-140429-initial-1 is invalid.
-recovered pasa_asmbl_47315.p1, initial, 140355, 140429
add_exon() Sorry, pasa_asmbl_47315.p1 135774-135904-terminal-2 is invalid.
-recovered pasa_asmbl_47315.p1, terminal, 135774, 135904
-recovered pasa_asmbl_47315.p1, internal, 134485, 134630
-recovered pasa_asmbl_47315.p1, internal, 135283, 135505
-recovered pasa_asmbl_47315.p1, internal, 135774, 135904
-recovered pasa_asmbl_47315.p1, internal, 136125, 136165
-recovered pasa_asmbl_47315.p1, internal, 136954, 137098
-recovered pasa_asmbl_47315.p1, internal, 139786, 139857
-recovered pasa_asmbl_47315.p1, internal, 140122, 140175
-recovered pasa_asmbl_47315.p1, internal, 140355, 140429
-recovered pasa_asmbl_47315.p1, internal, 140652, 140754
Valid prediction for Augustus_model.g10705.t1
Valid prediction for GeneMark_model.26801_t
Valid prediction for snap_scaffold_6-snap.2549-T1
Valid prediction for Augustus_model.g10699.t1
Valid prediction for GlimmerHMM_glimmerT_15980-T1
Valid prediction for Augustus_model.g10703.t1
Valid prediction for GeneMark_model.26807_t
Valid prediction for GeneMark_model.26794_t
Valid prediction for GlimmerHMM_glimmerT_15978-T1
Valid prediction for snap_scaffold_6-snap.2547-T1
Valid prediction for GeneMark_model.26783_t
Valid prediction for snap_scaffold_6-snap.2548-T1
Valid prediction for GlimmerHMM_glimmerT_15961-T1
Valid prediction for GeneMark_model.26803_t
Valid prediction for GlimmerHMM_glimmerT_15983-T1
Valid prediction for GeneMark_model.26789_t
Valid prediction for Augustus_model.g10697.t1
Valid prediction for GeneMark_model.26787_t
Valid prediction for GlimmerHMM_glimmerT_15974-T1
Valid prediction for GlimmerHMM_glimmerT_15948-T1
Valid prediction for Augustus_model.g10722.t1
Valid prediction for snap_scaffold_6-snap.2541-T1
Valid prediction for GlimmerHMM_glimmerT_15952-T1
Valid prediction for GlimmerHMM_glimmerT_15954-T1
Valid prediction for GlimmerHMM_glimmerT_15945-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_6-snap.2550-T1
Valid prediction for snap_scaffold_6-snap.2545-T1
Couldn't classify 230440, 230519
Sorry, prediction pasa_asmbl_48720.p1 fails validation.
(AAT)	 AG	230440-230519	GT	AGG
(ATT)	 AG	231193-231364	GT	AAG
(ATA)	 AG	231543-231689	CC	AAC
-recovered pasa_asmbl_48720.p1, terminal, 231543, 231689
-recovered pasa_asmbl_48720.p1, internal, 230440, 230519
-recovered pasa_asmbl_48720.p1, internal, 231193, 231364
Valid prediction for CodingQuarry_transcript_55097-T1
Valid prediction for CodingQuarry_transcript_55098-T1
Valid prediction for HiQ_model.g10698.t1
Valid prediction for pasa_asmbl_48730.p1
Valid prediction for snap_scaffold_6-snap.2553-T1
Valid prediction for GeneMark_model.26777_t
Couldn't classify 191739, 191949
Sorry, prediction pasa_asmbl_48732.p1 fails validation.
(CAG)	 CT	191739-191949	GT	GGG
(GCG)	 AG	192298-192385	GT	AGG
(GCA)	 AG	194401-194518	CT	AGC
add_exon() Sorry, pasa_asmbl_48732.p1 192298-192385-terminal-3 is invalid.
-recovered pasa_asmbl_48732.p1, terminal, 192298, 192385
-recovered pasa_asmbl_48732.p1, terminal, 194401, 194518
-recovered pasa_asmbl_48732.p1, internal, 192298, 192385
Valid prediction for snap_scaffold_6-snap.2542-T1
Valid prediction for snap_scaffold_6-snap.2555-T1
Valid prediction for snap_scaffold_6-snap.2564-T1
Valid prediction for GlimmerHMM_glimmerT_15975-T1
Valid prediction for GeneMark_model.26778_t
Valid prediction for GlimmerHMM_glimmerT_15949-T1
Valid prediction for Augustus_model.g10710.t1
Valid prediction for GeneMark_model.26782_t
Valid prediction for Augustus_model.g10720.t1
Valid prediction for GeneMark_model.26791_t
Valid prediction for GlimmerHMM_glimmerT_15946-T1
Valid prediction for GlimmerHMM_glimmerT_15972-T1
Valid prediction for snap_scaffold_6-snap.2535-T1
Valid prediction for snap_scaffold_6-snap.2568-T1
Valid prediction for GeneMark_model.26806_t
Valid prediction for GeneMark_model.26802_t
Valid prediction for GeneMark_model.26795_t
Valid prediction for GeneMark_model.26800_t
Valid prediction for GlimmerHMM_glimmerT_15985-T1
Valid prediction for GeneMark_model.26797_t
Valid prediction for GeneMark_model.26779_t
Valid prediction for GlimmerHMM_glimmerT_15960-T1
Valid prediction for snap_scaffold_6-snap.2556-T1
Valid prediction for snap_scaffold_6-snap.2536-T1
Valid prediction for GeneMark_model.26804_t
Valid prediction for snap_scaffold_6-snap.2539-T1
Valid prediction for GlimmerHMM_glimmerT_15951-T1
Valid prediction for GlimmerHMM_glimmerT_15944-T1
Valid prediction for GlimmerHMM_glimmerT_15967-T1
Valid prediction for GeneMark_model.26805_t
Valid prediction for GeneMark_model.26790_t
Valid prediction for GlimmerHMM_glimmerT_15958-T1
Valid prediction for GlimmerHMM_glimmerT_15979-T1
Valid prediction for GeneMark_model.26780_t
Valid prediction for snap_scaffold_6-snap.2540-T1
Valid prediction for Augustus_model.g10712.t1
Valid prediction for Augustus_model.g10704.t1
Valid prediction for Augustus_model.g10717.t1
Valid prediction for snap_scaffold_6-snap.2552-T1
Valid prediction for GlimmerHMM_glimmerT_15956-T1
Valid prediction for snap_scaffold_6-snap.2538-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15977-T1
Valid prediction for snap_scaffold_6-snap.2554-T1
Valid prediction for Augustus_model.g10716.t1
Valid prediction for snap_scaffold_6-snap.2565-T1
Valid prediction for snap_scaffold_6-snap.2561-T1
Valid prediction for Augustus_model.g10700.t1
Valid prediction for GlimmerHMM_glimmerT_15969-T1
Valid prediction for GlimmerHMM_glimmerT_15982-T1
Valid prediction for GeneMark_model.26798_t
Valid prediction for GeneMark_model.26792_t
Valid prediction for GlimmerHMM_glimmerT_15981-T1
Valid prediction for snap_scaffold_6-snap.2562-T1
Valid prediction for Augustus_model.g10706.t1
Valid prediction for GlimmerHMM_glimmerT_15965-T1
Valid prediction for snap_scaffold_6-snap.2551-T1
Valid prediction for Augustus_model.g10714.t1
Valid prediction for GeneMark_model.26785_t
Valid prediction for GlimmerHMM_glimmerT_15970-T1
Valid prediction for snap_scaffold_6-snap.2570-T1
Valid prediction for Augustus_model.g10702.t1
Valid prediction for GlimmerHMM_glimmerT_15964-T1
Valid prediction for GlimmerHMM_glimmerT_15953-T1
Valid prediction for GeneMark_model.26793_t
Valid prediction for Augustus_model.g10711.t1
Valid prediction for snap_scaffold_6-snap.2558-T1
Valid prediction for Augustus_model.g10701.t1
Couldn't classify 206914, 207130
Sorry, prediction pasa_asmbl_48725.p1 fails validation.
(GAC)	 AC	206914-207130	GT	TGG
(AGT)	 AG	208046-208184	GT	AAG
(GAT)	 AG	208417-208529	GT	TGG
(GTG)	 AG	208620-208885	GT	AGG
-recovered pasa_asmbl_48725.p1, terminal, 208620, 208885
-recovered pasa_asmbl_48725.p1, internal, 208046, 208184
-recovered pasa_asmbl_48725.p1, internal, 208417, 208529
-recovered pasa_asmbl_48725.p1, internal, 208620, 208885

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 54348, rend_intergenic: 54345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240370
-exon list size: 452


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.5    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.5    
3.7    
4.0    
4.2    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.7    
5.9    
6.2    
6.4    
6.6    
6.8    
7.0    
7.3    
7.5    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.3    
9.5    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.2    
13.4    
13.7    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.5    
16.7    
17.0    
17.2    
17.4    
17.6    
17.8    
18.1    
18.3    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.8    
20.0    
20.3    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.3    
27.5    
27.8    
28.0    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.1    
34.4    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.7    
54.0    
54.2    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.3    
59.5    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.4    
63.7    
63.9    
64.1    
64.3    
64.5    
64.8    
65.0    
65.2    
65.4    
65.6    
65.9    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.0    
72.2    
72.5    
72.7    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.3    
83.5    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.3    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 54348, rend_intergenic: 54345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 216101 - 240370
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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 216274 - 240370
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 216274 - 236823
-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

-building DP trellis

-building trellis in range 223366 - 236823
-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