-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_8/scaffold_8_15685514-15846583

-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_8-snap.2879-T1
Valid prediction for GeneMark_model.36644_t
Valid prediction for GeneMark_model.36624_t
Valid prediction for CodingQuarry_transcript_59762-T1
Valid prediction for HiQ_model.g14363.t1
Valid prediction for Augustus_model.g14369.t1
Valid prediction for CodingQuarry_transcript_59763-T1
Valid prediction for snap_scaffold_8-snap.2870-T1
Valid prediction for GlimmerHMM_glimmerT_21471-T1
Valid prediction for snap_scaffold_8-snap.2890-T1
Valid prediction for snap_scaffold_8-snap.2884-T1
Valid prediction for Augustus_model.g14366.t1
Valid prediction for GeneMark_model.36629_t
Valid prediction for GeneMark_model.36639_t
Couldn't classify 54250, 54372
Sorry, prediction pasa_asmbl_52412.p1 fails validation.
(AGA)	 GC	54250-54372	GT	ATG
(TCG)	 AG	54507-54734	GT	AGG
(AAA)	 AG	54996-55175	GT	AGG
(GTG)	 AG	55391-55535	GT	AGG
(GTG)	 AG	55677-55796	GT	CGG
(TGT)	 AG	55901-56046	GT	AGG
(GTG)	 AG	56188-56277	GT	AGG
(GCA)	 AG	56696-56851	GT	AGG
(GGC)	 AG	57051-57110	AG	GAA
add_exon() Sorry, pasa_asmbl_52412.p1 55391-55535-terminal-3 is invalid.
-recovered pasa_asmbl_52412.p1, terminal, 55391, 55535
-recovered pasa_asmbl_52412.p1, terminal, 57051, 57110
-recovered pasa_asmbl_52412.p1, internal, 54507, 54734
-recovered pasa_asmbl_52412.p1, internal, 54996, 55175
-recovered pasa_asmbl_52412.p1, internal, 55391, 55535
-recovered pasa_asmbl_52412.p1, internal, 55677, 55796
-recovered pasa_asmbl_52412.p1, internal, 55901, 56046
-recovered pasa_asmbl_52412.p1, internal, 56188, 56277
-recovered pasa_asmbl_52412.p1, internal, 56696, 56851
Valid prediction for Augustus_model.g14364.t1
Valid prediction for snap_scaffold_8-snap.2888-T1
Valid prediction for snap_scaffold_8-snap.2869-T1
Valid prediction for GeneMark_model.36635_t
Valid prediction for snap_scaffold_8-snap.2881-T1
Valid prediction for GeneMark_model.36637_t
Valid prediction for snap_scaffold_8-snap.2871-T1
Couldn't classify 77362, 77452
Sorry, prediction pasa_asmbl_52414.p1 fails validation.
(CAG)	 TG	77362-77452	GT	CAG
(TTC)	 AG	77886-77988	GT	AGG
(CTT)	 AG	79573-79681	GT	AGG
(GTG)	 AG	80751-80869	GT	AGG
(GAA)	 AG	81096-81183	GT	GAG
-recovered pasa_asmbl_52414.p1, terminal, 81096, 81183
-recovered pasa_asmbl_52414.p1, internal, 77886, 77988
-recovered pasa_asmbl_52414.p1, internal, 79573, 79681
-recovered pasa_asmbl_52414.p1, internal, 80751, 80869
-recovered pasa_asmbl_52414.p1, internal, 81096, 81183
Valid prediction for Augustus_model.g14357.t1
Couldn't classify 8106, 8436
Sorry, prediction pasa_asmbl_52407.p1 fails validation.
(GAG)	 CA	8106-8436	GT	GGG
(GGA)	 AG	9010-9191	AC	GAA
-recovered pasa_asmbl_52407.p1, terminal, 9010, 9191
Valid prediction for snap_scaffold_8-snap.2867-T1
Valid prediction for GeneMark_model.36641_t
Valid prediction for Augustus_model.g14361.t1
Valid prediction for Augustus_model.g14367.t1
Valid prediction for GlimmerHMM_glimmerT_21473-T1
Valid prediction for snap_scaffold_8-snap.2865-T1
Valid prediction for GeneMark_model.36614_t
Valid prediction for GeneMark_model.36616_t
Valid prediction for GeneMark_model.36636_t
Valid prediction for GlimmerHMM_glimmerT_21470-T1
Valid prediction for GlimmerHMM_glimmerT_21460-T1
Valid prediction for GeneMark_model.36645_t
Valid prediction for GeneMark_model.36633_t
Valid prediction for GlimmerHMM_glimmerT_21461-T1
Valid prediction for GeneMark_model.36626_t
Valid prediction for GlimmerHMM_glimmerT_21464-T1
Valid prediction for snap_scaffold_8-snap.2883-T1
Valid prediction for GeneMark_model.36631_t
Valid prediction for snap_scaffold_8-snap.2886-T1
Couldn't classify 7167, 7696
Sorry, prediction pasa_asmbl_52405.p1 fails validation.
(ATG)	 CC	6109-6345	GT	CGG
(ATC)	 AG	6872-7013	GT	CGG
(GCC)	 AG	7167-7696	CT	ACC
-recovered pasa_asmbl_52405.p1, initial, 6109, 6345
-recovered pasa_asmbl_52405.p1, internal, 6872, 7013
Valid prediction for GlimmerHMM_glimmerT_21452-T1
Valid prediction for GeneMark_model.36634_t
Valid prediction for GeneMark_model.36623_t
Valid prediction for GeneMark_model.36646_t
Valid prediction for pasa_asmbl_52408.p1
Couldn't classify 53897, 53941
Sorry, prediction pasa_asmbl_52411.p1 fails validation.
(ATG)	 CA	50193-50283	GT	AGG
(AAA)	 AG	50522-50751	GT	AGG
(GAC)	 AG	51129-51298	GT	AGG
(GAA)	 AG	51627-51741	GT	AGG
(GAC)	 AG	51852-51944	GT	AGG
(GTG)	 AG	52143-52280	GT	AGG
(GCT)	 AG	52673-52792	GT	AGG
(GAC)	 AG	52892-52999	GT	AGG
(CTG)	 AG	53186-53332	GT	TGG
(CTG)	 AG	53429-53574	GT	AAG
(GAT)	 AG	53694-53790	GT	AGG
(ATC)	 AG	53897-53941	GA	CGG
-recovered pasa_asmbl_52411.p1, initial, 50193, 50283
-recovered pasa_asmbl_52411.p1, internal, 50522, 50751
-recovered pasa_asmbl_52411.p1, internal, 51129, 51298
-recovered pasa_asmbl_52411.p1, internal, 51627, 51741
-recovered pasa_asmbl_52411.p1, internal, 51852, 51944
-recovered pasa_asmbl_52411.p1, internal, 52143, 52280
-recovered pasa_asmbl_52411.p1, internal, 52673, 52792
-recovered pasa_asmbl_52411.p1, internal, 52892, 52999
-recovered pasa_asmbl_52411.p1, internal, 53186, 53332
-recovered pasa_asmbl_52411.p1, internal, 53429, 53574
-recovered pasa_asmbl_52411.p1, internal, 53694, 53790
Valid prediction for GeneMark_model.36638_t
Valid prediction for GeneMark_model.36621_t
Valid prediction for snap_scaffold_8-snap.2895-T1
Valid prediction for HiQ_model.g14362.t1
Valid prediction for snap_scaffold_8-snap.2873-T1
Valid prediction for GeneMark_model.36643_t
Valid prediction for GlimmerHMM_glimmerT_21453-T1
Valid prediction for GeneMark_model.36619_t
Valid prediction for GeneMark_model.36632_t
Valid prediction for snap_scaffold_8-snap.2875-T1
Valid prediction for snap_scaffold_8-snap.2874-T1
Valid prediction for GlimmerHMM_glimmerT_21457-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_21463-T1
Valid prediction for snap_scaffold_8-snap.2892-T1
Valid prediction for GeneMark_model.36618_t
Valid prediction for GlimmerHMM_glimmerT_21475-T1
Valid prediction for snap_scaffold_8-snap.2877-T1
Valid prediction for GlimmerHMM_glimmerT_21455-T1
Couldn't classify 158632, 158697
Sorry, prediction pasa_asmbl_53343.p1 fails validation.
(CAA)	 CA	158632-158697	GT	TGG
(GGC)	 AG	159429-159520	GT	AGG
(AAC)	 AG	160333-160498	CT	AAC
-recovered pasa_asmbl_53343.p1, terminal, 160333, 160498
-recovered pasa_asmbl_53343.p1, internal, 159429, 159520
Valid prediction for Augustus_model.g14368.t1
Valid prediction for snap_scaffold_8-snap.2868-T1
Valid prediction for GeneMark_model.36620_t
Valid prediction for Augustus_model.g14358.t1
Couldn't classify 116263, 117147
Sorry, prediction pasa_asmbl_53348.p1 fails validation.
(ATG)	 AC	116263-117147	GA	GGG
Couldn't classify 141339, 141568
Sorry, prediction pasa_asmbl_53345.p1 fails validation.
(GGC)	 TA	141339-141568	GT	AGG
(CTG)	 AG	141723-141814	GT	AGG
(GTG)	 AG	142061-142221	GT	AGG
(GGT)	 AG	142566-142700	GT	ATG
(GTG)	 AG	143605-143716	GT	CTG
(ACC)	 AG	143940-144053	GT	AGG
(ATT)	 AG	144805-145004	GT	AGG
(GCG)	 AG	145649-145852	GT	AGG
(GTG)	 AG	146012-146173	GT	AGG
(GGA)	 AG	146276-146525	GT	AAG
(AAA)	 AG	146723-146934	CA	AGC
-recovered pasa_asmbl_53345.p1, terminal, 146723, 146934
-recovered pasa_asmbl_53345.p1, internal, 141723, 141814
-recovered pasa_asmbl_53345.p1, internal, 142061, 142221
-recovered pasa_asmbl_53345.p1, internal, 142566, 142700
-recovered pasa_asmbl_53345.p1, internal, 143605, 143716
-recovered pasa_asmbl_53345.p1, internal, 143940, 144053
-recovered pasa_asmbl_53345.p1, internal, 144805, 145004
-recovered pasa_asmbl_53345.p1, internal, 145649, 145852
-recovered pasa_asmbl_53345.p1, internal, 146012, 146173
-recovered pasa_asmbl_53345.p1, internal, 146276, 146525
Valid prediction for GlimmerHMM_glimmerT_21458-T1
Valid prediction for GlimmerHMM_glimmerT_21454-T1
Valid prediction for snap_scaffold_8-snap.2882-T1
Valid prediction for GlimmerHMM_glimmerT_21456-T1
Valid prediction for Augustus_model.g14360.t1
Valid prediction for Augustus_model.g14365.t1
Valid prediction for GeneMark_model.36630_t
Valid prediction for snap_scaffold_8-snap.2893-T1
Valid prediction for GeneMark_model.36640_t
Valid prediction for snap_scaffold_8-snap.2878-T1
Valid prediction for GlimmerHMM_glimmerT_21472-T1
Valid prediction for snap_scaffold_8-snap.2894-T1
Valid prediction for snap_scaffold_8-snap.2896-T1
Valid prediction for GeneMark_model.36617_t
Valid prediction for GeneMark_model.36642_t
Valid prediction for GeneMark_model.36622_t
Valid prediction for Augustus_model.g14370.t1
Valid prediction for GeneMark_model.36625_t
Valid prediction for snap_scaffold_8-snap.2887-T1
Valid prediction for GlimmerHMM_glimmerT_21468-T1
Valid prediction for GlimmerHMM_glimmerT_21469-T1
Couldn't classify 138774, 138827
Couldn't classify 141096, 141135
Sorry, prediction pasa_asmbl_53347.p1 fails validation.
(CAG)	 TT	138774-138827	GT	AGG
(GGT)	 AG	139866-140114	GT	AGG
(GGG)	 AG	140372-140514	GT	AGG
(TCC)	 AG	141096-141135	AC	TGA
add_exon() Sorry, pasa_asmbl_53347.p1 140372-140514-terminal-2 is invalid.
-recovered pasa_asmbl_53347.p1, terminal, 140372, 140514
-recovered pasa_asmbl_53347.p1, internal, 139866, 140114
-recovered pasa_asmbl_53347.p1, internal, 140372, 140514
Valid prediction for snap_scaffold_8-snap.2889-T1
Valid prediction for GlimmerHMM_glimmerT_21474-T1
Valid prediction for Augustus_model.g14359.t1
Valid prediction for snap_scaffold_8-snap.2885-T1
Valid prediction for GlimmerHMM_glimmerT_21466-T1
Valid prediction for snap_scaffold_8-snap.2866-T1
Valid prediction for GeneMark_model.36615_t
Valid prediction for GlimmerHMM_glimmerT_21459-T1
Valid prediction for GlimmerHMM_glimmerT_21467-T1
Valid prediction for GeneMark_model.36628_t
Valid prediction for GlimmerHMM_glimmerT_21465-T1
Valid prediction for GeneMark_model.36627_t
Valid prediction for snap_scaffold_8-snap.2891-T1
Valid prediction for snap_scaffold_8-snap.2872-T1
Valid prediction for snap_scaffold_8-snap.2880-T1
Valid prediction for snap_scaffold_8-snap.2876-T1
Valid prediction for GlimmerHMM_glimmerT_21462-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9191, rend_intergenic: 7163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13292, rend_intergenic: 12463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15530, rend_intergenic: 14137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27375, rend_intergenic: 16382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57110, rend_intergenic: 51071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72308, rend_intergenic: 70227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78083, rend_intergenic: 75547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81183, rend_intergenic: 78263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104643, rend_intergenic: 98712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109155, rend_intergenic: 104921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111656, rend_intergenic: 109775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126979, rend_intergenic: 117856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161070
-exon list size: 489


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.2    
2.4    
2.6    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.6    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 9191, rend_intergenic: 7163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13292, rend_intergenic: 12463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15530, rend_intergenic: 14137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27375, rend_intergenic: 16382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57110, rend_intergenic: 51071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72308, rend_intergenic: 70227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78083, rend_intergenic: 75547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81183, rend_intergenic: 78263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104643, rend_intergenic: 98712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109155, rend_intergenic: 104921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111656, rend_intergenic: 109775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126979, rend_intergenic: 117856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support