-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_4781849-5033788

-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: +)Couldn't classify 241260, 241301
Couldn't classify 245001, 245051
Sorry, prediction pasa_asmbl_16791.p1 fails validation.
(GCT)	 GT	241260-241301	GT	AGG
(CCA)	 AG	243116-243298	GT	AGG
(GTG)	 AG	244584-244760	GT	AGG
(TTT)	 AG	245001-245051	CG	ACC
-recovered pasa_asmbl_16791.p1, internal, 243116, 243298
-recovered pasa_asmbl_16791.p1, internal, 244584, 244760
Valid prediction for snap_scaffold_16-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_38277-T1
Valid prediction for snap_scaffold_16-snap.941-T1
Valid prediction for snap_scaffold_16-snap.931-T1
Valid prediction for GlimmerHMM_glimmerT_38302-T1
Valid prediction for GlimmerHMM_glimmerT_38294-T1
Couldn't classify 174105, 174138
Sorry, prediction pasa_asmbl_16205.p1 fails validation.
(GAA)	 CA	174105-174138	GT	AGG
(GTC)	 AG	174294-174465	GT	AGG
(GTG)	 AG	175518-175713	GT	AGG
(GAC)	 AG	177582-177792	GT	AGG
(GGG)	 AG	177891-177964	GT	AAG
(CTC)	 AG	178861-179016	GT	AGG
(ATT)	 AG	180066-180287	GC	AGG
-recovered pasa_asmbl_16205.p1, terminal, 180066, 180287
-recovered pasa_asmbl_16205.p1, internal, 174294, 174465
-recovered pasa_asmbl_16205.p1, internal, 175518, 175713
-recovered pasa_asmbl_16205.p1, internal, 177582, 177792
-recovered pasa_asmbl_16205.p1, internal, 177891, 177964
-recovered pasa_asmbl_16205.p1, internal, 178861, 179016
-recovered pasa_asmbl_16205.p1, internal, 180066, 180287
Valid prediction for snap_scaffold_16-snap.948-T1
Couldn't classify 119597, 119822
Couldn't classify 120588, 120847
Sorry, prediction pasa_asmbl_16202.p1 fails validation.
(GTG)	 GG	119597-119822	GT	AGG
(GGT)	 AG	120588-120847	TG	ACT
Valid prediction for snap_scaffold_16-snap.969-T1
Valid prediction for GlimmerHMM_glimmerT_38292-T1
Couldn't classify 236100, 236308
Couldn't classify 237407, 237554
Sorry, prediction pasa_asmbl_16745.p1 fails validation.
(GGC)	 CA	236100-236308	GT	AAG
(ACT)	 AG	237407-237554	GT	AGG
-recovered pasa_asmbl_16745.p1, internal, 237407, 237554
Valid prediction for GlimmerHMM_glimmerT_38299-T1
Valid prediction for GlimmerHMM_glimmerT_38295-T1
Valid prediction for snap_scaffold_16-snap.934-T1
Valid prediction for GlimmerHMM_glimmerT_38281-T1
Valid prediction for snap_scaffold_16-snap.965-T1
Valid prediction for Augustus_model.g25549.t1
Valid prediction for GlimmerHMM_glimmerT_38300-T1
Valid prediction for Augustus_model.g25557.t1
Valid prediction for Augustus_model.g25545.t1
Valid prediction for Augustus_model.g25558.t1
Valid prediction for GlimmerHMM_glimmerT_38286-T1
Valid prediction for snap_scaffold_16-snap.930-T1
Valid prediction for snap_scaffold_16-snap.937-T1
Valid prediction for GlimmerHMM_glimmerT_38291-T1
Valid prediction for snap_scaffold_16-snap.952-T1
Valid prediction for snap_scaffold_16-snap.936-T1
Valid prediction for snap_scaffold_16-snap.943-T1
Valid prediction for GlimmerHMM_glimmerT_38287-T1
Valid prediction for snap_scaffold_16-snap.960-T1
Valid prediction for Augustus_model.g25554.t1
Valid prediction for Augustus_model.g25548.t1
Valid prediction for GlimmerHMM_glimmerT_38276-T1
Couldn't classify 246092, 246427
Sorry, prediction pasa_asmbl_16209.p3 fails validation.
(ATC)	 GG	246092-246427	TA	AAT
Valid prediction for snap_scaffold_16-snap.959-T1
Valid prediction for snap_scaffold_16-snap.955-T1
Valid prediction for snap_scaffold_16-snap.958-T1
Couldn't classify 104951, 105048
Couldn't classify 105182, 105446
Sorry, prediction pasa_asmbl_16201.p1 fails validation.
(GTG)	 TT	104951-105048	GT	AGG
(ATG)	 AG	105182-105446	CC	AGC
Valid prediction for Augustus_model.g25556.t1
Valid prediction for snap_scaffold_16-snap.935-T1
Valid prediction for snap_scaffold_16-snap.950-T1
Valid prediction for snap_scaffold_16-snap.944-T1
Valid prediction for snap_scaffold_16-snap.963-T1
Valid prediction for Augustus_model.g25544.t1
Valid prediction for snap_scaffold_16-snap.932-T1
Valid prediction for snap_scaffold_16-snap.940-T1
Valid prediction for snap_scaffold_16-snap.942-T1
Valid prediction for GlimmerHMM_glimmerT_38280-T1
Couldn't classify 165636, 165669
Couldn't classify 166828, 167039
Sorry, prediction pasa_asmbl_16204.p1 fails validation.
(AAA)	 AG	165636-165669	GT	GAG
(TGG)	 AG	166394-166591	GT	CAG
(GTC)	 AG	166828-167039	AT	AGA
-recovered pasa_asmbl_16204.p1, internal, 165636, 165669
-recovered pasa_asmbl_16204.p1, internal, 166394, 166591
Valid prediction for Augustus_model.g25553.t1
Valid prediction for GlimmerHMM_glimmerT_38297-T1
Valid prediction for GlimmerHMM_glimmerT_38301-T1
Valid prediction for snap_scaffold_16-snap.929-T1
Valid prediction for GlimmerHMM_glimmerT_38288-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.946-T1
Valid prediction for snap_scaffold_16-snap.933-T1
Valid prediction for HiQ_model.g25546.t1
Valid prediction for GlimmerHMM_glimmerT_38298-T1
Valid prediction for GlimmerHMM_glimmerT_38284-T1
Valid prediction for pasa_asmbl_17076.p1
Valid prediction for HiQ_model.g25551.t1
Valid prediction for snap_scaffold_16-snap.951-T1
Valid prediction for snap_scaffold_16-snap.966-T1
Valid prediction for snap_scaffold_16-snap.964-T1
Valid prediction for snap_scaffold_16-snap.947-T1
Valid prediction for snap_scaffold_16-snap.949-T1
Valid prediction for GlimmerHMM_glimmerT_38285-T1
Valid prediction for snap_scaffold_16-snap.971-T1
Valid prediction for GlimmerHMM_glimmerT_38303-T1
Valid prediction for GlimmerHMM_glimmerT_38283-T1
Valid prediction for snap_scaffold_16-snap.938-T1
Valid prediction for snap_scaffold_16-snap.967-T1
Valid prediction for GlimmerHMM_glimmerT_38282-T1
Valid prediction for GlimmerHMM_glimmerT_38296-T1
Valid prediction for snap_scaffold_16-snap.970-T1
Valid prediction for snap_scaffold_16-snap.962-T1
Valid prediction for snap_scaffold_16-snap.953-T1
Valid prediction for Augustus_model.g25560.t1
Valid prediction for snap_scaffold_16-snap.968-T1
Valid prediction for GlimmerHMM_glimmerT_38289-T1
Valid prediction for GlimmerHMM_glimmerT_38293-T1
Valid prediction for Augustus_model.g25559.t1
Valid prediction for snap_scaffold_16-snap.939-T1
Valid prediction for snap_scaffold_16-snap.961-T1
Valid prediction for GlimmerHMM_glimmerT_38278-T1
Valid prediction for CodingQuarry_transcript_19957-T1
Couldn't classify 130435, 130806
Sorry, prediction pasa_asmbl_16203.p2 fails validation.
(ATG)	 AA	130435-130806	CC	GGC
Valid prediction for CodingQuarry_transcript_19959-T1
Valid prediction for CodingQuarry_transcript_19961-T1
Valid prediction for Augustus_model.g25550.t1
Valid prediction for GlimmerHMM_glimmerT_38290-T1
Couldn't classify 164471, 164803
Sorry, prediction pasa_asmbl_17072.p1 fails validation.
(TAC)	 GC	164471-164803	CC	CCC
Valid prediction for snap_scaffold_16-snap.956-T1
Valid prediction for Augustus_model.g25555.t1
Valid prediction for snap_scaffold_16-snap.954-T1
Valid prediction for Augustus_model.g25552.t1
Valid prediction for CodingQuarry_transcript_19960-T1
Valid prediction for snap_scaffold_16-snap.945-T1
Valid prediction for CodingQuarry_transcript_19958-T1
Valid prediction for HiQ_model.g25547.t1
Valid prediction for pasa_asmbl_17080.p1
Valid prediction for GlimmerHMM_glimmerT_38279-T1
Couldn't classify 160413, 160624
Couldn't classify 163638, 163819
Sorry, prediction pasa_asmbl_17584.p1 fails validation.
(AAG)	 AC	160413-160624	GT	AGG
(CTT)	 AG	160752-160910	GT	AAG
(GAT)	 AG	161034-161173	GT	AGG
(CTG)	 AG	161428-161598	GT	AGG
(GTG)	 AG	161722-161911	GT	AAG
(GGG)	 AG	162065-162121	GT	AGG
(CCG)	 AG	162301-162402	GT	GGG
(GTG)	 AG	162632-162709	GT	AGG
(TCG)	 AG	162849-162965	GT	TTG
(TAT)	 AG	163075-163206	GT	GAG
(TCT)	 AG	163349-163545	GT	AGG
(ACC)	 AG	163638-163819	CC	CCC
add_exon() Sorry, pasa_asmbl_17584.p1 163075-163206-terminal-1 is invalid.
-recovered pasa_asmbl_17584.p1, terminal, 163075, 163206
-recovered pasa_asmbl_17584.p1, terminal, 163349, 163545
-recovered pasa_asmbl_17584.p1, internal, 160752, 160910
-recovered pasa_asmbl_17584.p1, internal, 161034, 161173
-recovered pasa_asmbl_17584.p1, internal, 161428, 161598
-recovered pasa_asmbl_17584.p1, internal, 161722, 161911
-recovered pasa_asmbl_17584.p1, internal, 162065, 162121
-recovered pasa_asmbl_17584.p1, internal, 162301, 162402
-recovered pasa_asmbl_17584.p1, internal, 162632, 162709
-recovered pasa_asmbl_17584.p1, internal, 162849, 162965
-recovered pasa_asmbl_17584.p1, internal, 163075, 163206
-recovered pasa_asmbl_17584.p1, internal, 163349, 163545
Couldn't classify 126941, 126982
Sorry, prediction pasa_asmbl_17078.p1 fails validation.
(GCA)	 GG	126941-126982	GT	AGG
(GTC)	 AG	127197-127325	GT	AGG
(TGG)	 AG	127458-127583	GT	AGG
(GTC)	 AG	127863-127940	GT	AGG
(GCC)	 AG	128253-128378	GT	AGG
(CTC)	 AG	128486-128614	CC	AAC
-recovered pasa_asmbl_17078.p1, terminal, 128486, 128614
-recovered pasa_asmbl_17078.p1, internal, 127197, 127325
-recovered pasa_asmbl_17078.p1, internal, 127458, 127583
-recovered pasa_asmbl_17078.p1, internal, 127863, 127940
-recovered pasa_asmbl_17078.p1, internal, 128253, 128378

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 87107, rend_intergenic: 87006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138511, rend_intergenic: 135759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153934, rend_intergenic: 152100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164061, rend_intergenic: 156662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173673, rend_intergenic: 164307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180531, rend_intergenic: 174017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187952, rend_intergenic: 180630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204416, rend_intergenic: 200867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207417, rend_intergenic: 204948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211280, rend_intergenic: 208002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221600, rend_intergenic: 211859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245440, rend_intergenic: 235069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 251940
-exon list size: 391


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 87107, rend_intergenic: 87006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138511, rend_intergenic: 135759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153934, rend_intergenic: 152100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164061, rend_intergenic: 156662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173673, rend_intergenic: 164307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180531, rend_intergenic: 174017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187952, rend_intergenic: 180630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204416, rend_intergenic: 200867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207417, rend_intergenic: 204948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211280, rend_intergenic: 208002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221600, rend_intergenic: 211859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245440, rend_intergenic: 235069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support