-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_8/scaffold_8_13197041-13390813

-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 GlimmerHMM_glimmerT_20714-T1
Valid prediction for Augustus_model.g13819.t1
Valid prediction for GlimmerHMM_glimmerT_20716-T1
Valid prediction for GlimmerHMM_glimmerT_20703-T1
Couldn't classify 80051, 80461
Couldn't classify 80852, 81010
Sorry, prediction pasa_asmbl_53352.p1 fails validation.
(CTC)	 CT	80051-80461	GT	AGG
(GTG)	 AG	80852-81010	CA	ACC
Valid prediction for Augustus_model.g13820.t1
Valid prediction for GlimmerHMM_glimmerT_20713-T1
Valid prediction for Augustus_model.g13814.t1
Valid prediction for Augustus_model.g13823.t1
Valid prediction for snap_scaffold_8-snap.2404-T1
Valid prediction for GlimmerHMM_glimmerT_20706-T1
Valid prediction for Augustus_model.g13813.t1
Valid prediction for GlimmerHMM_glimmerT_20702-T1
Valid prediction for HiQ_model.g13811.t1
Valid prediction for GlimmerHMM_glimmerT_20705-T1
Valid prediction for snap_scaffold_8-snap.2411-T1
Valid prediction for GlimmerHMM_glimmerT_20707-T1
Couldn't classify 92497, 92646
Couldn't classify 94846, 94966
Sorry, prediction pasa_asmbl_53575.p1 fails validation.
(GTG)	 AT	92497-92646	GT	AGG
(CTG)	 AG	92784-92887	GT	AGG
(TCT)	 AG	94846-94966	TG	TTT
-recovered pasa_asmbl_53575.p1, internal, 92784, 92887
Valid prediction for snap_scaffold_8-snap.2400-T1
Valid prediction for GlimmerHMM_glimmerT_20709-T1
Valid prediction for GlimmerHMM_glimmerT_20710-T1
Valid prediction for snap_scaffold_8-snap.2401-T1
Couldn't classify 83002, 83144
Couldn't classify 84764, 84970
Sorry, prediction pasa_asmbl_53353.p1 fails validation.
(AGC)	 AC	83002-83144	GT	GAG
(AGA)	 AG	83366-83474	GC	AGG
(GTG)	 AG	84201-84317	GT	AGG
(ATG)	 AG	84764-84970	AA	ACA
-recovered pasa_asmbl_53353.p1, internal, 83366, 83474
-recovered pasa_asmbl_53353.p1, internal, 84201, 84317
Valid prediction for snap_scaffold_8-snap.2389-T1
Valid prediction for GlimmerHMM_glimmerT_20704-T1
Valid prediction for GlimmerHMM_glimmerT_20719-T1
Valid prediction for Augustus_model.g13812.t1
Couldn't classify 59151, 59184
Sorry, prediction pasa_asmbl_53350.p1 fails validation.
(GAA)	 TC	59151-59184	GT	AAG
(TTA)	 AG	59686-60032	GT	AGG
(GTG)	 AG	60231-60383	GT	GAG
-recovered pasa_asmbl_53350.p1, terminal, 60231, 60383
-recovered pasa_asmbl_53350.p1, internal, 59686, 60032
-recovered pasa_asmbl_53350.p1, internal, 60231, 60383
Valid prediction for GlimmerHMM_glimmerT_20712-T1
Valid prediction for snap_scaffold_8-snap.2413-T1
Valid prediction for GlimmerHMM_glimmerT_20697-T1
Valid prediction for snap_scaffold_8-snap.2397-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.2410-T1
Valid prediction for Augustus_model.g13816.t1
Valid prediction for Augustus_model.g13821.t1
Valid prediction for snap_scaffold_8-snap.2405-T1
Valid prediction for snap_scaffold_8-snap.2396-T1
Valid prediction for GlimmerHMM_glimmerT_20693-T1
Valid prediction for GlimmerHMM_glimmerT_20692-T1
Valid prediction for snap_scaffold_8-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_20708-T1
Valid prediction for CodingQuarry_transcript_59884-T1
Valid prediction for Augustus_model.g13815.t1
Valid prediction for Augustus_model.g13822.t1
Valid prediction for GlimmerHMM_glimmerT_20699-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_8-snap.2408-T1
Valid prediction for snap_scaffold_8-snap.2391-T1
Valid prediction for pasa_asmbl_52285.p1
Valid prediction for snap_scaffold_8-snap.2390-T1
Valid prediction for Augustus_model.g13809.t1
Valid prediction for GlimmerHMM_glimmerT_20694-T1
Valid prediction for snap_scaffold_8-snap.2399-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_8-snap.2409-T1
Valid prediction for snap_scaffold_8-snap.2416-T1
Valid prediction for GlimmerHMM_glimmerT_20715-T1
Valid prediction for GlimmerHMM_glimmerT_20698-T1
Valid prediction for Augustus_model.g13808.t1
Valid prediction for snap_scaffold_8-snap.2414-T1
Valid prediction for snap_scaffold_8-snap.2415-T1
Valid prediction for snap_scaffold_8-snap.2412-T1
Valid prediction for snap_scaffold_8-snap.2398-T1
Valid prediction for GlimmerHMM_glimmerT_20711-T1
Valid prediction for GlimmerHMM_glimmerT_20718-T1
Couldn't classify 153586, 153670
Sorry, prediction pasa_asmbl_52284.p1 fails validation.
(ATG)	 AC	147541-147579	GT	AGG
(ACA)	 AG	150258-150365	GT	AGG
(GAG)	 AG	151890-151958	GT	TGG
(GAC)	 AG	152330-152428	GT	AGG
(GCC)	 AG	152522-152707	GT	TAG
(GTG)	 AG	152853-152972	GT	ATG
(TGT)	 AG	153089-153204	GT	AGG
(GAA)	 AG	153586-153670	GT	GCG
-recovered pasa_asmbl_52284.p1, initial, 147541, 147579
-recovered pasa_asmbl_52284.p1, internal, 150258, 150365
-recovered pasa_asmbl_52284.p1, internal, 151890, 151958
-recovered pasa_asmbl_52284.p1, internal, 152330, 152428
-recovered pasa_asmbl_52284.p1, internal, 152522, 152707
-recovered pasa_asmbl_52284.p1, internal, 152853, 152972
-recovered pasa_asmbl_52284.p1, internal, 153089, 153204
-recovered pasa_asmbl_52284.p1, internal, 153586, 153670
Valid prediction for Augustus_model.g13817.t1
Valid prediction for GlimmerHMM_glimmerT_20700-T1
Valid prediction for snap_scaffold_8-snap.2393-T1
Valid prediction for snap_scaffold_8-snap.2407-T1
Couldn't classify 157026, 157134
Couldn't classify 158434, 158628
Sorry, prediction pasa_asmbl_52282.p1 fails validation.
(AGC)	 GC	157026-157134	GT	GGG
(TCA)	 AG	157327-157532	GT	ATG
(GCC)	 AG	157689-157891	GT	AGG
(GTA)	 AG	158134-158239	GT	AGG
(CAC)	 AG	158434-158628	AA	ACA
-recovered pasa_asmbl_52282.p1, internal, 157327, 157532
-recovered pasa_asmbl_52282.p1, internal, 157689, 157891
-recovered pasa_asmbl_52282.p1, internal, 158134, 158239
Valid prediction for GlimmerHMM_glimmerT_20717-T1
Valid prediction for snap_scaffold_8-snap.2402-T1
Valid prediction for snap_scaffold_8-snap.2403-T1
Valid prediction for snap_scaffold_8-snap.2395-T1
Valid prediction for GlimmerHMM_glimmerT_20696-T1
Couldn't classify 153958, 154056
Couldn't classify 155803, 156030
Sorry, prediction pasa_asmbl_52283.p1 fails validation.
(ATC)	 AG	153958-154056	GT	GGG
(CAA)	 AG	154582-154642	GT	GGG
(TGA)	 AG	155095-155246	GT	AGG
(GAA)	 AG	155492-155566	GT	GGG
(ATG)	 AG	155803-156030	GG	TCG
-recovered pasa_asmbl_52283.p1, internal, 153958, 154056
-recovered pasa_asmbl_52283.p1, internal, 154582, 154642
-recovered pasa_asmbl_52283.p1, internal, 155095, 155246
-recovered pasa_asmbl_52283.p1, internal, 155492, 155566
Valid prediction for snap_scaffold_8-snap.2417-T1
Valid prediction for GlimmerHMM_glimmerT_20695-T1
Valid prediction for snap_scaffold_8-snap.2392-T1
Valid prediction for HiQ_model.g13810.t1
Valid prediction for Augustus_model.g13818.t1
Valid prediction for GlimmerHMM_glimmerT_20701-T1
Valid prediction for snap_scaffold_8-snap.2388-T1
Valid prediction for snap_scaffold_8-snap.2406-T1
Valid prediction for CodingQuarry_transcript_59883-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11227, rend_intergenic: 9774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15622, rend_intergenic: 11341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50859, rend_intergenic: 45933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77553, rend_intergenic: 63802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92114, rend_intergenic: 77787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98515, rend_intergenic: 92182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110003, rend_intergenic: 98654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135342, rend_intergenic: 111833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146771, rend_intergenic: 145549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155569, rend_intergenic: 151683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165545, rend_intergenic: 155766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183881, rend_intergenic: 168184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193773
-exon list size: 332


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
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    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
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    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
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    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
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    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
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    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 11227, rend_intergenic: 9774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15622, rend_intergenic: 11341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50859, rend_intergenic: 45933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77553, rend_intergenic: 63802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92114, rend_intergenic: 77787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98515, rend_intergenic: 92182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110003, rend_intergenic: 98654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135342, rend_intergenic: 111833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146771, rend_intergenic: 145549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155569, rend_intergenic: 151683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165545, rend_intergenic: 155766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183881, rend_intergenic: 168184  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

-building DP trellis

-building trellis in range 1 - 16852
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 2 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 1 - 11985
-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