-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_11426410-11621282

-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_15-snap.2352-T1
Valid prediction for snap_scaffold_15-snap.2379-T1
Valid prediction for snap_scaffold_15-snap.2374-T1
Valid prediction for GlimmerHMM_glimmerT_36995-T1
Valid prediction for GlimmerHMM_glimmerT_36996-T1
Valid prediction for snap_scaffold_15-snap.2380-T1
Valid prediction for GlimmerHMM_glimmerT_36992-T1
Valid prediction for snap_scaffold_15-snap.2361-T1
Valid prediction for GlimmerHMM_glimmerT_37017-T1
Valid prediction for Augustus_model.g24633.t1
Valid prediction for snap_scaffold_15-snap.2365-T1
Valid prediction for GlimmerHMM_glimmerT_37003-T1
Valid prediction for GlimmerHMM_glimmerT_37010-T1
Valid prediction for snap_scaffold_15-snap.2373-T1
Valid prediction for Augustus_model.g24631.t1
Couldn't classify 9840, 10196
Sorry, prediction pasa_asmbl_14511.p1 fails validation.
(ATG)	 TC	9840-10196	CT	AGC
Valid prediction for snap_scaffold_15-snap.2368-T1
Valid prediction for snap_scaffold_15-snap.2371-T1
Valid prediction for GlimmerHMM_glimmerT_37005-T1
Valid prediction for snap_scaffold_15-snap.2384-T1
Valid prediction for snap_scaffold_15-snap.2355-T1
Valid prediction for snap_scaffold_15-snap.2353-T1
Valid prediction for snap_scaffold_15-snap.2385-T1
Valid prediction for GlimmerHMM_glimmerT_37016-T1
Valid prediction for GlimmerHMM_glimmerT_37013-T1
Valid prediction for pasa_asmbl_15499.p1
Valid prediction for snap_scaffold_15-snap.2381-T1
Valid prediction for snap_scaffold_15-snap.2369-T1
Valid prediction for GlimmerHMM_glimmerT_36987-T1
Valid prediction for GlimmerHMM_glimmerT_37011-T1
Valid prediction for Augustus_model.g24628.t1
Valid prediction for HiQ_model.g24635.t1
Valid prediction for GlimmerHMM_glimmerT_36988-T1
Valid prediction for GlimmerHMM_glimmerT_37004-T1
Valid prediction for snap_scaffold_15-snap.2350-T1
Valid prediction for snap_scaffold_15-snap.2358-T1
Valid prediction for GlimmerHMM_glimmerT_37015-T1
Valid prediction for Augustus_model.g24629.t1
Valid prediction for CodingQuarry_transcript_18146-T1
Valid prediction for Augustus_model.g24640.t1
Valid prediction for snap_scaffold_15-snap.2387-T1
Valid prediction for GlimmerHMM_glimmerT_37012-T1
Valid prediction for Augustus_model.g24644.t1
Valid prediction for snap_scaffold_15-snap.2363-T1
Valid prediction for Augustus_model.g24646.t1
Valid prediction for Augustus_model.g24634.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 HiQ_model.g24636.t1
Valid prediction for CodingQuarry_transcript_18147-T1
Valid prediction for snap_scaffold_15-snap.2375-T1
Valid prediction for Augustus_model.g24645.t1
Valid prediction for GlimmerHMM_glimmerT_36993-T1
Valid prediction for snap_scaffold_15-snap.2372-T1
Valid prediction for snap_scaffold_15-snap.2359-T1
Valid prediction for GlimmerHMM_glimmerT_37009-T1
Valid prediction for snap_scaffold_15-snap.2351-T1
Valid prediction for GlimmerHMM_glimmerT_36989-T1
Valid prediction for snap_scaffold_15-snap.2366-T1
Valid prediction for snap_scaffold_15-snap.2383-T1
Valid prediction for GlimmerHMM_glimmerT_37002-T1
Valid prediction for snap_scaffold_15-snap.2382-T1
Valid prediction for GlimmerHMM_glimmerT_37006-T1
Couldn't classify 54311, 54417
Sorry, prediction pasa_asmbl_14522.p1 fails validation.
(GCT)	 CA	54311-54417	GT	AGG
(CCT)	 AG	54598-54839	GT	AGG
(GCC)	 AG	55351-55516	GT	AGG
(AGG)	 AG	55656-55773	GT	AGG
(GCG)	 AG	56534-56680	GT	AGG
(GTG)	 AG	56790-56864	GT	AGG
(GAC)	 AG	56986-57103	GT	CGG
(ATT)	 AG	57694-57762	GT	AGG
(ACC)	 AG	57884-57988	GT	AGG
(GCA)	 AG	58474-58564	GT	AAG
(TGT)	 AG	58705-58813	GT	CTG
(GTA)	 AG	58970-59070	GT	AAG
(GTG)	 AG	61080-61224	GT	AGG
(ATT)	 AG	61753-61764	CG	AAC
add_exon() Sorry, pasa_asmbl_14522.p1 54598-54839-terminal-2 is invalid.
-recovered pasa_asmbl_14522.p1, terminal, 54598, 54839
-recovered pasa_asmbl_14522.p1, terminal, 61753, 61764
-recovered pasa_asmbl_14522.p1, internal, 54598, 54839
-recovered pasa_asmbl_14522.p1, internal, 55351, 55516
-recovered pasa_asmbl_14522.p1, internal, 55656, 55773
-recovered pasa_asmbl_14522.p1, internal, 56534, 56680
-recovered pasa_asmbl_14522.p1, internal, 56790, 56864
-recovered pasa_asmbl_14522.p1, internal, 56986, 57103
-recovered pasa_asmbl_14522.p1, internal, 57694, 57762
-recovered pasa_asmbl_14522.p1, internal, 57884, 57988
-recovered pasa_asmbl_14522.p1, internal, 58474, 58564
-recovered pasa_asmbl_14522.p1, internal, 58705, 58813
-recovered pasa_asmbl_14522.p1, internal, 58970, 59070
-recovered pasa_asmbl_14522.p1, internal, 61080, 61224
Valid prediction for snap_scaffold_15-snap.2386-T1
Valid prediction for GlimmerHMM_glimmerT_37000-T1
Valid prediction for snap_scaffold_15-snap.2349-T1
Valid prediction for snap_scaffold_15-snap.2377-T1
Valid prediction for Augustus_model.g24630.t1
Valid prediction for snap_scaffold_15-snap.2378-T1
Valid prediction for GlimmerHMM_glimmerT_36991-T1
Couldn't classify 151667, 152008
Sorry, prediction pasa_asmbl_14515.p2 fails validation.
(ATG)	 TC	151667-152008	GA	TGG
Valid prediction for CodingQuarry_transcript_18148-T1
Valid prediction for snap_scaffold_15-snap.2364-T1
Valid prediction for Augustus_model.g24638.t1
Valid prediction for GlimmerHMM_glimmerT_37001-T1
Couldn't classify 47566, 47687
Sorry, prediction pasa_asmbl_14525.p1 fails validation.
(ATG)	 AA	45408-45450	GT	AGG
(ACT)	 AG	46216-46281	GT	AGG
(CGG)	 AG	46440-46571	GT	GGG
(GCA)	 AG	47090-47341	GT	AGG
(GAG)	 AG	47566-47687	CT	AAC
-recovered pasa_asmbl_14525.p1, initial, 45408, 45450
-recovered pasa_asmbl_14525.p1, internal, 46216, 46281
-recovered pasa_asmbl_14525.p1, internal, 46440, 46571
-recovered pasa_asmbl_14525.p1, internal, 47090, 47341
Valid prediction for GlimmerHMM_glimmerT_36990-T1
Valid prediction for HiQ_model.g24642.t1
Valid prediction for Augustus_model.g24637.t1
Valid prediction for HiQ_model.g24641.t1
Valid prediction for pasa_asmbl_14516.p1
Valid prediction for snap_scaffold_15-snap.2354-T1
Valid prediction for snap_scaffold_15-snap.2367-T1
Valid prediction for GlimmerHMM_glimmerT_37008-T1
Valid prediction for snap_scaffold_15-snap.2370-T1
Valid prediction for snap_scaffold_15-snap.2360-T1
Valid prediction for GlimmerHMM_glimmerT_37007-T1
Valid prediction for snap_scaffold_15-snap.2357-T1
Valid prediction for GlimmerHMM_glimmerT_36999-T1
Couldn't classify 63531, 63590
Couldn't classify 66531, 66659
Sorry, prediction pasa_asmbl_14520.p1 fails validation.
(TCA)	 AC	63531-63590	GT	AGG
(GTG)	 AG	64139-64286	GT	AGG
(GGA)	 AG	64801-64956	GT	GGG
(CTG)	 AG	65167-65316	GT	CGG
(GCA)	 AG	65510-65766	GT	AGG
(GGC)	 AG	66127-66288	GT	AGG
(GTG)	 AG	66531-66659	GT	GCG
-recovered pasa_asmbl_14520.p1, internal, 64139, 64286
-recovered pasa_asmbl_14520.p1, internal, 64801, 64956
-recovered pasa_asmbl_14520.p1, internal, 65167, 65316
-recovered pasa_asmbl_14520.p1, internal, 65510, 65766
-recovered pasa_asmbl_14520.p1, internal, 66127, 66288
-recovered pasa_asmbl_14520.p1, internal, 66531, 66659
Valid prediction for GlimmerHMM_glimmerT_36994-T1
Valid prediction for Augustus_model.g24632.t1
Valid prediction for GlimmerHMM_glimmerT_37014-T1
Valid prediction for snap_scaffold_15-snap.2376-T1
Couldn't classify 116731, 116920
Couldn't classify 117125, 117255
Sorry, prediction CodingQuarry_transcript_18149-T1 fails validation.
(ATG)	 GA	116027-116082	GT	CAG
(CCC)	 AG	116328-116403	GT	CTG
(CCC)	 AG	116731-116920	TG	GGT
(AGA)	 GG	117125-117255	GT	AGG
(TTG)	 AG	118067-118303	GT	AGG
(TAC)	 AG	118461-118556	GT	TGG
(CCT)	 AG	118759-118914	GT	TTG
(ACT)	 AG	119030-119119	GT	TGG
(ACG)	 AG	119249-119416	GA	AGG
-recovered CodingQuarry_transcript_18149-T1, initial, 116027, 116082
-recovered CodingQuarry_transcript_18149-T1, terminal, 119249, 119416
-recovered CodingQuarry_transcript_18149-T1, internal, 116328, 116403
-recovered CodingQuarry_transcript_18149-T1, internal, 118067, 118303
-recovered CodingQuarry_transcript_18149-T1, internal, 118461, 118556
-recovered CodingQuarry_transcript_18149-T1, internal, 118759, 118914
-recovered CodingQuarry_transcript_18149-T1, internal, 119030, 119119
Valid prediction for HiQ_model.g24643.t1
Valid prediction for snap_scaffold_15-snap.2388-T1
Valid prediction for GlimmerHMM_glimmerT_36998-T1
Valid prediction for Augustus_model.g24647.t1
Valid prediction for Augustus_model.g24639.t1
Valid prediction for snap_scaffold_15-snap.2362-T1
Valid prediction for GlimmerHMM_glimmerT_36997-T1
Valid prediction for snap_scaffold_15-snap.2356-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9283, rend_intergenic: 3321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14046, rend_intergenic: 9445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37762, rend_intergenic: 30241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53442, rend_intergenic: 45147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59376, rend_intergenic: 56625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79480, rend_intergenic: 75458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95085, rend_intergenic: 81824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104951, rend_intergenic: 95117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108955, rend_intergenic: 105462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115544, rend_intergenic: 109576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122680, rend_intergenic: 116056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129428, rend_intergenic: 122975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145320, rend_intergenic: 138152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162611, rend_intergenic: 155421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178120, rend_intergenic: 167350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180695, rend_intergenic: 178342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193977, rend_intergenic: 181204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 178345, rend_intergenic: 178342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194873
-exon list size: 381


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.4    
4.7    
5.0    
5.2    
5.5    
5.7    
6.0    
6.3    
6.5    
6.8    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.3    
12.5    
12.8    
13.1    
13.3    
13.6    
13.8    
14.1    
14.4    
14.6    
14.9    
15.1    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
17.0    
17.2    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.7    
23.0    
23.2    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.1    
31.3    
31.6    
31.9    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.6    
42.8    
43.1    
43.3    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.7    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.7    
53.0    
53.3    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
58.0    
58.2    
58.5    
58.7    
59.0    
59.3    
59.5    
59.8    
60.1    
60.3    
60.6    
60.8    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.0    
65.3    
65.5    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.1    
68.4    
68.7    
68.9    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.8    
71.0    
71.3    
71.5    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.8    
83.0    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.9    
85.1    
85.4    
85.6    
85.9    
86.2    
86.4    
86.7    
86.9    
87.2    
87.5    
87.7    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.7    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 9283, rend_intergenic: 3321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14046, rend_intergenic: 9445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37762, rend_intergenic: 30241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53442, rend_intergenic: 45147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59376, rend_intergenic: 56625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79480, rend_intergenic: 75458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95085, rend_intergenic: 81824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104951, rend_intergenic: 95117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108955, rend_intergenic: 105462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115544, rend_intergenic: 109576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122680, rend_intergenic: 116056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129428, rend_intergenic: 122975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145320, rend_intergenic: 138152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162611, rend_intergenic: 155421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178120, rend_intergenic: 167350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180695, rend_intergenic: 178342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193977, rend_intergenic: 181204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 178345, rend_intergenic: 178342  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