-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_11888937-12107216

-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_7419-T1
Valid prediction for GlimmerHMM_glimmerT_7431-T1
Valid prediction for snap_scaffold_3-snap.2355-T1
Valid prediction for GlimmerHMM_glimmerT_7416-T1
Valid prediction for snap_scaffold_3-snap.2335-T1
Valid prediction for snap_scaffold_3-snap.2337-T1
Valid prediction for Augustus_model.g4838.t1
Valid prediction for snap_scaffold_3-snap.2347-T1
Valid prediction for HiQ_model.g4828.t1
Couldn't classify 98691, 98881
Couldn't classify 101961, 102135
Sorry, prediction pasa_asmbl_40387.p1 fails validation.
(AGA)	 AG	98691-98881	GT	AGG
(GGT)	 AG	101052-101219	GT	TGG
(CTT)	 AG	101961-102135	TC	GGT
-recovered pasa_asmbl_40387.p1, internal, 98691, 98881
-recovered pasa_asmbl_40387.p1, internal, 101052, 101219
Couldn't classify 82889, 82958
Couldn't classify 84648, 84847
Sorry, prediction pasa_asmbl_40382.p1 fails validation.
(GAT)	 CA	82889-82958	GT	AGG
(TCA)	 AG	84063-84269	GT	TGG
(ACC)	 AG	84648-84847	CC	AGC
-recovered pasa_asmbl_40382.p1, internal, 84063, 84269
Valid prediction for GlimmerHMM_glimmerT_7414-T1
Valid prediction for snap_scaffold_3-snap.2350-T1
Valid prediction for HiQ_model.g4837.t1
Couldn't classify 126655, 126969
Sorry, prediction pasa_asmbl_40392.p1 fails validation.
(ATG)	 AG	126655-126969	AT	ACA
Valid prediction for GlimmerHMM_glimmerT_7404-T1
Valid prediction for snap_scaffold_3-snap.2361-T1
Valid prediction for snap_scaffold_3-snap.2339-T1
Valid prediction for GlimmerHMM_glimmerT_7429-T1
Valid prediction for Augustus_model.g4827.t1
Valid prediction for Augustus_model.g4831.t1
Valid prediction for Augustus_model.g4830.t1
Valid prediction for GlimmerHMM_glimmerT_7415-T1
Valid prediction for pasa_asmbl_40393.p1
Valid prediction for snap_scaffold_3-snap.2358-T1
Valid prediction for snap_scaffold_3-snap.2371-T1
Valid prediction for snap_scaffold_3-snap.2368-T1
Valid prediction for snap_scaffold_3-snap.2357-T1
Valid prediction for GlimmerHMM_glimmerT_7418-T1
Couldn't classify 86699, 86732
Sorry, prediction pasa_asmbl_40384.p1 fails validation.
(CAT)	 AA	86699-86732	GT	CGG
(GTG)	 AG	87081-89044	GT	AGG
(GGT)	 AG	89419-89599	GT	AGG
(GCA)	 AG	91608-92206	TT	GAT
-recovered pasa_asmbl_40384.p1, terminal, 91608, 92206
-recovered pasa_asmbl_40384.p1, internal, 87081, 89044
-recovered pasa_asmbl_40384.p1, internal, 89419, 89599
Valid prediction for snap_scaffold_3-snap.2359-T1
Valid prediction for snap_scaffold_3-snap.2352-T1
Valid prediction for snap_scaffold_3-snap.2353-T1
Valid prediction for snap_scaffold_3-snap.2365-T1
Valid prediction for GlimmerHMM_glimmerT_7420-T1
Valid prediction for Augustus_model.g4834.t1
Valid prediction for snap_scaffold_3-snap.2376-T1
Valid prediction for Augustus_model.g4821.t1
Valid prediction for CodingQuarry_transcript_46293-T1
Valid prediction for snap_scaffold_3-snap.2345-T1
Valid prediction for snap_scaffold_3-snap.2336-T1
Valid prediction for GlimmerHMM_glimmerT_7410-T1
Valid prediction for GlimmerHMM_glimmerT_7423-T1
Valid prediction for snap_scaffold_3-snap.2375-T1
Valid prediction for snap_scaffold_3-snap.2366-T1
Valid prediction for GlimmerHMM_glimmerT_7427-T1
Valid prediction for GlimmerHMM_glimmerT_7421-T1
Valid prediction for snap_scaffold_3-snap.2372-T1
Valid prediction for Augustus_model.g4829.t1
Valid prediction for snap_scaffold_3-snap.2374-T1
Valid prediction for GlimmerHMM_glimmerT_7426-T1
Valid prediction for GlimmerHMM_glimmerT_7405-T1
Valid prediction for HiQ_model.g4826.t1
Valid prediction for GlimmerHMM_glimmerT_7412-T1
Valid prediction for Augustus_model.g4825.t1
Valid prediction for snap_scaffold_3-snap.2343-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_3-snap.2367-T1
Valid prediction for snap_scaffold_3-snap.2377-T1
Valid prediction for GlimmerHMM_glimmerT_7430-T1
Valid prediction for Augustus_model.g4823.t1
Valid prediction for snap_scaffold_3-snap.2351-T1
Valid prediction for snap_scaffold_3-snap.2342-T1
Valid prediction for GlimmerHMM_glimmerT_7422-T1
Valid prediction for snap_scaffold_3-snap.2364-T1
Valid prediction for GlimmerHMM_glimmerT_7417-T1
Valid prediction for snap_scaffold_3-snap.2349-T1
Valid prediction for Augustus_model.g4836.t1
Valid prediction for GlimmerHMM_glimmerT_7425-T1
Valid prediction for snap_scaffold_3-snap.2344-T1
Couldn't classify 109390, 109689
Sorry, prediction pasa_asmbl_40388.p1 fails validation.
(TTT)	 CC	109390-109689	TC	GAT
Valid prediction for snap_scaffold_3-snap.2340-T1
Valid prediction for snap_scaffold_3-snap.2373-T1
Valid prediction for snap_scaffold_3-snap.2360-T1
Valid prediction for GlimmerHMM_glimmerT_7406-T1
Valid prediction for snap_scaffold_3-snap.2354-T1
Valid prediction for Augustus_model.g4832.t1
Couldn't classify 63731, 63829
Couldn't classify 72121, 72254
Sorry, prediction pasa_asmbl_39199.p1 fails validation.
(ATA)	 AG	63731-63829	GT	TGG
(TCT)	 AG	64129-64282	GT	CCG
(TTC)	 AG	66015-66137	GT	AGG
(ATC)	 AG	68033-68131	GT	AGG
(GCT)	 AG	70024-70101	GT	AGG
(AGG)	 AG	72121-72254	AG	TCA
-recovered pasa_asmbl_39199.p1, internal, 63731, 63829
-recovered pasa_asmbl_39199.p1, internal, 64129, 64282
-recovered pasa_asmbl_39199.p1, internal, 66015, 66137
-recovered pasa_asmbl_39199.p1, internal, 68033, 68131
-recovered pasa_asmbl_39199.p1, internal, 70024, 70101
Valid prediction for snap_scaffold_3-snap.2346-T1
Valid prediction for GlimmerHMM_glimmerT_7413-T1
Valid prediction for Augustus_model.g4833.t1
Valid prediction for snap_scaffold_3-snap.2363-T1
Valid prediction for GlimmerHMM_glimmerT_7428-T1
Valid prediction for Augustus_model.g4835.t1
Valid prediction for Augustus_model.g4822.t1
Valid prediction for snap_scaffold_3-snap.2341-T1
Valid prediction for GlimmerHMM_glimmerT_7424-T1
Valid prediction for snap_scaffold_3-snap.2369-T1
Couldn't classify 54897, 54971
Sorry, prediction pasa_asmbl_39203.p1 fails validation.
(ATG)	 GA	49291-49304	GT	AGG
(AAT)	 AG	50470-50644	GT	CTG
(ATT)	 AG	52696-52761	GT	CTG
(GGG)	 AG	53009-53158	GT	TGG
(AAA)	 AG	54897-54971	AA	GGA
-recovered pasa_asmbl_39203.p1, initial, 49291, 49304
-recovered pasa_asmbl_39203.p1, internal, 50470, 50644
-recovered pasa_asmbl_39203.p1, internal, 52696, 52761
-recovered pasa_asmbl_39203.p1, internal, 53009, 53158
Valid prediction for snap_scaffold_3-snap.2338-T1
Valid prediction for GlimmerHMM_glimmerT_7411-T1
Valid prediction for snap_scaffold_3-snap.2362-T1
Valid prediction for Augustus_model.g4824.t1
Valid prediction for GlimmerHMM_glimmerT_7408-T1
Valid prediction for GlimmerHMM_glimmerT_7409-T1
Valid prediction for GlimmerHMM_glimmerT_7407-T1
Valid prediction for snap_scaffold_3-snap.2370-T1
Valid prediction for snap_scaffold_3-snap.2348-T1
Valid prediction for snap_scaffold_3-snap.2356-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 53879, rend_intergenic: 49633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57280, rend_intergenic: 56846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60116, rend_intergenic: 57936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73998, rend_intergenic: 62048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79217, rend_intergenic: 76288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101223, rend_intergenic: 98508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102080, rend_intergenic: 101808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114197, rend_intergenic: 112057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138018, rend_intergenic: 135612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218280
-exon list size: 287


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.8    
5.2    
5.5    
5.9    
6.2    
6.6    
6.9    
7.3    
7.6    
8.0    
8.3    
8.7    
9.0    
9.3    
9.7    
10.0    
10.4    
10.7    
11.1    
11.4    
11.8    
12.1    
12.5    
12.8    
13.1    
13.5    
13.8    
14.2    
14.5    
14.9    
15.2    
15.6    
15.9    
16.3    
16.6    
17.0    
17.3    
17.6    
18.0    
18.3    
18.7    
19.0    
19.4    
19.7    
20.1    
20.4    
20.8    
21.1    
21.5    
21.8    
22.1    
22.5    
22.8    
23.2    
23.5    
23.9    
24.2    
24.6    
24.9    
25.3    
25.6    
26.0    
26.3    
26.6    
27.0    
27.3    
27.7    
28.0    
28.4    
28.7    
29.1    
29.4    
29.8    
30.1    
30.4    
30.8    
31.1    
31.5    
31.8    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.6    
34.9    
35.3    
35.6    
36.0    
36.3    
36.7    
37.0    
37.4    
37.7    
38.1    
38.4    
38.8    
39.1    
39.4    
39.8    
40.1    
40.5    
40.8    
41.2    
41.5    
41.9    
42.2    
42.6    
42.9    
43.3    
43.6    
43.9    
44.3    
44.6    
45.0    
45.3    
45.7    
46.0    
46.4    
46.7    
47.1    
47.4    
47.8    
48.1    
48.4    
48.8    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.2    
51.6    
51.9    
52.2    
52.6    
52.9    
53.3    
53.6    
54.0    
54.3    
54.7    
55.0    
55.4    
55.7    
56.1    
56.4    
56.7    
57.1    
57.4    
57.8    
58.1    
58.5    
58.8    
59.2    
59.5    
59.9    
60.2    
60.6    
60.9    
61.2    
61.6    
61.9    
62.3    
62.6    
63.0    
63.3    
63.7    
64.0    
64.4    
64.7    
65.1    
65.4    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.2    
68.5    
68.9    
69.2    
69.6    
69.9    
70.2    
70.6    
70.9    
71.3    
71.6    
72.0    
72.3    
72.7    
73.0    
73.4    
73.7    
74.0    
74.4    
74.7    
75.1    
75.4    
75.8    
76.1    
76.5    
76.8    
77.2    
77.5    
77.9    
78.2    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.3    
81.7    
82.0    
82.4    
82.7    
83.0    
83.4    
83.7    
84.1    
84.4    
84.8    
85.1    
85.5    
85.8    
86.2    
86.5    
86.9    
87.2    
87.5    
87.9    
88.2    
88.6    
88.9    
89.3    
89.6    
90.0    
90.3    
90.7    
91.0    
91.3    
91.7    
92.0    
92.4    
92.7    
93.1    
93.4    
93.8    
94.1    
94.5    
94.8    
95.2    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 53879, rend_intergenic: 49633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57280, rend_intergenic: 56846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60116, rend_intergenic: 57936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73998, rend_intergenic: 62048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79217, rend_intergenic: 76288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101223, rend_intergenic: 98508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102080, rend_intergenic: 101808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114197, rend_intergenic: 112057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138018, rend_intergenic: 135612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support