-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_1348870-1608671

-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 pasa_asmbl_31340.p1
Valid prediction for snap_scaffold_23-snap.213-T1
Valid prediction for GlimmerHMM_glimmerT_50503-T1
Valid prediction for GlimmerHMM_glimmerT_50490-T1
Valid prediction for snap_scaffold_23-snap.200-T1
Valid prediction for Augustus_model.g33711.t1
Valid prediction for GlimmerHMM_glimmerT_50493-T1
Valid prediction for snap_scaffold_23-snap.230-T1
Valid prediction for snap_scaffold_23-snap.233-T1
Valid prediction for snap_scaffold_23-snap.215-T1
Valid prediction for Augustus_model.g33719.t1
Valid prediction for GlimmerHMM_glimmerT_50500-T1
Valid prediction for Augustus_model.g33712.t1
Valid prediction for CodingQuarry_transcript_35555-T1
Valid prediction for snap_scaffold_23-snap.241-T1
Couldn't classify 151480, 151567
Sorry, prediction pasa_asmbl_31333.p2 fails validation.
(GCT)	 CA	151480-151567	GT	TGG
(AAG)	 AG	153059-153229	GT	AGG
(ACT)	 AG	153522-153644	GT	GGG
(GAG)	 AG	153926-154020	AC	AGA
-recovered pasa_asmbl_31333.p2, terminal, 153926, 154020
-recovered pasa_asmbl_31333.p2, internal, 153059, 153229
-recovered pasa_asmbl_31333.p2, internal, 153522, 153644
Couldn't classify 117430, 117984
Sorry, prediction pasa_asmbl_31329.p1 fails validation.
(GAC)	 CC	117430-117984	CA	GAC
Valid prediction for Augustus_model.g33740.t1
Valid prediction for GlimmerHMM_glimmerT_50482-T1
Couldn't classify 145688, 145763
Sorry, prediction pasa_asmbl_31331.p1 fails validation.
(ATG)	 AC	141736-141898	GT	AGG
(GGG)	 AG	143753-143871	GT	TGG
(AAG)	 AG	143982-144090	GT	AGG
(GGG)	 AG	144661-144803	GC	AGG
(GTG)	 AG	145223-145344	GT	AAG
(GTA)	 AG	145688-145763	AT	ACA
-recovered pasa_asmbl_31331.p1, initial, 141736, 141898
-recovered pasa_asmbl_31331.p1, internal, 143753, 143871
-recovered pasa_asmbl_31331.p1, internal, 143982, 144090
-recovered pasa_asmbl_31331.p1, internal, 144661, 144803
-recovered pasa_asmbl_31331.p1, internal, 145223, 145344
Valid prediction for Augustus_model.g33720.t1
Valid prediction for snap_scaffold_23-snap.239-T1
Valid prediction for snap_scaffold_23-snap.229-T1
Valid prediction for HiQ_model.g33734.t1
Valid prediction for pasa_asmbl_31339.p1
Valid prediction for snap_scaffold_23-snap.216-T1
Valid prediction for CodingQuarry_transcript_35553-T1
Valid prediction for GlimmerHMM_glimmerT_50502-T1
Valid prediction for pasa_asmbl_31348.p1
Valid prediction for Augustus_model.g33730.t1
Valid prediction for GlimmerHMM_glimmerT_50475-T1
Valid prediction for GlimmerHMM_glimmerT_50492-T1
Valid prediction for snap_scaffold_23-snap.199-T1
Valid prediction for snap_scaffold_23-snap.221-T1
Valid prediction for Augustus_model.g33735.t1
Valid prediction for snap_scaffold_23-snap.207-T1
Valid prediction for GlimmerHMM_glimmerT_50480-T1
Couldn't classify 108588, 110402
Sorry, prediction pasa_asmbl_31326.p1 fails validation.
(ATG)	 TG	108588-110402	TT	GGT
Valid prediction for GlimmerHMM_glimmerT_50494-T1
Valid prediction for snap_scaffold_23-snap.227-T1
Valid prediction for snap_scaffold_23-snap.220-T1
Valid prediction for snap_scaffold_23-snap.243-T1
Valid prediction for Augustus_model.g33718.t1
Couldn't classify 235613, 235727
Sorry, prediction pasa_asmbl_31343.p1 fails validation.
(AAG)	 TG	235613-235727	GT	GGG
(GAG)	 AG	235889-236043	GT	AGG
(GTC)	 AG	236368-236706	CA	GAC
-recovered pasa_asmbl_31343.p1, terminal, 236368, 236706
-recovered pasa_asmbl_31343.p1, internal, 235889, 236043
Valid prediction for GlimmerHMM_glimmerT_50486-T1
Valid prediction for Augustus_model.g33725.t1
Valid prediction for snap_scaffold_23-snap.245-T1
Valid prediction for snap_scaffold_23-snap.234-T1
Valid prediction for snap_scaffold_23-snap.222-T1
Valid prediction for snap_scaffold_23-snap.212-T1
Valid prediction for Augustus_model.g33731.t1
Valid prediction for snap_scaffold_23-snap.236-T1
Valid prediction for snap_scaffold_23-snap.238-T1
Valid prediction for Augustus_model.g33724.t1
Couldn't classify 149008, 149098
Couldn't classify 150709, 150773
Sorry, prediction pasa_asmbl_31332.p1 fails validation.
(CCC)	 CC	149008-149098	GT	TGG
(GTC)	 AG	149229-149312	GT	AGG
(CGG)	 AG	149477-149572	GT	AGG
(AGA)	 AG	150709-150773	GT	TGG
-recovered pasa_asmbl_31332.p1, internal, 149229, 149312
-recovered pasa_asmbl_31332.p1, internal, 149477, 149572
-recovered pasa_asmbl_31332.p1, internal, 150709, 150773
Valid prediction for GlimmerHMM_glimmerT_50476-T1
Valid prediction for GlimmerHMM_glimmerT_50489-T1
Valid prediction for GlimmerHMM_glimmerT_50498-T1
Valid prediction for GlimmerHMM_glimmerT_50481-T1
Valid prediction for snap_scaffold_23-snap.228-T1
Valid prediction for Augustus_model.g33732.t1
Valid prediction for Augustus_model.g33728.t1
Valid prediction for GlimmerHMM_glimmerT_50496-T1
Valid prediction for Augustus_model.g33739.t1
Valid prediction for Augustus_model.g33717.t1
Valid prediction for GlimmerHMM_glimmerT_50504-T1
Valid prediction for Augustus_model.g33727.t1
Valid prediction for snap_scaffold_23-snap.202-T1
Valid prediction for Augustus_model.g33737.t1
Valid prediction for GlimmerHMM_glimmerT_50495-T1
Valid prediction for snap_scaffold_23-snap.235-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_23-snap.201-T1
Valid prediction for GlimmerHMM_glimmerT_50487-T1
Valid prediction for GlimmerHMM_glimmerT_50488-T1
Valid prediction for Augustus_model.g33714.t1
Valid prediction for Augustus_model.g33721.t1
Couldn't classify 65399, 66169
Sorry, prediction pasa_asmbl_30659.p1 fails validation.
(CTG)	 GA	65399-66169	GT	GGG
(GCA)	 AG	66659-66754	GT	AGG
(GAG)	 AG	66905-67138	GT	GGG
(AAC)	 AG	67676-67698	GT	AGG
(GCC)	 AG	67796-67911	GT	AGG
(TTC)	 AG	68042-68586	GC	GAG
-recovered pasa_asmbl_30659.p1, terminal, 68042, 68586
-recovered pasa_asmbl_30659.p1, internal, 66659, 66754
-recovered pasa_asmbl_30659.p1, internal, 66905, 67138
-recovered pasa_asmbl_30659.p1, internal, 67676, 67698
-recovered pasa_asmbl_30659.p1, internal, 67796, 67911
-recovered pasa_asmbl_30659.p1, internal, 68042, 68586
Valid prediction for snap_scaffold_23-snap.214-T1
Couldn't classify 227768, 228283
Sorry, prediction pasa_asmbl_30638.p1 fails validation.
(AGT)	 TG	227768-228283	CT	AGC
Valid prediction for snap_scaffold_23-snap.224-T1
Valid prediction for snap_scaffold_23-snap.210-T1
Valid prediction for GlimmerHMM_glimmerT_50491-T1
Valid prediction for CodingQuarry_transcript_35549-T1
Valid prediction for GlimmerHMM_glimmerT_50497-T1
Valid prediction for CodingQuarry_transcript_35552-T1
Valid prediction for snap_scaffold_23-snap.209-T1
Valid prediction for pasa_asmbl_30652.p1
Couldn't classify 182841, 182982
Sorry, prediction pasa_asmbl_30646.p1 fails validation.
(CTG)	 GT	182841-182982	GT	CAG
(CTG)	 AG	185655-185843	GT	AGG
(ACA)	 AG	185965-186143	GT	TGG
(GTG)	 AG	186504-186629	GT	TGG
(GTG)	 AG	188276-188389	GT	GGG
(GAT)	 AG	188497-188591	GT	AGG
(ATT)	 AG	191458-191527	CA	GAC
-recovered pasa_asmbl_30646.p1, terminal, 191458, 191527
-recovered pasa_asmbl_30646.p1, internal, 185655, 185843
-recovered pasa_asmbl_30646.p1, internal, 185965, 186143
-recovered pasa_asmbl_30646.p1, internal, 186504, 186629
-recovered pasa_asmbl_30646.p1, internal, 188276, 188389
-recovered pasa_asmbl_30646.p1, internal, 188497, 188591
Valid prediction for snap_scaffold_23-snap.232-T1
Couldn't classify 96969, 97169
Sorry, prediction pasa_asmbl_30655.p1 fails validation.
(ATG)	 TG	86268-86422	GT	AAG
(GTC)	 AG	88129-88200	GT	AGG
(CCC)	 AG	88980-89051	GT	AGG
(GGA)	 AG	89272-89353	GT	AGG
(GCC)	 AG	89514-89547	GT	CGG
(GTT)	 AG	89884-89963	GT	AGG
(GCA)	 AG	90819-90887	GT	AGG
(CTT)	 AG	91239-91319	GT	CGG
(ATC)	 AG	91528-91588	GT	AGG
(AAT)	 AG	91716-91814	GT	GAG
(TGA)	 AG	92892-92961	GT	ACG
(GAC)	 AG	93219-93297	GT	GTG
(TCT)	 AG	93614-93709	GT	TGG
(ATC)	 AG	93888-93929	GT	CTG
(GAT)	 AG	94117-94209	GT	AGG
(GTC)	 AG	94481-94648	GT	AGG
(GGC)	 AG	95957-96037	GT	AGG
(GGA)	 AG	96969-97169	CC	CCC
-recovered pasa_asmbl_30655.p1, initial, 86268, 86422
-recovered pasa_asmbl_30655.p1, terminal, 91716, 91814
-recovered pasa_asmbl_30655.p1, internal, 88129, 88200
-recovered pasa_asmbl_30655.p1, internal, 88980, 89051
-recovered pasa_asmbl_30655.p1, internal, 89272, 89353
-recovered pasa_asmbl_30655.p1, internal, 89514, 89547
-recovered pasa_asmbl_30655.p1, internal, 89884, 89963
-recovered pasa_asmbl_30655.p1, internal, 90819, 90887
-recovered pasa_asmbl_30655.p1, internal, 91239, 91319
-recovered pasa_asmbl_30655.p1, internal, 91528, 91588
-recovered pasa_asmbl_30655.p1, internal, 91716, 91814
-recovered pasa_asmbl_30655.p1, internal, 92892, 92961
-recovered pasa_asmbl_30655.p1, internal, 93219, 93297
-recovered pasa_asmbl_30655.p1, internal, 93614, 93709
-recovered pasa_asmbl_30655.p1, internal, 93888, 93929
-recovered pasa_asmbl_30655.p1, internal, 94117, 94209
-recovered pasa_asmbl_30655.p1, internal, 94481, 94648
-recovered pasa_asmbl_30655.p1, internal, 95957, 96037
Valid prediction for snap_scaffold_23-snap.208-T1
Valid prediction for HiQ_model.g33726.t1
Valid prediction for GlimmerHMM_glimmerT_50483-T1
Valid prediction for snap_scaffold_23-snap.240-T1
Valid prediction for snap_scaffold_23-snap.242-T1
Valid prediction for GlimmerHMM_glimmerT_50477-T1
Valid prediction for Augustus_model.g33715.t1
Valid prediction for snap_scaffold_23-snap.205-T1
Valid prediction for snap_scaffold_23-snap.237-T1
Valid prediction for snap_scaffold_23-snap.204-T1
Valid prediction for GlimmerHMM_glimmerT_50499-T1
Couldn't classify 204487, 204669
Sorry, prediction pasa_asmbl_30642.p1 fails validation.
(GCC)	 AG	204487-204669	GT	TGG
(GTG)	 AG	206169-206282	GT	AGG
(AAG)	 AG	207230-207379	GT	GAG
-recovered pasa_asmbl_30642.p1, terminal, 207230, 207379
-recovered pasa_asmbl_30642.p1, internal, 204487, 204669
-recovered pasa_asmbl_30642.p1, internal, 206169, 206282
-recovered pasa_asmbl_30642.p1, internal, 207230, 207379
Valid prediction for snap_scaffold_23-snap.219-T1
Valid prediction for CodingQuarry_transcript_35551-T1
Valid prediction for snap_scaffold_23-snap.225-T1
Valid prediction for snap_scaffold_23-snap.206-T1
Valid prediction for Augustus_model.g33736.t1
Valid prediction for GlimmerHMM_glimmerT_50485-T1
Valid prediction for snap_scaffold_23-snap.218-T1
Valid prediction for GlimmerHMM_glimmerT_50501-T1
Valid prediction for snap_scaffold_23-snap.211-T1
Valid prediction for snap_scaffold_23-snap.231-T1
Valid prediction for Augustus_model.g33738.t1
Valid prediction for Augustus_model.g33729.t1
Valid prediction for snap_scaffold_23-snap.203-T1
Valid prediction for GlimmerHMM_glimmerT_50479-T1
Valid prediction for Augustus_model.g33716.t1
Valid prediction for GlimmerHMM_glimmerT_50478-T1
Valid prediction for CodingQuarry_transcript_35550-T1
Valid prediction for Augustus_model.g33713.t1
Valid prediction for snap_scaffold_23-snap.217-T1
Valid prediction for snap_scaffold_23-snap.226-T1
Valid prediction for HiQ_model.g33723.t1
Couldn't classify 175139, 175139
Sorry, prediction pasa_asmbl_30648.p1 fails validation.
(AGT)	 TA	175139-175139	GT	AAG
(TGG)	 AG	175797-175890	GT	GAG
(TCA)	 AG	176407-176540	GT	TGG
(ATA)	 AG	177011-177087	GT	GAG
-recovered pasa_asmbl_30648.p1, terminal, 177011, 177087
-recovered pasa_asmbl_30648.p1, internal, 175797, 175890
-recovered pasa_asmbl_30648.p1, internal, 176407, 176540
-recovered pasa_asmbl_30648.p1, internal, 177011, 177087
Valid prediction for snap_scaffold_23-snap.244-T1
Couldn't classify 217263, 217333
Sorry, prediction pasa_asmbl_30639.p1 fails validation.
(ATG)	 GC	213213-213678	GT	CGG
(AGT)	 AG	214702-214755	GT	TGG
(ATT)	 AG	217263-217333	GG	CAG
-recovered pasa_asmbl_30639.p1, initial, 213213, 213678
-recovered pasa_asmbl_30639.p1, internal, 214702, 214755
Valid prediction for GlimmerHMM_glimmerT_50484-T1
Valid prediction for Augustus_model.g33733.t1
Valid prediction for snap_scaffold_23-snap.223-T1
Valid prediction for Augustus_model.g33722.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 110619, rend_intergenic: 105007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204685, rend_intergenic: 202055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243114, rend_intergenic: 238625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 259802
-exon list size: 415


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.2    
2.4    
2.6    
2.9    
3.1    
3.4    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.0    
5.3    
5.5    
5.8    
6.0    
6.2    
6.5    
6.7    
7.0    
7.2    
7.4    
7.7    
7.9    
8.2    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.8    
10.1    
10.3    
10.6    
10.8    
11.0    
11.3    
11.5    
11.8    
12.0    
12.2    
12.5    
12.7    
12.9    
13.2    
13.4    
13.7    
13.9    
14.1    
14.4    
14.6    
14.9    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.5    
16.8    
17.0    
17.3    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
30.9    
31.2    
31.4    
31.7    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.2    
53.5    
53.7    
54.0    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.8    
57.1    
57.3    
57.6    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.6    
61.9    
62.1    
62.4    
62.6    
62.8    
63.1    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.9    
68.1    
68.3    
68.6    
68.8    
69.1    
69.3    
69.5    
69.8    
70.0    
70.3    
70.5    
70.7    
71.0    
71.2    
71.5    
71.7    
71.9    
72.2    
72.4    
72.7    
72.9    
73.1    
73.4    
73.6    
73.9    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.7    
83.0    
83.2    
83.5    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.2    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 110619, rend_intergenic: 105007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204685, rend_intergenic: 202055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243114, rend_intergenic: 238625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support