-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_5768795-5930594

-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_57390-T1
Valid prediction for pasa_asmbl_36363.p1
Valid prediction for snap_scaffold_27-snap.1385-T1
Valid prediction for snap_scaffold_27-snap.1377-T1
Valid prediction for GlimmerHMM_glimmerT_57389-T1
Valid prediction for snap_scaffold_27-snap.1375-T1
Valid prediction for CodingQuarry_transcript_41906-T1
Valid prediction for snap_scaffold_27-snap.1389-T1
Valid prediction for snap_scaffold_27-snap.1373-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1378-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g38028.t1
Valid prediction for GlimmerHMM_glimmerT_57401-T1
Valid prediction for snap_scaffold_27-snap.1382-T1
Valid prediction for CodingQuarry_transcript_41907-T1
Valid prediction for GlimmerHMM_glimmerT_57404-T1
Valid prediction for snap_scaffold_27-snap.1381-T1
Valid prediction for snap_scaffold_27-snap.1359-T1
Valid prediction for snap_scaffold_27-snap.1371-T1
Valid prediction for snap_scaffold_27-snap.1372-T1
Valid prediction for snap_scaffold_27-snap.1370-T1
Valid prediction for snap_scaffold_27-snap.1392-T1
Valid prediction for snap_scaffold_27-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_57399-T1
Valid prediction for snap_scaffold_27-snap.1387-T1
Valid prediction for GlimmerHMM_glimmerT_57403-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_27-snap.1376-T1
Valid prediction for Augustus_model.g38024.t1
Valid prediction for Augustus_model.g38026.t1
Valid prediction for CodingQuarry_transcript_41905-T1
Valid prediction for Augustus_model.g38020.t1
Valid prediction for CodingQuarry_transcript_41904-T1
Valid prediction for Augustus_model.g38022.t1
Valid prediction for HiQ_model.g38025.t1
Valid prediction for snap_scaffold_27-snap.1369-T1
Valid prediction for Augustus_model.g38030.t1
Valid prediction for snap_scaffold_27-snap.1390-T1
Valid prediction for Augustus_model.g38029.t1
Valid prediction for snap_scaffold_27-snap.1368-T1
Valid prediction for GlimmerHMM_glimmerT_57392-T1
Valid prediction for snap_scaffold_27-snap.1379-T1
Valid prediction for snap_scaffold_27-snap.1365-T1
Valid prediction for CodingQuarry_transcript_41908-T1
Valid prediction for GlimmerHMM_glimmerT_57386-T1
Couldn't classify 126130, 126270
Sorry, prediction pasa_asmbl_37203.p1 fails validation.
(ATG)	 AG	124573-124735	GT	CGG
(GGG)	 AG	124941-125428	GT	TGG
(TCA)	 AG	125603-125668	GT	AGG
(GTG)	 AG	126130-126270	TT	CCT
-recovered pasa_asmbl_37203.p1, initial, 124573, 124735
-recovered pasa_asmbl_37203.p1, internal, 124573, 124735
-recovered pasa_asmbl_37203.p1, internal, 124941, 125428
-recovered pasa_asmbl_37203.p1, internal, 125603, 125668
Valid prediction for GlimmerHMM_glimmerT_57396-T1
Valid prediction for GlimmerHMM_glimmerT_57394-T1
Valid prediction for snap_scaffold_27-snap.1384-T1
Valid prediction for CodingQuarry_transcript_41899-T1
Valid prediction for pasa_asmbl_37019.p1
Valid prediction for CodingQuarry_transcript_41900-T1
Valid prediction for GlimmerHMM_glimmerT_57385-T1
Valid prediction for GlimmerHMM_glimmerT_57384-T1
Valid prediction for CodingQuarry_transcript_41901-T1
Valid prediction for CodingQuarry_transcript_41903-T1
Couldn't classify 31655, 31969
Sorry, prediction pasa_asmbl_37039.p1 fails validation.
(CAG)	 GA	31655-31969	GT	AAG
Couldn't classify 88476, 88898
Sorry, prediction pasa_asmbl_37037.p1 fails validation.
(TCC)	 TC	88476-88898	AC	AAA
Valid prediction for snap_scaffold_27-snap.1366-T1
Valid prediction for GlimmerHMM_glimmerT_57388-T1
Couldn't classify 130271, 130392
Sorry, prediction pasa_asmbl_37024.p1 fails validation.
(GAG)	 CA	130271-130392	GT	AGG
(GCA)	 AG	130618-130793	GT	GGG
(CTG)	 AG	131103-131224	GT	AGG
(ATA)	 AG	131452-131530	GT	CGG
(GTC)	 AG	132669-132751	GT	AGG
(GTG)	 AG	132974-133138	GT	TGG
(CTG)	 AG	133861-134023	GT	AGG
(GCA)	 AG	134371-134564	GT	AGG
(GGT)	 AG	134705-134842	GT	CCG
(GAA)	 AG	135145-135294	GT	ACG
(ATC)	 AG	135615-135842	GT	AGG
(GAT)	 AG	136010-136228	GT	AGG
(ACT)	 AG	136399-136543	GT	GAG
(GTG)	 AG	136704-136777	GT	TTG
(CAA)	 AG	137262-137309	AG	AGA
-recovered pasa_asmbl_37024.p1, terminal, 137262, 137309
-recovered pasa_asmbl_37024.p1, internal, 130618, 130793
-recovered pasa_asmbl_37024.p1, internal, 131103, 131224
-recovered pasa_asmbl_37024.p1, internal, 131452, 131530
-recovered pasa_asmbl_37024.p1, internal, 132669, 132751
-recovered pasa_asmbl_37024.p1, internal, 132974, 133138
-recovered pasa_asmbl_37024.p1, internal, 133861, 134023
-recovered pasa_asmbl_37024.p1, internal, 134371, 134564
-recovered pasa_asmbl_37024.p1, internal, 134705, 134842
-recovered pasa_asmbl_37024.p1, internal, 135145, 135294
-recovered pasa_asmbl_37024.p1, internal, 135615, 135842
-recovered pasa_asmbl_37024.p1, internal, 136010, 136228
-recovered pasa_asmbl_37024.p1, internal, 136399, 136543
-recovered pasa_asmbl_37024.p1, internal, 136704, 136777
Couldn't classify 115858, 115972
Couldn't classify 118126, 118142
Sorry, prediction pasa_asmbl_37032.p1 fails validation.
(GTG)	 TG	115858-115972	GT	TGG
(TGC)	 AG	116298-116407	GT	TGG
(CTG)	 AG	116703-116815	GT	GCG
(GCT)	 AG	116992-117110	GT	CGG
(ATA)	 AG	117400-117455	GT	AGG
(CTG)	 AG	117615-117821	GT	AGG
(GAT)	 AG	117908-118031	GT	TGG
(GGT)	 AG	118126-118142	TC	ACT
-recovered pasa_asmbl_37032.p1, internal, 116298, 116407
-recovered pasa_asmbl_37032.p1, internal, 116703, 116815
-recovered pasa_asmbl_37032.p1, internal, 116992, 117110
-recovered pasa_asmbl_37032.p1, internal, 117400, 117455
-recovered pasa_asmbl_37032.p1, internal, 117615, 117821
-recovered pasa_asmbl_37032.p1, internal, 117908, 118031
Valid prediction for CodingQuarry_transcript_41902-T1
Valid prediction for GlimmerHMM_glimmerT_57397-T1
Valid prediction for snap_scaffold_27-snap.1361-T1
Valid prediction for snap_scaffold_27-snap.1374-T1
Valid prediction for snap_scaffold_27-snap.1386-T1
Couldn't classify 61119, 61631
Sorry, prediction pasa_asmbl_37038.p1 fails validation.
(GGG)	 AC	61119-61631	AG	TGA
Valid prediction for GlimmerHMM_glimmerT_57393-T1
Couldn't classify 111807, 112023
Couldn't classify 113201, 113388
Sorry, prediction pasa_asmbl_37033.p2 fails validation.
(GGA)	 AC	111807-112023	GT	AGG
(GCT)	 AG	113201-113388	CC	CCC
Valid prediction for GlimmerHMM_glimmerT_57391-T1
Valid prediction for GlimmerHMM_glimmerT_57395-T1
Valid prediction for GlimmerHMM_glimmerT_57405-T1
Valid prediction for snap_scaffold_27-snap.1380-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for pasa_asmbl_37041.p1
Valid prediction for GlimmerHMM_glimmerT_57387-T1
Valid prediction for Augustus_model.g38021.t1
Valid prediction for snap_scaffold_27-snap.1367-T1
Valid prediction for GlimmerHMM_glimmerT_57402-T1
Valid prediction for snap_scaffold_27-snap.1388-T1
Valid prediction for snap_scaffold_27-snap.1363-T1
Valid prediction for snap_scaffold_27-snap.1393-T1
Valid prediction for snap_scaffold_27-snap.1364-T1
Valid prediction for snap_scaffold_27-snap.1383-T1
Valid prediction for HiQ_model.g38031.t1
Couldn't classify 111430, 111677
Sorry, prediction pasa_asmbl_37034.p1 fails validation.
(ATG)	 AA	108438-108498	GT	TGG
(GCC)	 AG	111430-111677	CC	GCC
-recovered pasa_asmbl_37034.p1, initial, 108438, 108498
Valid prediction for snap_scaffold_27-snap.1360-T1
Valid prediction for GlimmerHMM_glimmerT_57406-T1
Valid prediction for snap_scaffold_27-snap.1362-T1
Valid prediction for GlimmerHMM_glimmerT_57398-T1
Valid prediction for Augustus_model.g38023.t1
Couldn't classify 118236, 118284
Sorry, prediction pasa_asmbl_37031.p1 fails validation.
(ACG)	 TG	118236-118284	GT	AGG
(GCC)	 AG	118390-118563	GT	AGG
(GAG)	 AG	118855-118965	GT	GGG
(CTG)	 AG	119074-119249	GT	AGG
(ATG)	 AG	119624-119761	GT	AGG
(GGG)	 AG	119976-120080	GT	CGG
(GTC)	 AG	120162-120254	GT	TGG
(AAC)	 AG	120865-120968	GT	AGG
(GGA)	 AG	121444-121558	AG	AAA
-recovered pasa_asmbl_37031.p1, initial, 119624, 119761
-recovered pasa_asmbl_37031.p1, terminal, 121444, 121558
-recovered pasa_asmbl_37031.p1, internal, 118390, 118563
-recovered pasa_asmbl_37031.p1, internal, 118855, 118965
-recovered pasa_asmbl_37031.p1, internal, 119074, 119249
-recovered pasa_asmbl_37031.p1, internal, 119624, 119761
-recovered pasa_asmbl_37031.p1, internal, 119976, 120080
-recovered pasa_asmbl_37031.p1, internal, 120162, 120254
-recovered pasa_asmbl_37031.p1, internal, 120865, 120968
Valid prediction for Augustus_model.g38027.t1
Valid prediction for GlimmerHMM_glimmerT_57400-T1
Valid prediction for GlimmerHMM_glimmerT_57383-T1
Couldn't classify 129326, 129594
Sorry, prediction pasa_asmbl_37028.p1 fails validation.
(ATG)	 AC	128062-128078	GT	AGG
(ACA)	 AG	128337-128519	GT	AGG
(GCG)	 AG	128602-128724	GT	AAG
(GTC)	 AG	128833-128920	GT	ACG
(CAA)	 AG	129020-129188	GT	CGG
(ACG)	 AG	129326-129594	GT	AGG
-recovered pasa_asmbl_37028.p1, initial, 128062, 128078
-recovered pasa_asmbl_37028.p1, internal, 128337, 128519
-recovered pasa_asmbl_37028.p1, internal, 128602, 128724
-recovered pasa_asmbl_37028.p1, internal, 128833, 128920
-recovered pasa_asmbl_37028.p1, internal, 129020, 129188
-recovered pasa_asmbl_37028.p1, internal, 129326, 129594

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6025, rend_intergenic: 2903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50871, rend_intergenic: 39989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66225, rend_intergenic: 63952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66914, rend_intergenic: 66311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76041, rend_intergenic: 68661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100740, rend_intergenic: 76062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109367, rend_intergenic: 100936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132508, rend_intergenic: 111494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133608, rend_intergenic: 133063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139973, rend_intergenic: 133907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141777, rend_intergenic: 140020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147329, rend_intergenic: 142450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153403, rend_intergenic: 150879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159483, rend_intergenic: 156824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 64907, rend_intergenic: 64904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 148722, rend_intergenic: 148719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161800
-exon list size: 363


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.7    
4.9    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.8    
7.1    
7.4    
7.7    
7.9    
8.2    
8.5    
8.8    
9.0    
9.3    
9.6    
9.9    
10.1    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.5    
19.7    
20.0    
20.3    
20.5    
20.8    
21.1    
21.4    
21.6    
21.9    
22.2    
22.5    
22.7    
23.0    
23.3    
23.6    
23.8    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.8    
26.0    
26.3    
26.6    
26.8    
27.1    
27.4    
27.7    
27.9    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.9    
30.1    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.2    
36.4    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.4    
38.6    
38.9    
39.2    
39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.7    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.3    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.7    
60.0    
60.3    
60.5    
60.8    
61.1    
61.4    
61.6    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.6    
63.8    
64.1    
64.4    
64.7    
64.9    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.9    
70.1    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.1    
72.3    
72.6    
72.9    
73.2    
73.4    
73.7    
74.0    
74.2    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.2    
76.4    
76.7    
77.0    
77.3    
77.5    
77.8    
78.1    
78.4    
78.6    
78.9    
79.2    
79.5    
79.7    
80.0    
80.3    
80.5    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.1    
90.4    
90.7    
91.0    
91.2    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.1    
95.3    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 6025, rend_intergenic: 2903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50871, rend_intergenic: 39989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66225, rend_intergenic: 63952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66914, rend_intergenic: 66311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76041, rend_intergenic: 68661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100740, rend_intergenic: 76062  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109367, rend_intergenic: 100936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132508, rend_intergenic: 111494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133608, rend_intergenic: 133063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139973, rend_intergenic: 133907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141777, rend_intergenic: 140020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147329, rend_intergenic: 142450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153403, rend_intergenic: 150879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159483, rend_intergenic: 156824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 64907, rend_intergenic: 64904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 148722, rend_intergenic: 148719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support