-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_571989-749224

-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_20-snap.136-T1
Valid prediction for GlimmerHMM_glimmerT_45348-T1
Valid prediction for snap_scaffold_20-snap.131-T1
Valid prediction for GlimmerHMM_glimmerT_45358-T1
Valid prediction for snap_scaffold_20-snap.148-T1
Valid prediction for Augustus_model.g30102.t1
Valid prediction for snap_scaffold_20-snap.125-T1
Valid prediction for GlimmerHMM_glimmerT_45349-T1
Valid prediction for snap_scaffold_20-snap.154-T1
Valid prediction for Augustus_model.g30107.t1
Valid prediction for snap_scaffold_20-snap.137-T1
Valid prediction for snap_scaffold_20-snap.120-T1
Valid prediction for GlimmerHMM_glimmerT_45355-T1
Valid prediction for Augustus_model.g30101.t1
Valid prediction for Augustus_model.g30104.t1
Valid prediction for snap_scaffold_20-snap.134-T1
Valid prediction for Augustus_model.g30112.t1
Valid prediction for Augustus_model.g30114.t1
Valid prediction for GlimmerHMM_glimmerT_45344-T1
Couldn't classify 116698, 116814
Couldn't classify 117429, 117680
Sorry, prediction pasa_asmbl_27166.p1 fails validation.
(GCA)	 CG	116698-116814	GT	TGG
(GTA)	 AG	117429-117680	AG	GGA
Couldn't classify 38188, 38305
Couldn't classify 40488, 40572
Sorry, prediction pasa_asmbl_27220.p2 fails validation.
(AGG)	 CG	38188-38305	GT	AGG
(GTG)	 AG	38428-38562	GT	AGG
(GGG)	 AG	39148-39284	GT	GGG
(AAC)	 AG	39807-39943	GT	AGG
(GGT)	 AG	40488-40572	GA	GTG
-recovered pasa_asmbl_27220.p2, internal, 38428, 38562
-recovered pasa_asmbl_27220.p2, internal, 39148, 39284
-recovered pasa_asmbl_27220.p2, internal, 39807, 39943
Valid prediction for snap_scaffold_20-snap.127-T1
Valid prediction for snap_scaffold_20-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_45345-T1
Valid prediction for snap_scaffold_20-snap.132-T1
Valid prediction for GlimmerHMM_glimmerT_45351-T1
Couldn't classify 151304, 151375
Sorry, prediction pasa_asmbl_26376.p1 fails validation.
(AGA)	 AG	151304-151375	GT	TGG
(GTC)	 AG	152426-153751	GT	AGG
(GCG)	 AG	154235-154300	GT	CGG
(GCG)	 AG	154617-154922	GT	GAG
-recovered pasa_asmbl_26376.p1, terminal, 154617, 154922
-recovered pasa_asmbl_26376.p1, internal, 151304, 151375
-recovered pasa_asmbl_26376.p1, internal, 152426, 153751
-recovered pasa_asmbl_26376.p1, internal, 154235, 154300
-recovered pasa_asmbl_26376.p1, internal, 154617, 154922
Valid prediction for Augustus_model.g30111.t1
Valid prediction for snap_scaffold_20-snap.123-T1
Valid prediction for snap_scaffold_20-snap.142-T1
Valid prediction for snap_scaffold_20-snap.143-T1
Valid prediction for snap_scaffold_20-snap.146-T1
Valid prediction for Augustus_model.g30108.t1
Couldn't classify 37482, 37618
Sorry, prediction pasa_asmbl_26372.p1 fails validation.
(ATG)	 GG	36829-37025	GT	GGG
(GTA)	 AG	37195-37391	GT	TGG
(GTC)	 AG	37482-37618	GT	AGG
-recovered pasa_asmbl_26372.p1, initial, 36829, 37025
-recovered pasa_asmbl_26372.p1, internal, 37195, 37391
-recovered pasa_asmbl_26372.p1, internal, 37482, 37618
Valid prediction for GlimmerHMM_glimmerT_45343-T1
Valid prediction for snap_scaffold_20-snap.128-T1
Valid prediction for snap_scaffold_20-snap.141-T1
Valid prediction for Augustus_model.g30105.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_20-snap.138-T1
Valid prediction for snap_scaffold_20-snap.139-T1
Valid prediction for GlimmerHMM_glimmerT_45361-T1
Couldn't classify 101116, 101505
Sorry, prediction pasa_asmbl_25505.p2 fails validation.
(GAT)	 CA	101116-101505	AA	AGA
Valid prediction for Augustus_model.g30110.t1
Valid prediction for snap_scaffold_20-snap.135-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.152-T1
Valid prediction for snap_scaffold_20-snap.126-T1
Valid prediction for Augustus_model.g30109.t1
Couldn't classify 116177, 116271
Sorry, prediction pasa_asmbl_25503.p1 fails validation.
(TTA)	 GA	116177-116271	GT	AGG
(GTT)	 AG	116605-116717	GT	AGG
(TGG)	 AG	117011-117129	GT	AGG
(GAC)	 AG	117819-117890	GT	AGG
(GAA)	 AG	118043-118063	GT	AGG
(GAG)	 AG	120375-120516	GT	GGG
(GGA)	 AG	120749-120795	GT	GAG
(AGG)	 AG	121001-121082	GT	AGG
(CTC)	 AG	121879-121949	GA	GAG
-recovered pasa_asmbl_25503.p1, terminal, 121879, 121949
-recovered pasa_asmbl_25503.p1, internal, 116605, 116717
-recovered pasa_asmbl_25503.p1, internal, 117011, 117129
-recovered pasa_asmbl_25503.p1, internal, 117819, 117890
-recovered pasa_asmbl_25503.p1, internal, 118043, 118063
-recovered pasa_asmbl_25503.p1, internal, 120375, 120516
-recovered pasa_asmbl_25503.p1, internal, 120749, 120795
-recovered pasa_asmbl_25503.p1, internal, 121001, 121082
Valid prediction for snap_scaffold_20-snap.140-T1
Couldn't classify 115364, 115530
Sorry, prediction pasa_asmbl_26280.p1 fails validation.
(ATG)	 AG	114446-114702	GT	GGG
(ATG)	 AG	114962-115032	GT	AGG
(TGG)	 AG	115364-115530	AT	CCA
-recovered pasa_asmbl_26280.p1, initial, 114446, 114702
-recovered pasa_asmbl_26280.p1, initial, 114962, 115032
-recovered pasa_asmbl_26280.p1, internal, 114446, 114702
-recovered pasa_asmbl_26280.p1, internal, 114962, 115032
Valid prediction for snap_scaffold_20-snap.147-T1
Valid prediction for Augustus_model.g30106.t1
Valid prediction for snap_scaffold_20-snap.124-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_45346-T1
Couldn't classify 15856, 16116
Sorry, prediction pasa_asmbl_25514.p1 fails validation.
(TTT)	 AG	15856-16116	GT	AGG
(GAC)	 AG	16887-17067	GT	GGG
(GTA)	 AG	17559-17728	AC	AAA
-recovered pasa_asmbl_25514.p1, terminal, 17559, 17728
-recovered pasa_asmbl_25514.p1, internal, 15856, 16116
-recovered pasa_asmbl_25514.p1, internal, 16887, 17067
Valid prediction for snap_scaffold_20-snap.121-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_20-snap.151-T1
Valid prediction for GlimmerHMM_glimmerT_45352-T1
Valid prediction for snap_scaffold_20-snap.130-T1
Valid prediction for GlimmerHMM_glimmerT_45342-T1
Valid prediction for snap_scaffold_20-snap.129-T1
Valid prediction for GlimmerHMM_glimmerT_45354-T1
Valid prediction for GlimmerHMM_glimmerT_45353-T1
Valid prediction for CodingQuarry_transcript_30382-T1
Valid prediction for GlimmerHMM_glimmerT_45350-T1
Couldn't classify 144278, 144341
Sorry, prediction pasa_asmbl_25500.p2 fails validation.
(GGG)	 GC	144278-144341	GT	AGG
(CTC)	 AG	144828-144923	GT	AGG
(ACT)	 AG	145098-145238	GT	GGG
(ATC)	 AG	146329-146381	AG	GAA
-recovered pasa_asmbl_25500.p2, terminal, 146329, 146381
-recovered pasa_asmbl_25500.p2, internal, 144828, 144923
-recovered pasa_asmbl_25500.p2, internal, 145098, 145238
Couldn't classify 84394, 84546
Couldn't classify 87149, 87199
Sorry, prediction pasa_asmbl_25512.p1 fails validation.
(CTA)	 GT	84394-84546	GT	AGG
(AAC)	 AG	84751-84884	GT	AGG
(ACG)	 AG	85408-85538	GT	CGG
(GTT)	 AG	86468-86627	GT	AGG
(CAC)	 AG	86816-86987	GT	CGG
(AGC)	 AG	87149-87199	GC	ACG
-recovered pasa_asmbl_25512.p1, internal, 84751, 84884
-recovered pasa_asmbl_25512.p1, internal, 85408, 85538
-recovered pasa_asmbl_25512.p1, internal, 86468, 86627
-recovered pasa_asmbl_25512.p1, internal, 86816, 86987
-recovered pasa_asmbl_25512.p1, internal, 87149, 87199
Valid prediction for GlimmerHMM_glimmerT_45359-T1
Valid prediction for snap_scaffold_20-snap.150-T1
Valid prediction for Augustus_model.g30113.t1
Valid prediction for Augustus_model.g30103.t1
Valid prediction for snap_scaffold_20-snap.133-T1
Couldn't classify 95254, 95496
Couldn't classify 99030, 99113
Sorry, prediction pasa_asmbl_25507.p1 fails validation.
(AGT)	 AA	95254-95496	GT	GGG
(AAG)	 AG	96929-97129	GT	GGG
(GTG)	 AG	98516-98647	GT	AGG
(GTG)	 AG	99030-99113	GG	AGG
-recovered pasa_asmbl_25507.p1, internal, 96929, 97129
-recovered pasa_asmbl_25507.p1, internal, 98516, 98647
Valid prediction for snap_scaffold_20-snap.149-T1
Valid prediction for Augustus_model.g30115.t1
Valid prediction for CodingQuarry_transcript_30383-T1
Valid prediction for snap_scaffold_20-snap.145-T1
Valid prediction for GlimmerHMM_glimmerT_45357-T1
Valid prediction for Augustus_model.g30100.t1
Valid prediction for GlimmerHMM_glimmerT_45356-T1
Valid prediction for GlimmerHMM_glimmerT_45360-T1
Valid prediction for snap_scaffold_20-snap.122-T1
Valid prediction for GlimmerHMM_glimmerT_45347-T1
Valid prediction for snap_scaffold_20-snap.144-T1
Valid prediction for Augustus_model.g30116.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4744, rend_intergenic: 2030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8338, rend_intergenic: 6288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25103, rend_intergenic: 10095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26487, rend_intergenic: 25395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28886, rend_intergenic: 27043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35727, rend_intergenic: 30506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53871, rend_intergenic: 36832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62866, rend_intergenic: 55209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70709, rend_intergenic: 65213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82154, rend_intergenic: 72817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118828, rend_intergenic: 86262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132970, rend_intergenic: 118950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140418, rend_intergenic: 134427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155828, rend_intergenic: 151659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161480, rend_intergenic: 159509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176879, rend_intergenic: 165322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177236
-exon list size: 369


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.4    
8.6    
8.9    
9.2    
9.4    
9.7    
10.0    
10.2    
10.5    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.3    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.6    
22.9    
23.2    
23.5    
23.7    
24.0    
24.3    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
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    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
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    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 4744, rend_intergenic: 2030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8338, rend_intergenic: 6288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25103, rend_intergenic: 10095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26487, rend_intergenic: 25395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28886, rend_intergenic: 27043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35727, rend_intergenic: 30506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53871, rend_intergenic: 36832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62866, rend_intergenic: 55209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70709, rend_intergenic: 65213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82154, rend_intergenic: 72817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118828, rend_intergenic: 86262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132970, rend_intergenic: 118950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140418, rend_intergenic: 134427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155828, rend_intergenic: 151659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161480, rend_intergenic: 159509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176879, rend_intergenic: 165322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support