-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_1718822-1904478

-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_37859-T1
Valid prediction for GlimmerHMM_glimmerT_37845-T1
Valid prediction for GlimmerHMM_glimmerT_37834-T1
Valid prediction for GlimmerHMM_glimmerT_37847-T1
Valid prediction for snap_scaffold_16-snap.245-T1
Valid prediction for snap_scaffold_16-snap.252-T1
Valid prediction for snap_scaffold_16-snap.243-T1
Valid prediction for snap_scaffold_16-snap.248-T1
Valid prediction for snap_scaffold_16-snap.261-T1
Valid prediction for GlimmerHMM_glimmerT_37836-T1
Valid prediction for snap_scaffold_16-snap.258-T1
Valid prediction for Augustus_model.g25234.t1
Valid prediction for snap_scaffold_16-snap.270-T1
Valid prediction for HiQ_model.g25236.t1
Valid prediction for HiQ_model.g25243.t1
Valid prediction for Augustus_model.g25231.t1
Valid prediction for Augustus_model.g25238.t1
Valid prediction for HiQ_model.g25240.t1
Couldn't classify 73371, 73772
Sorry, prediction pasa_asmbl_16094.p2 fails validation.
(ATG)	 TC	73371-73772	TG	CCT
Valid prediction for snap_scaffold_16-snap.260-T1
Valid prediction for snap_scaffold_16-snap.274-T1
Valid prediction for GlimmerHMM_glimmerT_37855-T1
Valid prediction for Augustus_model.g25230.t1
Valid prediction for GlimmerHMM_glimmerT_37854-T1
Valid prediction for snap_scaffold_16-snap.256-T1
Valid prediction for pasa_asmbl_16087.p1
Valid prediction for GlimmerHMM_glimmerT_37837-T1
Valid prediction for GlimmerHMM_glimmerT_37846-T1
Valid prediction for GlimmerHMM_glimmerT_37856-T1
Valid prediction for snap_scaffold_16-snap.246-T1
Valid prediction for snap_scaffold_16-snap.266-T1
Valid prediction for snap_scaffold_16-snap.269-T1
Valid prediction for snap_scaffold_16-snap.262-T1
Valid prediction for snap_scaffold_16-snap.264-T1
Valid prediction for Augustus_model.g25233.t1
Valid prediction for GlimmerHMM_glimmerT_37843-T1
Valid prediction for GlimmerHMM_glimmerT_37853-T1
Valid prediction for GlimmerHMM_glimmerT_37841-T1
Valid prediction for snap_scaffold_16-snap.257-T1
Valid prediction for GlimmerHMM_glimmerT_37851-T1
Valid prediction for snap_scaffold_16-snap.254-T1
Valid prediction for GlimmerHMM_glimmerT_37850-T1
Valid prediction for snap_scaffold_16-snap.244-T1
Couldn't classify 159277, 159372
Sorry, prediction pasa_asmbl_16102.p1 fails validation.
(ATG)	 AA	154301-154308	GT	GGG
(TGA)	 AG	155606-155627	GT	AGG
(AGG)	 AG	157121-157190	GT	TGG
(ACG)	 AG	157868-158040	GC	AGG
(GCC)	 AG	158290-158430	GT	AGG
(AGG)	 AG	158637-158801	GT	AAG
(ATC)	 AG	159277-159372	GC	CCG
-recovered pasa_asmbl_16102.p1, initial, 154301, 154308
-recovered pasa_asmbl_16102.p1, internal, 155606, 155627
-recovered pasa_asmbl_16102.p1, internal, 157121, 157190
-recovered pasa_asmbl_16102.p1, internal, 157868, 158040
-recovered pasa_asmbl_16102.p1, internal, 158290, 158430
-recovered pasa_asmbl_16102.p1, internal, 158637, 158801
-recovered pasa_asmbl_16102.p1, internal, 159277, 159372
Couldn't classify 86970, 87105
Sorry, prediction pasa_asmbl_16098.p1 fails validation.
(ATG)	 CG	85039-85202	GT	AGG
(TCG)	 AG	85361-85406	GT	AGG
(AAA)	 AG	85495-85584	GT	AGG
(TTG)	 AG	85703-85812	GT	AGG
(AAA)	 AG	85935-86021	GT	AGG
(TCA)	 AG	86141-86225	GT	CAG
(GCC)	 AG	86457-86561	GT	CGG
(TGT)	 AG	86738-86865	GT	AAG
(GTA)	 AG	86970-87105	GT	AGG
-recovered pasa_asmbl_16098.p1, initial, 85039, 85202
-recovered pasa_asmbl_16098.p1, internal, 85361, 85406
-recovered pasa_asmbl_16098.p1, internal, 85495, 85584
-recovered pasa_asmbl_16098.p1, internal, 85703, 85812
-recovered pasa_asmbl_16098.p1, internal, 85935, 86021
-recovered pasa_asmbl_16098.p1, internal, 86141, 86225
-recovered pasa_asmbl_16098.p1, internal, 86457, 86561
-recovered pasa_asmbl_16098.p1, internal, 86738, 86865
-recovered pasa_asmbl_16098.p1, internal, 86970, 87105
Couldn't classify 159630, 159819
Sorry, prediction pasa_asmbl_16104.p1 fails validation.
(GCT)	 AG	159630-159819	GT	CGG
(GTG)	 AG	160338-160453	GT	AGG
(ATG)	 AG	162242-162275	GT	CGG
(GCG)	 AG	162810-162902	GT	AGG
(CCA)	 AG	163197-163413	GT	CCG
(TCA)	 AG	163579-163656	GT	CAG
(AGA)	 AG	163928-164057	GT	GAG
-recovered pasa_asmbl_16104.p1, initial, 162242, 162275
-recovered pasa_asmbl_16104.p1, terminal, 162810, 162902
-recovered pasa_asmbl_16104.p1, terminal, 163928, 164057
-recovered pasa_asmbl_16104.p1, internal, 159630, 159819
-recovered pasa_asmbl_16104.p1, internal, 160338, 160453
-recovered pasa_asmbl_16104.p1, internal, 162242, 162275
-recovered pasa_asmbl_16104.p1, internal, 162810, 162902
-recovered pasa_asmbl_16104.p1, internal, 163197, 163413
-recovered pasa_asmbl_16104.p1, internal, 163579, 163656
-recovered pasa_asmbl_16104.p1, internal, 163928, 164057
Couldn't classify 73857, 74513
Sorry, prediction pasa_asmbl_16095.p2 fails validation.
(CGA)	 GA	73857-74513	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_37839-T1
Valid prediction for Augustus_model.g25241.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 GlimmerHMM_glimmerT_37860-T1
Valid prediction for GlimmerHMM_glimmerT_37838-T1
Valid prediction for HiQ_model.g25239.t1
Valid prediction for snap_scaffold_16-snap.268-T1
Valid prediction for snap_scaffold_16-snap.263-T1
Valid prediction for snap_scaffold_16-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_37833-T1
Valid prediction for snap_scaffold_16-snap.255-T1
Valid prediction for snap_scaffold_16-snap.251-T1
Couldn't classify 107209, 107306
Sorry, prediction pasa_asmbl_16954.p1 fails validation.
(ATG)	 GC	100893-101158	GT	AGG
(CGC)	 AG	101240-101339	GT	AGG
(GTT)	 AG	102361-102486	GT	AGG
(GGG)	 AG	102697-102858	GT	AGG
(GTG)	 AG	103227-103391	GT	AGG
(GCA)	 AG	103494-103635	GT	AGG
(GTG)	 AG	103832-103953	GC	AGG
(GGG)	 AG	104251-104357	GT	AGG
(TCT)	 AG	104545-104659	GT	AGG
(GAA)	 AG	104840-104917	GT	AGG
(GGG)	 AG	105689-105827	GT	TGG
(ACA)	 AG	106112-106219	GT	CGG
(AGC)	 AG	107209-107306	GG	GCG
-recovered pasa_asmbl_16954.p1, initial, 100893, 101158
-recovered pasa_asmbl_16954.p1, internal, 101240, 101339
-recovered pasa_asmbl_16954.p1, internal, 102361, 102486
-recovered pasa_asmbl_16954.p1, internal, 102697, 102858
-recovered pasa_asmbl_16954.p1, internal, 103227, 103391
-recovered pasa_asmbl_16954.p1, internal, 103494, 103635
-recovered pasa_asmbl_16954.p1, internal, 103832, 103953
-recovered pasa_asmbl_16954.p1, internal, 104251, 104357
-recovered pasa_asmbl_16954.p1, internal, 104545, 104659
-recovered pasa_asmbl_16954.p1, internal, 104840, 104917
-recovered pasa_asmbl_16954.p1, internal, 105689, 105827
-recovered pasa_asmbl_16954.p1, internal, 106112, 106219
Valid prediction for snap_scaffold_16-snap.265-T1
Valid prediction for GlimmerHMM_glimmerT_37858-T1
Valid prediction for snap_scaffold_16-snap.249-T1
Valid prediction for snap_scaffold_16-snap.273-T1
Couldn't classify 106112, 106112
Sorry, prediction CodingQuarry_transcript_19902-T1 fails validation.
(ATG)	 AG	104884-104917	GT	AGG
(GGG)	 AG	105689-105827	GT	TGG
(ACA)	 AG	106112-106112	CA	GAC
-recovered CodingQuarry_transcript_19902-T1, initial, 104884, 104917
-recovered CodingQuarry_transcript_19902-T1, internal, 104884, 104917
-recovered CodingQuarry_transcript_19902-T1, internal, 105689, 105827
Couldn't classify 115686, 115774
Sorry, prediction pasa_asmbl_16952.p1 fails validation.
(GGT)	 AT	115686-115774	GT	AGG
(ACA)	 AG	116185-116270	GT	TGG
(ACG)	 AG	116397-116468	GT	GGG
(GGG)	 AG	116587-116741	GT	ATG
(GAG)	 AG	116925-117041	GT	AGG
(ATT)	 AG	117221-117330	GT	ATG
(GTA)	 AG	117529-117643	GA	GAG
-recovered pasa_asmbl_16952.p1, terminal, 117529, 117643
-recovered pasa_asmbl_16952.p1, internal, 116185, 116270
-recovered pasa_asmbl_16952.p1, internal, 116397, 116468
-recovered pasa_asmbl_16952.p1, internal, 116587, 116741
-recovered pasa_asmbl_16952.p1, internal, 116925, 117041
-recovered pasa_asmbl_16952.p1, internal, 117221, 117330
Valid prediction for CodingQuarry_transcript_19903-T1
Valid prediction for GlimmerHMM_glimmerT_37842-T1
Valid prediction for snap_scaffold_16-snap.253-T1
Valid prediction for GlimmerHMM_glimmerT_37835-T1
Valid prediction for snap_scaffold_16-snap.247-T1
Valid prediction for Augustus_model.g25242.t1
Valid prediction for GlimmerHMM_glimmerT_37844-T1
Valid prediction for snap_scaffold_16-snap.267-T1
Valid prediction for Augustus_model.g25232.t1
Valid prediction for GlimmerHMM_glimmerT_37852-T1
Valid prediction for GlimmerHMM_glimmerT_37848-T1
Valid prediction for snap_scaffold_16-snap.250-T1
Valid prediction for snap_scaffold_16-snap.259-T1
Valid prediction for snap_scaffold_16-snap.271-T1
Valid prediction for Augustus_model.g25235.t1
Valid prediction for Augustus_model.g25237.t1
Valid prediction for GlimmerHMM_glimmerT_37849-T1
Valid prediction for GlimmerHMM_glimmerT_37840-T1
Valid prediction for Augustus_model.g25244.t1
Valid prediction for GlimmerHMM_glimmerT_37857-T1
Valid prediction for snap_scaffold_16-snap.275-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 47095, rend_intergenic: 38003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100092, rend_intergenic: 99097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103281, rend_intergenic: 100578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113403, rend_intergenic: 113074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124224, rend_intergenic: 113516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130001, rend_intergenic: 129161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144327, rend_intergenic: 130020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170265, rend_intergenic: 159650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178168, rend_intergenic: 174343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185657
-exon list size: 362


building trellis

0.3    
0.5    
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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    
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5.5    
5.8    
6.0    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.1    
9.3    
9.6    
9.9    
10.2    
10.4    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.7    
15.9    
16.2    
16.5    
16.8    
17.0    
17.3    
17.6    
17.9    
18.1    
18.4    
18.7    
19.0    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.4    
23.6    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.0    
31.3    
31.6    
31.9    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.1    
59.3    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.7    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.1    
68.4    
68.7    
69.0    
69.2    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.2    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.0    
81.3    
81.6    
81.9    
82.1    
82.4    
82.7    
83.0    
83.2    
83.5    
83.8    
84.1    
84.3    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.9    
93.1    
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 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 47095, rend_intergenic: 38003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100092, rend_intergenic: 99097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103281, rend_intergenic: 100578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113403, rend_intergenic: 113074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124224, rend_intergenic: 113516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130001, rend_intergenic: 129161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144327, rend_intergenic: 130020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170265, rend_intergenic: 159650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178168, rend_intergenic: 174343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support