-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_5810473-5937557

-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 CodingQuarry_transcript_57364-T1
Valid prediction for GeneMark_model.30012_t
Valid prediction for snap_scaffold_7-snap.1228-T1
Valid prediction for snap_scaffold_7-snap.1221-T1
Valid prediction for snap_scaffold_7-snap.1214-T1
Valid prediction for GeneMark_model.30019_t
Valid prediction for CodingQuarry_transcript_57369-T1
Valid prediction for snap_scaffold_7-snap.1227-T1
Valid prediction for GeneMark_model.30016_t
Valid prediction for Augustus_model.g11999.t1
Valid prediction for CodingQuarry_transcript_57359-T1
Valid prediction for snap_scaffold_7-snap.1211-T1
Couldn't classify 64810, 64945
Sorry, prediction pasa_asmbl_50710.p1 fails validation.
(GCG)	 TC	64810-64945	GT	AAG
(ATA)	 AG	65487-65664	GT	AAG
(GAT)	 AG	66772-66917	GT	AGG
(CTA)	 AG	67029-67202	GT	AAG
(GCA)	 AG	67304-67383	GT	AAG
(GGA)	 AG	67465-67574	GT	CCG
(GTC)	 AG	67699-67871	GT	GAG
(AGG)	 AG	67987-68108	AA	AGA
-recovered pasa_asmbl_50710.p1, terminal, 67987, 68108
-recovered pasa_asmbl_50710.p1, internal, 65487, 65664
-recovered pasa_asmbl_50710.p1, internal, 66772, 66917
-recovered pasa_asmbl_50710.p1, internal, 67029, 67202
-recovered pasa_asmbl_50710.p1, internal, 67304, 67383
-recovered pasa_asmbl_50710.p1, internal, 67465, 67574
-recovered pasa_asmbl_50710.p1, internal, 67699, 67871
Couldn't classify 116046, 116069
Sorry, prediction pasa_asmbl_50714.p1 fails validation.
(CTG)	 CC	116046-116069	GT	TGG
(AAC)	 AG	116878-116943	GT	TGG
(GTT)	 AG	117026-117235	GT	GGG
(CAC)	 AG	117535-117648	GT	AGG
(TGA)	 AG	119394-119396	GA	GAG
-recovered pasa_asmbl_50714.p1, terminal, 119394, 119396
-recovered pasa_asmbl_50714.p1, internal, 116878, 116943
-recovered pasa_asmbl_50714.p1, internal, 117026, 117235
-recovered pasa_asmbl_50714.p1, internal, 117535, 117648
Valid prediction for GeneMark_model.30026_t
Valid prediction for GeneMark_model.30022_t
Valid prediction for snap_scaffold_7-snap.1224-T1
Valid prediction for GlimmerHMM_glimmerT_17887-T1
Valid prediction for HiQ_model.g12005.t1
Valid prediction for Augustus_model.g12007.t1
Valid prediction for GlimmerHMM_glimmerT_17880-T1
Valid prediction for GlimmerHMM_glimmerT_17879-T1
Valid prediction for GeneMark_model.30020_t
Valid prediction for GlimmerHMM_glimmerT_17873-T1
Valid prediction for GeneMark_model.30014_t
Valid prediction for GlimmerHMM_glimmerT_17872-T1
Couldn't classify 111565, 111865
Sorry, prediction pasa_asmbl_50711.p1 fails validation.
(CTG)	 GC	111565-111865	GT	AGG
(GCA)	 AG	112415-112594	GT	TGG
(GTG)	 AG	112772-112803	AG	GAA
-recovered pasa_asmbl_50711.p1, terminal, 112772, 112803
-recovered pasa_asmbl_50711.p1, internal, 112415, 112594
Valid prediction for CodingQuarry_transcript_57360-T1
Valid prediction for GlimmerHMM_glimmerT_17882-T1
Valid prediction for snap_scaffold_7-snap.1222-T1
Valid prediction for snap_scaffold_7-snap.1232-T1
Valid prediction for GeneMark_model.30023_t
Valid prediction for GlimmerHMM_glimmerT_17884-T1
Valid prediction for GlimmerHMM_glimmerT_17874-T1
Valid prediction for snap_scaffold_7-snap.1213-T1
Valid prediction for HiQ_model.g12011.t1
Valid prediction for HiQ_model.g12012.t1
Valid prediction for GeneMark_model.30028_t
Valid prediction for GeneMark_model.30013_t
Valid prediction for Augustus_model.g12000.t1
Valid prediction for pasa_asmbl_50708.p1
Valid prediction for snap_scaffold_7-snap.1226-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_17877-T1
Valid prediction for GlimmerHMM_glimmerT_17883-T1
Valid prediction for GeneMark_model.30017_t
Valid prediction for pasa_asmbl_49714.p1
Valid prediction for GeneMark_model.30011_t
Valid prediction for GlimmerHMM_glimmerT_17881-T1
Valid prediction for snap_scaffold_7-snap.1217-T1
Valid prediction for CodingQuarry_transcript_57367-T1
Valid prediction for HiQ_model.g12003.t1
Valid prediction for HiQ_model.g12010.t1
Valid prediction for CodingQuarry_transcript_57362-T1
Valid prediction for GlimmerHMM_glimmerT_17878-T1
Valid prediction for GlimmerHMM_glimmerT_17876-T1
Valid prediction for snap_scaffold_7-snap.1233-T1
Valid prediction for snap_scaffold_7-snap.1219-T1
Valid prediction for GlimmerHMM_glimmerT_17870-T1
Valid prediction for HiQ_model.g12001.t1
Valid prediction for GeneMark_model.30025_t
Valid prediction for Augustus_model.g12006.t1
Valid prediction for GlimmerHMM_glimmerT_17871-T1
Valid prediction for snap_scaffold_7-snap.1223-T1
Valid prediction for HiQ_model.g12009.t1
Valid prediction for CodingQuarry_transcript_57361-T1
Valid prediction for GeneMark_model.30015_t
Valid prediction for CodingQuarry_transcript_57363-T1
Valid prediction for pasa_asmbl_49709.p1
Valid prediction for snap_scaffold_7-snap.1212-T1
Valid prediction for GeneMark_model.30021_t
Valid prediction for pasa_asmbl_49707.p1
Valid prediction for CodingQuarry_transcript_57366-T1
Valid prediction for GeneMark_model.30024_t
Valid prediction for Augustus_model.g11998.t1
Valid prediction for CodingQuarry_transcript_57368-T1
Valid prediction for snap_scaffold_7-snap.1215-T1
Valid prediction for snap_scaffold_7-snap.1231-T1
Valid prediction for GlimmerHMM_glimmerT_17875-T1
Valid prediction for snap_scaffold_7-snap.1216-T1
Valid prediction for snap_scaffold_7-snap.1210-T1
Valid prediction for GeneMark_model.30018_t
Valid prediction for GeneMark_model.30010_t
Valid prediction for GlimmerHMM_glimmerT_17886-T1
Valid prediction for HiQ_model.g12004.t1
Valid prediction for snap_scaffold_7-snap.1234-T1
Valid prediction for Augustus_model.g12002.t1
Valid prediction for snap_scaffold_7-snap.1218-T1
Couldn't classify 57295, 57630
Sorry, prediction pasa_asmbl_49708.p1 fails validation.
(CAG)	 GA	57295-57630	CT	AAC
Valid prediction for Augustus_model.g12013.t1
Valid prediction for pasa_asmbl_49705.p1
Valid prediction for snap_scaffold_7-snap.1229-T1
Valid prediction for pasa_asmbl_49719.p1
Valid prediction for GlimmerHMM_glimmerT_17885-T1
Valid prediction for GeneMark_model.30027_t
Valid prediction for snap_scaffold_7-snap.1225-T1
Valid prediction for HiQ_model.g12008.t1
Valid prediction for snap_scaffold_7-snap.1230-T1
Valid prediction for pasa_asmbl_49706.p1
Valid prediction for snap_scaffold_7-snap.1220-T1
Valid prediction for CodingQuarry_transcript_57365-T1
Valid prediction for GlimmerHMM_glimmerT_17888-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13357, rend_intergenic: 8994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96148, rend_intergenic: 90155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 127085
-exon list size: 294


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.0    
2.4    
2.7    
3.0    
3.4    
3.7    
4.1    
4.4    
4.7    
5.1    
5.4    
5.7    
6.1    
6.4    
6.8    
7.1    
7.4    
7.8    
8.1    
8.4    
8.8    
9.1    
9.5    
9.8    
10.1    
10.5    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.5    
14.9    
15.2    
15.5    
15.9    
16.2    
16.6    
16.9    
17.2    
17.6    
17.9    
18.2    
18.6    
18.9    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.3    
21.6    
22.0    
22.3    
22.6    
23.0    
23.3    
23.6    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.4    
26.7    
27.0    
27.4    
27.7    
28.0    
28.4    
28.7    
29.1    
29.4    
29.7    
30.1    
30.4    
30.7    
31.1    
31.4    
31.8    
32.1    
32.4    
32.8    
33.1    
33.4    
33.8    
34.1    
34.5    
34.8    
35.1    
35.5    
35.8    
36.1    
36.5    
36.8    
37.2    
37.5    
37.8    
38.2    
38.5    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.9    
41.2    
41.6    
41.9    
42.2    
42.6    
42.9    
43.2    
43.6    
43.9    
44.3    
44.6    
44.9    
45.3    
45.6    
45.9    
46.3    
46.6    
47.0    
47.3    
47.6    
48.0    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.0    
52.4    
52.7    
53.0    
53.4    
53.7    
54.1    
54.4    
54.7    
55.1    
55.4    
55.7    
56.1    
56.4    
56.8    
57.1    
57.4    
57.8    
58.1    
58.4    
58.8    
59.1    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.5    
61.8    
62.2    
62.5    
62.8    
63.2    
63.5    
63.9    
64.2    
64.5    
64.9    
65.2    
65.5    
65.9    
66.2    
66.6    
66.9    
67.2    
67.6    
67.9    
68.2    
68.6    
68.9    
69.3    
69.6    
69.9    
70.3    
70.6    
70.9    
71.3    
71.6    
72.0    
72.3    
72.6    
73.0    
73.3    
73.6    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.4    
76.7    
77.0    
77.4    
77.7    
78.0    
78.4    
78.7    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.1    
81.4    
81.8    
82.1    
82.4    
82.8    
83.1    
83.4    
83.8    
84.1    
84.5    
84.8    
85.1    
85.5    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.5    
89.9    
90.2    
90.5    
90.9    
91.2    
91.6    
91.9    
92.2    
92.6    
92.9    
93.2    
93.6    
93.9    
94.3    
94.6    
94.9    
95.3    
95.6    
95.9    
96.3    
96.6    
97.0    
97.3    
97.6    
98.0    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 13357, rend_intergenic: 8994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96148, rend_intergenic: 90155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support