-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_15162036-15505485

-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 HiQ_model.g18787.t1
Valid prediction for Augustus_model.g18778.t1
Valid prediction for snap_scaffold_11-snap.3112-T1
Valid prediction for snap_scaffold_11-snap.3128-T1
Valid prediction for snap_scaffold_11-snap.3115-T1
Valid prediction for Augustus_model.g18783.t1
Valid prediction for snap_scaffold_11-snap.3137-T1
Valid prediction for Augustus_model.g18788.t1
Valid prediction for snap_scaffold_11-snap.3140-T1
Couldn't classify 100046, 100322
Sorry, prediction pasa_asmbl_6112.p1 fails validation.
(GAG)	 AG	100046-100322	GT	CAG
(AAG)	 AG	101515-101567	GT	TGG
(GAT)	 AG	101849-101921	GT	AGG
(GAA)	 AG	102038-102144	GT	AGG
(AAC)	 AG	102228-102389	GT	AGG
(ATT)	 AG	103197-103295	GT	AGG
(GTA)	 AG	103384-103651	GT	AGG
(CAA)	 AG	104367-104452	GT	AGG
(GAC)	 AG	104622-104795	TG	AGT
-recovered pasa_asmbl_6112.p1, terminal, 104622, 104795
-recovered pasa_asmbl_6112.p1, internal, 100046, 100322
-recovered pasa_asmbl_6112.p1, internal, 101515, 101567
-recovered pasa_asmbl_6112.p1, internal, 101849, 101921
-recovered pasa_asmbl_6112.p1, internal, 102038, 102144
-recovered pasa_asmbl_6112.p1, internal, 102228, 102389
-recovered pasa_asmbl_6112.p1, internal, 103197, 103295
-recovered pasa_asmbl_6112.p1, internal, 103384, 103651
-recovered pasa_asmbl_6112.p1, internal, 104367, 104452
Valid prediction for Augustus_model.g18785.t1
Valid prediction for snap_scaffold_11-snap.3131-T1
Valid prediction for HiQ_model.g18784.t1
Valid prediction for GlimmerHMM_glimmerT_28360-T1
Valid prediction for GlimmerHMM_glimmerT_28350-T1
Valid prediction for HiQ_model.g18781.t1
Valid prediction for snap_scaffold_11-snap.3119-T1
Valid prediction for GlimmerHMM_glimmerT_28354-T1
Valid prediction for GlimmerHMM_glimmerT_28355-T1
Valid prediction for Augustus_model.g18789.t1
Valid prediction for snap_scaffold_11-snap.3136-T1
Valid prediction for GlimmerHMM_glimmerT_28366-T1
Valid prediction for snap_scaffold_11-snap.3117-T1
Valid prediction for GlimmerHMM_glimmerT_28353-T1
Valid prediction for snap_scaffold_11-snap.3123-T1
Valid prediction for GlimmerHMM_glimmerT_28349-T1
Valid prediction for GlimmerHMM_glimmerT_28373-T1
Valid prediction for GlimmerHMM_glimmerT_28352-T1
Valid prediction for GlimmerHMM_glimmerT_28367-T1
Valid prediction for GlimmerHMM_glimmerT_28363-T1
Valid prediction for snap_scaffold_11-snap.3138-T1
Valid prediction for GlimmerHMM_glimmerT_28371-T1
Valid prediction for snap_scaffold_11-snap.3122-T1
Valid prediction for GlimmerHMM_glimmerT_28374-T1
Valid prediction for GlimmerHMM_glimmerT_28356-T1
Valid prediction for GlimmerHMM_glimmerT_28347-T1
Valid prediction for snap_scaffold_11-snap.3116-T1
Valid prediction for snap_scaffold_11-snap.3120-T1
Valid prediction for snap_scaffold_11-snap.3125-T1
Valid prediction for snap_scaffold_11-snap.3130-T1
Valid prediction for Augustus_model.g18782.t1
Valid prediction for GlimmerHMM_glimmerT_28372-T1
Valid prediction for GlimmerHMM_glimmerT_28370-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_11-snap.3135-T1
Valid prediction for GlimmerHMM_glimmerT_28351-T1
Valid prediction for Augustus_model.g18777.t1
Valid prediction for Augustus_model.g18780.t1
Valid prediction for GlimmerHMM_glimmerT_28359-T1
Valid prediction for GlimmerHMM_glimmerT_28375-T1
Valid prediction for Augustus_model.g18790.t1
Valid prediction for GlimmerHMM_glimmerT_28346-T1
Valid prediction for snap_scaffold_11-snap.3113-T1
Valid prediction for snap_scaffold_11-snap.3108-T1
Valid prediction for Augustus_model.g18791.t1
Valid prediction for snap_scaffold_11-snap.3107-T1
Valid prediction for pasa_asmbl_7189.p1
Valid prediction for snap_scaffold_11-snap.3127-T1
Valid prediction for snap_scaffold_11-snap.3110-T1
Valid prediction for snap_scaffold_11-snap.3133-T1
Valid prediction for GlimmerHMM_glimmerT_28362-T1
Valid prediction for GlimmerHMM_glimmerT_28344-T1
Valid prediction for GlimmerHMM_glimmerT_28361-T1
Valid prediction for GlimmerHMM_glimmerT_28358-T1
Valid prediction for GlimmerHMM_glimmerT_28364-T1
Valid prediction for HiQ_model.g18776.t1
Valid prediction for GlimmerHMM_glimmerT_28348-T1
Valid prediction for GlimmerHMM_glimmerT_28345-T1
Valid prediction for snap_scaffold_11-snap.3126-T1
Valid prediction for snap_scaffold_11-snap.3106-T1
Valid prediction for Augustus_model.g18786.t1
Valid prediction for snap_scaffold_11-snap.3132-T1
Valid prediction for snap_scaffold_11-snap.3109-T1
Valid prediction for CodingQuarry_transcript_8319-T1
Couldn't classify 309666, 309701
Sorry, prediction pasa_asmbl_7192.p1 fails validation.
(ACC)	 GC	309666-309701	GT	TCG
(TCC)	 AG	310745-310864	GT	TGG
(GGT)	 AG	311023-311082	GT	ATG
(TCT)	 AG	311760-311828	GT	TGG
(GTG)	 AG	311941-312087	GT	AGG
(AAT)	 AG	313454-313578	GT	CGG
(AGA)	 AG	314359-314546	GT	TGG
(GGA)	 AG	314647-314733	GT	AGG
(GTG)	 AG	315748-316043	TG	GAT
-recovered pasa_asmbl_7192.p1, terminal, 315748, 316043
-recovered pasa_asmbl_7192.p1, internal, 310745, 310864
-recovered pasa_asmbl_7192.p1, internal, 311023, 311082
-recovered pasa_asmbl_7192.p1, internal, 311760, 311828
-recovered pasa_asmbl_7192.p1, internal, 311941, 312087
-recovered pasa_asmbl_7192.p1, internal, 313454, 313578
-recovered pasa_asmbl_7192.p1, internal, 314359, 314546
-recovered pasa_asmbl_7192.p1, internal, 314647, 314733
Valid prediction for snap_scaffold_11-snap.3134-T1
Valid prediction for GlimmerHMM_glimmerT_28368-T1
Valid prediction for snap_scaffold_11-snap.3124-T1
Valid prediction for GlimmerHMM_glimmerT_28369-T1
Valid prediction for Augustus_model.g18792.t1
Valid prediction for CodingQuarry_transcript_8318-T1
Valid prediction for snap_scaffold_11-snap.3118-T1
Valid prediction for snap_scaffold_11-snap.3121-T1
Valid prediction for snap_scaffold_11-snap.3139-T1
Valid prediction for GlimmerHMM_glimmerT_28357-T1
Valid prediction for snap_scaffold_11-snap.3114-T1
Valid prediction for GlimmerHMM_glimmerT_28365-T1
Valid prediction for snap_scaffold_11-snap.3129-T1
Couldn't classify 280320, 280487
Sorry, prediction pasa_asmbl_7194.p1 fails validation.
(GGC)	 AG	280320-280487	GT	TGG
(GAC)	 AG	280957-281056	GT	TGG
(AGC)	 AG	281250-281366	GT	AGG
(GTG)	 AG	281491-281672	AG	AGA
-recovered pasa_asmbl_7194.p1, terminal, 281491, 281672
-recovered pasa_asmbl_7194.p1, internal, 280320, 280487
-recovered pasa_asmbl_7194.p1, internal, 280957, 281056
-recovered pasa_asmbl_7194.p1, internal, 281250, 281366
Valid prediction for snap_scaffold_11-snap.3111-T1
Valid prediction for Augustus_model.g18779.t1
Couldn't classify 340055, 340078
Couldn't classify 341603, 341755
Sorry, prediction pasa_asmbl_7188.p1 fails validation.
(AGT)	 AG	340055-340078	GT	AAG
(TGC)	 AG	340518-340679	GT	AGG
(AGT)	 AG	340812-340968	GT	TGG
(GGA)	 AG	341307-341434	GT	AGG
(CTC)	 AG	341603-341755	CA	AGC
-recovered pasa_asmbl_7188.p1, internal, 340055, 340078
-recovered pasa_asmbl_7188.p1, internal, 340518, 340679
-recovered pasa_asmbl_7188.p1, internal, 340812, 340968
-recovered pasa_asmbl_7188.p1, internal, 341307, 341434

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 50905, rend_intergenic: 44787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98242, rend_intergenic: 95608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99694, rend_intergenic: 98579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138451, rend_intergenic: 135546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 338716, rend_intergenic: 336713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 343450
-exon list size: 310


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.2    
2.6    
2.9    
3.2    
3.5    
3.8    
4.2    
4.5    
4.8    
5.1    
5.4    
5.8    
6.1    
6.4    
6.7    
7.1    
7.4    
7.7    
8.0    
8.3    
8.7    
9.0    
9.3    
9.6    
9.9    
10.3    
10.6    
10.9    
11.2    
11.5    
11.9    
12.2    
12.5    
12.8    
13.1    
13.5    
13.8    
14.1    
14.4    
14.7    
15.1    
15.4    
15.7    
16.0    
16.3    
16.7    
17.0    
17.3    
17.6    
17.9    
18.3    
18.6    
18.9    
19.2    
19.6    
19.9    
20.2    
20.5    
20.8    
21.2    
21.5    
21.8    
22.1    
22.4    
22.8    
23.1    
23.4    
23.7    
24.0    
24.4    
24.7    
25.0    
25.3    
25.6    
26.0    
26.3    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.5    
28.8    
29.2    
29.5    
29.8    
30.1    
30.4    
30.8    
31.1    
31.4    
31.7    
32.1    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
34.9    
35.3    
35.6    
35.9    
36.2    
36.5    
36.9    
37.2    
37.5    
37.8    
38.1    
38.5    
38.8    
39.1    
39.4    
39.7    
40.1    
40.4    
40.7    
41.0    
41.3    
41.7    
42.0    
42.3    
42.6    
42.9    
43.3    
43.6    
43.9    
44.2    
44.6    
44.9    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.1    
47.4    
47.8    
48.1    
48.4    
48.7    
49.0    
49.4    
49.7    
50.0    
50.3    
50.6    
51.0    
51.3    
51.6    
51.9    
52.2    
52.6    
52.9    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.1    
55.4    
55.8    
56.1    
56.4    
56.7    
57.1    
57.4    
57.7    
58.0    
58.3    
58.7    
59.0    
59.3    
59.6    
59.9    
60.3    
60.6    
60.9    
61.2    
61.5    
61.9    
62.2    
62.5    
62.8    
63.1    
63.5    
63.8    
64.1    
64.4    
64.7    
65.1    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
67.9    
68.3    
68.6    
68.9    
69.2    
69.6    
69.9    
70.2    
70.5    
70.8    
71.2    
71.5    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.7    
74.0    
74.4    
74.7    
75.0    
75.3    
75.6    
76.0    
76.3    
76.6    
76.9    
77.2    
77.6    
77.9    
78.2    
78.5    
78.8    
79.2    
79.5    
79.8    
80.1    
80.4    
80.8    
81.1    
81.4    
81.7    
82.1    
82.4    
82.7    
83.0    
83.3    
83.7    
84.0    
84.3    
84.6    
84.9    
85.3    
85.6    
85.9    
86.2    
86.5    
86.9    
87.2    
87.5    
87.8    
88.1    
88.5    
88.8    
89.1    
89.4    
89.7    
90.1    
90.4    
90.7    
91.0    
91.3    
91.7    
92.0    
92.3    
92.6    
92.9    
93.3    
93.6    
93.9    
94.2    
94.6    
94.9    
95.2    
95.5    
95.8    
96.2    
96.5    
96.8    
97.1    
97.4    
97.8    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 50905, rend_intergenic: 44787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98242, rend_intergenic: 95608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99694, rend_intergenic: 98579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138451, rend_intergenic: 135546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 338716, rend_intergenic: 336713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 14342
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support
	-no exons in range 3397 - 14342