-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_8109624-8340974

-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 GeneMark_model.67599_t
Valid prediction for snap_scaffold_16-snap.1527-T1
Valid prediction for HiQ_model.g26551.t1
Valid prediction for pasa_asmbl_17180.p1
Valid prediction for snap_scaffold_16-snap.1505-T1
Valid prediction for snap_scaffold_16-snap.1494-T1
Valid prediction for GlimmerHMM_glimmerT_39497-T1
Valid prediction for GeneMark_model.67591_t
Valid prediction for Augustus_model.g26535.t1
Valid prediction for CodingQuarry_transcript_19983-T1
Valid prediction for snap_scaffold_16-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_39492-T1
Valid prediction for GlimmerHMM_glimmerT_39493-T1
Valid prediction for GeneMark_model.67578_t
Valid prediction for pasa_asmbl_17186.p1
Valid prediction for GeneMark_model.67574_t
Valid prediction for snap_scaffold_16-snap.1526-T1
Valid prediction for snap_scaffold_16-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_39487-T1
Valid prediction for snap_scaffold_16-snap.1524-T1
Valid prediction for HiQ_model.g26548.t1
Valid prediction for snap_scaffold_16-snap.1509-T1
Valid prediction for CodingQuarry_transcript_19985-T1
Valid prediction for HiQ_model.g26534.t1
Valid prediction for GlimmerHMM_glimmerT_39500-T1
Valid prediction for Augustus_model.g26544.t1
Valid prediction for Augustus_model.g26545.t1
Valid prediction for GeneMark_model.67571_t
Valid prediction for GeneMark_model.67593_t
Valid prediction for GeneMark_model.67583_t
Valid prediction for GlimmerHMM_glimmerT_39505-T1
Valid prediction for snap_scaffold_16-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_39504-T1
Valid prediction for snap_scaffold_16-snap.1512-T1
Valid prediction for snap_scaffold_16-snap.1519-T1
Valid prediction for GeneMark_model.67581_t
Valid prediction for snap_scaffold_16-snap.1493-T1
Valid prediction for Augustus_model.g26541.t1
Valid prediction for Augustus_model.g26552.t1
Valid prediction for GeneMark_model.67597_t
Valid prediction for GlimmerHMM_glimmerT_39490-T1
Valid prediction for snap_scaffold_16-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_39498-T1
Valid prediction for Augustus_model.g26540.t1
Valid prediction for CodingQuarry_transcript_19986-T1
Valid prediction for snap_scaffold_16-snap.1516-T1
Valid prediction for HiQ_model.g26549.t1
Valid prediction for GlimmerHMM_glimmerT_39501-T1
Valid prediction for snap_scaffold_16-snap.1515-T1
Valid prediction for snap_scaffold_16-snap.1497-T1
Valid prediction for Augustus_model.g26532.t1
Valid prediction for GeneMark_model.67573_t
Valid prediction for snap_scaffold_16-snap.1508-T1
Valid prediction for GeneMark_model.67592_t
Valid prediction for GlimmerHMM_glimmerT_39491-T1
Valid prediction for pasa_asmbl_17182.p1
Valid prediction for snap_scaffold_16-snap.1523-T1
Valid prediction for GeneMark_model.67586_t
Valid prediction for pasa_asmbl_17183.p1
Valid prediction for Augustus_model.g26547.t1
Valid prediction for CodingQuarry_transcript_19982-T1
Valid prediction for GeneMark_model.67594_t
Valid prediction for GlimmerHMM_glimmerT_39502-T1
Valid prediction for GlimmerHMM_glimmerT_39495-T1
Valid prediction for Augustus_model.g26537.t1
Valid prediction for snap_scaffold_16-snap.1521-T1
Valid prediction for CodingQuarry_transcript_19988-T1
Valid prediction for GlimmerHMM_glimmerT_39486-T1
Valid prediction for Augustus_model.g26543.t1
Valid prediction for GeneMark_model.67572_t
Valid prediction for HiQ_model.g26536.t1
Valid prediction for GeneMark_model.67579_t
Valid prediction for GlimmerHMM_glimmerT_39489-T1
Valid prediction for GeneMark_model.67588_t
Valid prediction for snap_scaffold_16-snap.1502-T1
Valid prediction for snap_scaffold_16-snap.1520-T1
Valid prediction for snap_scaffold_16-snap.1522-T1
Couldn't classify 202251, 202899
Sorry, prediction pasa_asmbl_17187.p1 fails validation.
(ACA)	 TA	202251-202899	GT	AGG
(AAG)	 AG	203302-203897	GC	AAG
-recovered pasa_asmbl_17187.p1, terminal, 203302, 203897
-recovered pasa_asmbl_17187.p1, internal, 203302, 203897
Valid prediction for GeneMark_model.67601_t
Valid prediction for GeneMark_model.67577_t
Valid prediction for CodingQuarry_transcript_19987-T1
Valid prediction for GeneMark_model.67580_t

-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_16-snap.1501-T1
Valid prediction for GlimmerHMM_glimmerT_39496-T1
Valid prediction for snap_scaffold_16-snap.1495-T1
Valid prediction for snap_scaffold_16-snap.1517-T1
Valid prediction for GeneMark_model.67589_t
Couldn't classify 142480, 143307
Sorry, prediction pasa_asmbl_16414.p1 fails validation.
(TGC)	 AA	142480-143307	GT	AGG
(ATA)	 AG	143423-143510	GT	TGG
(TTA)	 AG	143670-143835	GT	CAG
(AGG)	 AG	143931-144039	GT	TTG
(GAT)	 AG	144180-144311	GT	TGG
(GGA)	 AG	144725-144814	GT	AGG
(GTT)	 AG	145000-145143	GT	AGG
(GGT)	 AG	145287-145471	GT	AGG
(GAA)	 AG	145782-145947	TG	GAT
-recovered pasa_asmbl_16414.p1, terminal, 145782, 145947
-recovered pasa_asmbl_16414.p1, internal, 143423, 143510
-recovered pasa_asmbl_16414.p1, internal, 143670, 143835
-recovered pasa_asmbl_16414.p1, internal, 143931, 144039
-recovered pasa_asmbl_16414.p1, internal, 144180, 144311
-recovered pasa_asmbl_16414.p1, internal, 144725, 144814
-recovered pasa_asmbl_16414.p1, internal, 145000, 145143
-recovered pasa_asmbl_16414.p1, internal, 145287, 145471
Valid prediction for GeneMark_model.67582_t
Valid prediction for Augustus_model.g26538.t1
Valid prediction for GeneMark_model.67590_t
Valid prediction for GeneMark_model.67575_t
Valid prediction for GlimmerHMM_glimmerT_39494-T1
Valid prediction for GlimmerHMM_glimmerT_39488-T1
Valid prediction for Augustus_model.g26546.t1
Valid prediction for pasa_asmbl_16416.p1
Valid prediction for GeneMark_model.67600_t
Valid prediction for HiQ_model.g26533.t1
Valid prediction for GlimmerHMM_glimmerT_39503-T1
Valid prediction for snap_scaffold_16-snap.1492-T1
Valid prediction for GeneMark_model.67596_t
Valid prediction for snap_scaffold_16-snap.1514-T1
Valid prediction for snap_scaffold_16-snap.1518-T1
Valid prediction for Augustus_model.g26542.t1
Valid prediction for GeneMark_model.67576_t
Couldn't classify 141337, 141933
Sorry, prediction pasa_asmbl_16415.p1 fails validation.
(CCT)	 TG	141337-141933	GA	GTG
Valid prediction for snap_scaffold_16-snap.1507-T1
Valid prediction for CodingQuarry_transcript_19989-T1
Valid prediction for CodingQuarry_transcript_19984-T1
Valid prediction for snap_scaffold_16-snap.1510-T1
Valid prediction for snap_scaffold_16-snap.1506-T1
Valid prediction for GeneMark_model.67585_t
Valid prediction for HiQ_model.g26550.t1
Valid prediction for GeneMark_model.67595_t
Valid prediction for snap_scaffold_16-snap.1511-T1
Valid prediction for snap_scaffold_16-snap.1500-T1
Valid prediction for GeneMark_model.67587_t
Valid prediction for GeneMark_model.67584_t
Valid prediction for GlimmerHMM_glimmerT_39485-T1
Valid prediction for snap_scaffold_16-snap.1499-T1
Valid prediction for snap_scaffold_16-snap.1525-T1
Valid prediction for pasa_asmbl_16413.p1
Couldn't classify 35267, 35380
Sorry, prediction pasa_asmbl_16418.p1 fails validation.
(GGG)	 GG	35267-35380	GT	AGG
(GTT)	 AG	35708-35878	GT	GGG
(GGT)	 AG	36131-36268	GT	AGG
(GCT)	 AG	37145-37237	GT	AGG
(AAC)	 AG	37385-37477	GT	CCG
(CTT)	 AG	38906-39035	GT	TGG
(TGA)	 AG	39187-39310	GT	GGG
(GGT)	 AG	39586-39685	GT	AGG
(AGA)	 AG	39863-39985	GA	AGG
-recovered pasa_asmbl_16418.p1, terminal, 39863, 39985
-recovered pasa_asmbl_16418.p1, internal, 35708, 35878
-recovered pasa_asmbl_16418.p1, internal, 36131, 36268
-recovered pasa_asmbl_16418.p1, internal, 37145, 37237
-recovered pasa_asmbl_16418.p1, internal, 37385, 37477
-recovered pasa_asmbl_16418.p1, internal, 38906, 39035
-recovered pasa_asmbl_16418.p1, internal, 39187, 39310
-recovered pasa_asmbl_16418.p1, internal, 39586, 39685
Valid prediction for GlimmerHMM_glimmerT_39499-T1
Valid prediction for HiQ_model.g26539.t1
Valid prediction for snap_scaffold_16-snap.1496-T1
Valid prediction for snap_scaffold_16-snap.1513-T1
Valid prediction for CodingQuarry_transcript_19981-T1
Valid prediction for GeneMark_model.67598_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 111625, rend_intergenic: 110069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164883, rend_intergenic: 162803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231351
-exon list size: 471


building trellis

0.2    
0.4    
0.6    
0.8    
1.1    
1.3    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.4    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.3    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
8.0    
8.2    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 111625, rend_intergenic: 110069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164883, rend_intergenic: 162803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 28148
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11415
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10679
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10231
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 11422 - 28148
-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 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 11422 - 25978
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support