-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_17394278-17700088

-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_9-snap.3542-T1
Valid prediction for GeneMark_model.41587_t
Valid prediction for GlimmerHMM_glimmerT_24272-T1
Valid prediction for GlimmerHMM_glimmerT_24277-T1
Valid prediction for snap_scaffold_9-snap.3561-T1
Valid prediction for snap_scaffold_9-snap.3544-T1
Valid prediction for GeneMark_model.41604_t
Valid prediction for GlimmerHMM_glimmerT_24250-T1
Valid prediction for GlimmerHMM_glimmerT_24249-T1
Valid prediction for snap_scaffold_9-snap.3526-T1
Valid prediction for Augustus_model.g16230.t1
Valid prediction for GeneMark_model.41589_t
Valid prediction for GeneMark_model.41603_t
Valid prediction for GlimmerHMM_glimmerT_24259-T1
Valid prediction for GlimmerHMM_glimmerT_24268-T1
Valid prediction for snap_scaffold_9-snap.3521-T1
Valid prediction for pasa_asmbl_54610.p1
Valid prediction for GeneMark_model.41584_t
Valid prediction for GeneMark_model.41595_t
Valid prediction for snap_scaffold_9-snap.3559-T1
Valid prediction for GlimmerHMM_glimmerT_24280-T1
Valid prediction for GlimmerHMM_glimmerT_24269-T1
Valid prediction for GlimmerHMM_glimmerT_24247-T1
Valid prediction for GeneMark_model.41593_t
Valid prediction for snap_scaffold_9-snap.3539-T1
Valid prediction for snap_scaffold_9-snap.3538-T1
Valid prediction for snap_scaffold_9-snap.3522-T1
Valid prediction for snap_scaffold_9-snap.3545-T1
Valid prediction for CodingQuarry_transcript_62293-T1
Valid prediction for GeneMark_model.41598_t
Valid prediction for snap_scaffold_9-snap.3546-T1
Valid prediction for Augustus_model.g16248.t1
Valid prediction for GeneMark_model.41608_t
Valid prediction for GlimmerHMM_glimmerT_24261-T1
Valid prediction for snap_scaffold_9-snap.3529-T1
Valid prediction for snap_scaffold_9-snap.3556-T1
Valid prediction for GlimmerHMM_glimmerT_24251-T1
Valid prediction for GeneMark_model.41610_t
Valid prediction for snap_scaffold_9-snap.3554-T1
Valid prediction for Augustus_model.g16243.t1
Valid prediction for snap_scaffold_9-snap.3528-T1
Valid prediction for CodingQuarry_transcript_62291-T1
Valid prediction for snap_scaffold_9-snap.3536-T1
Valid prediction for GeneMark_model.41600_t
Valid prediction for GeneMark_model.41612_t
Valid prediction for snap_scaffold_9-snap.3560-T1
Valid prediction for snap_scaffold_9-snap.3547-T1
Valid prediction for GlimmerHMM_glimmerT_24254-T1
Valid prediction for snap_scaffold_9-snap.3541-T1
Valid prediction for GeneMark_model.41606_t
Valid prediction for Augustus_model.g16241.t1
Valid prediction for HiQ_model.g16233.t1
Valid prediction for Augustus_model.g16238.t1
Valid prediction for GlimmerHMM_glimmerT_24278-T1
Valid prediction for GlimmerHMM_glimmerT_24260-T1
Valid prediction for Augustus_model.g16246.t1
Valid prediction for GlimmerHMM_glimmerT_24262-T1
Valid prediction for Augustus_model.g16229.t1
Valid prediction for GlimmerHMM_glimmerT_24245-T1
Valid prediction for snap_scaffold_9-snap.3543-T1
Valid prediction for GlimmerHMM_glimmerT_24274-T1
Valid prediction for pasa_asmbl_54606.p1
Valid prediction for GeneMark_model.41590_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_9-snap.3553-T1
Valid prediction for GlimmerHMM_glimmerT_24256-T1
Valid prediction for GlimmerHMM_glimmerT_24248-T1
Valid prediction for GeneMark_model.41607_t
Valid prediction for Augustus_model.g16234.t1
Couldn't classify 242570, 242596
Sorry, prediction pasa_asmbl_55606.p1 fails validation.
(AAT)	 AG	242570-242596	GT	TGG
(AGG)	 AG	242813-243110	GT	GGG
(GAT)	 AG	243531-243596	GT	AGG
(AAT)	 AG	243917-243930	CA	GAC
-recovered pasa_asmbl_55606.p1, terminal, 243917, 243930
-recovered pasa_asmbl_55606.p1, internal, 242570, 242596
-recovered pasa_asmbl_55606.p1, internal, 242813, 243110
-recovered pasa_asmbl_55606.p1, internal, 243531, 243596
Valid prediction for GlimmerHMM_glimmerT_24252-T1
Valid prediction for GlimmerHMM_glimmerT_24258-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.41592_t
Valid prediction for GeneMark_model.41591_t
Valid prediction for GlimmerHMM_glimmerT_24276-T1
Valid prediction for Augustus_model.g16231.t1
Valid prediction for GlimmerHMM_glimmerT_24257-T1
Valid prediction for snap_scaffold_9-snap.3534-T1
Valid prediction for HiQ_model.g16236.t1
Valid prediction for GlimmerHMM_glimmerT_24266-T1
Valid prediction for Augustus_model.g16239.t1
Valid prediction for GeneMark_model.41601_t
Valid prediction for snap_scaffold_9-snap.3549-T1
Valid prediction for snap_scaffold_9-snap.3535-T1
Valid prediction for snap_scaffold_9-snap.3558-T1
Valid prediction for CodingQuarry_transcript_62296-T1
Valid prediction for snap_scaffold_9-snap.3524-T1
Valid prediction for snap_scaffold_9-snap.3527-T1
Valid prediction for HiQ_model.g16242.t1
Valid prediction for snap_scaffold_9-snap.3540-T1
Valid prediction for snap_scaffold_9-snap.3548-T1
Valid prediction for pasa_asmbl_55630.p1
Valid prediction for GlimmerHMM_glimmerT_24246-T1
Valid prediction for snap_scaffold_9-snap.3537-T1
Valid prediction for HiQ_model.g16249.t1
Couldn't classify 39227, 39319
Sorry, prediction pasa_asmbl_55632.p1 fails validation.
(AGA)	 CC	39227-39319	GT	AGG
(GCT)	 AG	40933-41542	GT	GCG
(CTC)	 AG	41665-41763	GT	AGG
(GTT)	 AG	41852-42084	GT	AGG
(AAA)	 AG	42252-42554	TA	AGT
-recovered pasa_asmbl_55632.p1, terminal, 42252, 42554
-recovered pasa_asmbl_55632.p1, internal, 40933, 41542
-recovered pasa_asmbl_55632.p1, internal, 41665, 41763
-recovered pasa_asmbl_55632.p1, internal, 41852, 42084
Valid prediction for GlimmerHMM_glimmerT_24275-T1
Valid prediction for snap_scaffold_9-snap.3552-T1
Valid prediction for CodingQuarry_transcript_62294-T1
Valid prediction for GlimmerHMM_glimmerT_24263-T1
Valid prediction for GeneMark_model.41609_t
Valid prediction for snap_scaffold_9-snap.3530-T1
Valid prediction for GlimmerHMM_glimmerT_24273-T1
Valid prediction for pasa_asmbl_55607.p1
Valid prediction for HiQ_model.g16237.t1
Valid prediction for GlimmerHMM_glimmerT_24244-T1
Valid prediction for GlimmerHMM_glimmerT_24264-T1
Valid prediction for Augustus_model.g16247.t1
Valid prediction for GlimmerHMM_glimmerT_24255-T1
Valid prediction for snap_scaffold_9-snap.3555-T1
Valid prediction for CodingQuarry_transcript_62292-T1
Valid prediction for HiQ_model.g16244.t1
Valid prediction for Augustus_model.g16245.t1
Valid prediction for snap_scaffold_9-snap.3551-T1
Valid prediction for GeneMark_model.41594_t
Valid prediction for snap_scaffold_9-snap.3550-T1
Valid prediction for GeneMark_model.41611_t
Valid prediction for CodingQuarry_transcript_62295-T1
Valid prediction for snap_scaffold_9-snap.3525-T1
Valid prediction for Augustus_model.g16232.t1
Valid prediction for GlimmerHMM_glimmerT_24253-T1
Valid prediction for snap_scaffold_9-snap.3532-T1
Valid prediction for pasa_asmbl_55614.p1
Valid prediction for GeneMark_model.41605_t
Valid prediction for GeneMark_model.41602_t
Valid prediction for Augustus_model.g16240.t1
Valid prediction for CodingQuarry_transcript_62297-T1
Valid prediction for snap_scaffold_9-snap.3531-T1
Valid prediction for GlimmerHMM_glimmerT_24270-T1
Valid prediction for snap_scaffold_9-snap.3523-T1
Couldn't classify 204153, 204649
Sorry, prediction pasa_asmbl_55616.p1 fails validation.
(ATG)	 AG	202745-202856	GT	GGG
(ATG)	 AG	204153-204649	CT	AGC
-recovered pasa_asmbl_55616.p1, initial, 202745, 202856
-recovered pasa_asmbl_55616.p1, internal, 202745, 202856
Valid prediction for Augustus_model.g16228.t1
Valid prediction for GeneMark_model.41596_t
Valid prediction for pasa_asmbl_55611.p1
Valid prediction for GeneMark_model.41588_t
Valid prediction for GeneMark_model.41597_t
Valid prediction for pasa_asmbl_55623.p1
Valid prediction for GlimmerHMM_glimmerT_24267-T1
Valid prediction for GeneMark_model.41586_t
Valid prediction for Augustus_model.g16235.t1
Valid prediction for GlimmerHMM_glimmerT_24271-T1
Valid prediction for GlimmerHMM_glimmerT_24265-T1
Valid prediction for GlimmerHMM_glimmerT_24279-T1
Valid prediction for snap_scaffold_9-snap.3533-T1
Valid prediction for snap_scaffold_9-snap.3557-T1
Couldn't classify 269405, 269466
Couldn't classify 273203, 273293
Sorry, prediction pasa_asmbl_55603.p1 fails validation.
(GCT)	 CT	269405-269466	GT	AAG
(CAT)	 AG	270705-270802	GT	TGG
(AGC)	 AG	271572-271635	GT	AAG
(TCT)	 AG	272020-272115	GT	CGG
(CCT)	 AG	273203-273293	CC	ACC
-recovered pasa_asmbl_55603.p1, internal, 270705, 270802
-recovered pasa_asmbl_55603.p1, internal, 271572, 271635
-recovered pasa_asmbl_55603.p1, internal, 272020, 272115
Valid prediction for GeneMark_model.41599_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 98750, rend_intergenic: 97528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 305811
-exon list size: 516


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
9.7    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 98750, rend_intergenic: 97528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 264853 - 305811
-exon list size: 49


building trellis

2.0    
3.9    
5.9    
7.8    
9.8    
11.8    
13.7    
15.7    
17.6    
19.6    
21.6    
23.5    
25.5    
27.5    
29.4    
31.4    
33.3    
35.3    
37.3    
39.2    
41.2    
43.1    
45.1    
47.1    
49.0    
51.0    
52.9    
54.9    
56.9    
58.8    
60.8    
62.7    
64.7    
66.7    
68.6    
70.6    
72.5    
74.5    
76.5    
78.4    
80.4    
82.4    
84.3    
86.3    
88.2    
90.2    
92.2    
94.1    
96.1    
98.0    
-found 4 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 3 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 264853 - 294598
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 2 predictions from path traversal
GOT 5prime partial gene.
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 264853 - 284272
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-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 264853 - 283811
-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 265701 - 283811
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 268908 - 283811
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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