-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_3630224-3713466

-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.101615_t
Valid prediction for GeneMark_model.101605_t
Valid prediction for snap_scaffold_27-snap.882-T1
Valid prediction for GeneMark_model.101620_t
Valid prediction for snap_scaffold_27-snap.874-T1
Valid prediction for snap_scaffold_27-snap.884-T1
Valid prediction for GlimmerHMM_glimmerT_58451-T1
Valid prediction for GeneMark_model.101625_t
Valid prediction for GeneMark_model.101606_t
Valid prediction for GeneMark_model.101611_t
Valid prediction for Augustus_model.g38943.t1
Valid prediction for GeneMark_model.101613_t
Valid prediction for Augustus_model.g38937.t1
Valid prediction for Augustus_model.g38931.t1
Valid prediction for GeneMark_model.101610_t
Valid prediction for GeneMark_model.101623_t
Valid prediction for GlimmerHMM_glimmerT_58453-T1
Valid prediction for GeneMark_model.101622_t
Valid prediction for snap_scaffold_27-snap.879-T1
Valid prediction for snap_scaffold_27-snap.883-T1
Valid prediction for GlimmerHMM_glimmerT_58446-T1
Valid prediction for GeneMark_model.101621_t
Valid prediction for GeneMark_model.101616_t
Valid prediction for Augustus_model.g38932.t1
Valid prediction for GeneMark_model.101618_t
Valid prediction for snap_scaffold_27-snap.886-T1
Valid prediction for GeneMark_model.101608_t
Valid prediction for GlimmerHMM_glimmerT_58450-T1
Valid prediction for GeneMark_model.101619_t
Valid prediction for snap_scaffold_27-snap.873-T1
Valid prediction for Augustus_model.g38939.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_27-snap.892-T1
Valid prediction for GlimmerHMM_glimmerT_58443-T1
Valid prediction for snap_scaffold_27-snap.880-T1
Valid prediction for snap_scaffold_27-snap.894-T1
Valid prediction for snap_scaffold_27-snap.885-T1
Valid prediction for GeneMark_model.101627_t
Valid prediction for Augustus_model.g38935.t1
Valid prediction for snap_scaffold_27-snap.876-T1
Valid prediction for HiQ_model.g38933.t1
Valid prediction for GeneMark_model.101612_t
Couldn't classify 48594, 48632
Couldn't classify 51724, 51886
Sorry, prediction pasa_asmbl_36870.p1 fails validation.
(ATT)	 CA	48594-48632	GT	ACG
(ATC)	 AG	48799-48849	GT	GTG
(GGG)	 AG	49252-49376	GT	CGG
(AGT)	 AG	51724-51886	CC	GAC
-recovered pasa_asmbl_36870.p1, internal, 48799, 48849
-recovered pasa_asmbl_36870.p1, internal, 49252, 49376
Valid prediction for snap_scaffold_27-snap.888-T1
Valid prediction for GeneMark_model.101614_t
Valid prediction for GeneMark_model.101607_t
Valid prediction for Augustus_model.g38941.t1
Valid prediction for GlimmerHMM_glimmerT_58447-T1
Valid prediction for GlimmerHMM_glimmerT_58448-T1
Valid prediction for snap_scaffold_27-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_58445-T1
Valid prediction for GeneMark_model.101609_t
Valid prediction for GlimmerHMM_glimmerT_58439-T1
Valid prediction for GlimmerHMM_glimmerT_58452-T1
Valid prediction for GlimmerHMM_glimmerT_58440-T1
Valid prediction for GlimmerHMM_glimmerT_58442-T1
Valid prediction for snap_scaffold_27-snap.890-T1
Valid prediction for CodingQuarry_transcript_41765-T1
Valid prediction for Augustus_model.g38934.t1
Valid prediction for Augustus_model.g38938.t1
Valid prediction for snap_scaffold_27-snap.887-T1
Valid prediction for snap_scaffold_27-snap.881-T1
Valid prediction for Augustus_model.g38940.t1
Valid prediction for snap_scaffold_27-snap.875-T1
Valid prediction for Augustus_model.g38942.t1
Valid prediction for GlimmerHMM_glimmerT_58449-T1
Valid prediction for GlimmerHMM_glimmerT_58438-T1
Valid prediction for GlimmerHMM_glimmerT_58444-T1
Valid prediction for snap_scaffold_27-snap.891-T1
Valid prediction for Augustus_model.g38936.t1
Valid prediction for GeneMark_model.101617_t
Valid prediction for GeneMark_model.101624_t
Valid prediction for snap_scaffold_27-snap.878-T1
Valid prediction for snap_scaffold_27-snap.877-T1
Valid prediction for snap_scaffold_27-snap.893-T1
Valid prediction for GlimmerHMM_glimmerT_58441-T1
Valid prediction for GeneMark_model.101626_t
Couldn't classify 64132, 64177
Sorry, prediction pasa_asmbl_36867.p1 fails validation.
(GAC)	 AG	64132-64177	GT	GAG
(GGA)	 AG	65697-65747	GT	AAG
(TAA)	 AG	65862-65963	GT	ACG
(ATA)	 AG	67442-67614	GT	GGG
(GGT)	 AG	67819-67928	GT	ATG
(GGA)	 AG	68663-68754	GT	AGG
(CCC)	 AG	68864-68970	GA	AAG
add_exon() Sorry, pasa_asmbl_36867.p1 64132-64177-terminal-3 is invalid.
-recovered pasa_asmbl_36867.p1, terminal, 64132, 64177
-recovered pasa_asmbl_36867.p1, terminal, 68864, 68970
-recovered pasa_asmbl_36867.p1, internal, 64132, 64177
-recovered pasa_asmbl_36867.p1, internal, 65697, 65747
-recovered pasa_asmbl_36867.p1, internal, 65862, 65963
-recovered pasa_asmbl_36867.p1, internal, 67442, 67614
-recovered pasa_asmbl_36867.p1, internal, 67819, 67928
-recovered pasa_asmbl_36867.p1, internal, 68663, 68754

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34539, rend_intergenic: 30028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 83243
-exon list size: 290


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.7    
3.1    
3.4    
3.8    
4.1    
4.5    
4.8    
5.1    
5.5    
5.8    
6.2    
6.5    
6.8    
7.2    
7.5    
7.9    
8.2    
8.6    
8.9    
9.2    
9.6    
9.9    
10.3    
10.6    
11.0    
11.3    
11.6    
12.0    
12.3    
12.7    
13.0    
13.4    
13.7    
14.0    
14.4    
14.7    
15.1    
15.4    
15.8    
16.1    
16.4    
16.8    
17.1    
17.5    
17.8    
18.2    
18.5    
18.8    
19.2    
19.5    
19.9    
20.2    
20.5    
20.9    
21.2    
21.6    
21.9    
22.3    
22.6    
22.9    
23.3    
23.6    
24.0    
24.3    
24.7    
25.0    
25.3    
25.7    
26.0    
26.4    
26.7    
27.1    
27.4    
27.7    
28.1    
28.4    
28.8    
29.1    
29.5    
29.8    
30.1    
30.5    
30.8    
31.2    
31.5    
31.8    
32.2    
32.5    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.3    
35.6    
36.0    
36.3    
36.6    
37.0    
37.3    
37.7    
38.0    
38.4    
38.7    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.1    
41.4    
41.8    
42.1    
42.5    
42.8    
43.2    
43.5    
43.8    
44.2    
44.5    
44.9    
45.2    
45.5    
45.9    
46.2    
46.6    
46.9    
47.3    
47.6    
47.9    
48.3    
48.6    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.4    
51.7    
52.1    
52.4    
52.7    
53.1    
53.4    
53.8    
54.1    
54.5    
54.8    
55.1    
55.5    
55.8    
56.2    
56.5    
56.8    
57.2    
57.5    
57.9    
58.2    
58.6    
58.9    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.3    
61.6    
62.0    
62.3    
62.7    
63.0    
63.4    
63.7    
64.0    
64.4    
64.7    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.5    
67.8    
68.2    
68.5    
68.8    
69.2    
69.5    
69.9    
70.2    
70.5    
70.9    
71.2    
71.6    
71.9    
72.3    
72.6    
72.9    
73.3    
73.6    
74.0    
74.3    
74.7    
75.0    
75.3    
75.7    
76.0    
76.4    
76.7    
77.1    
77.4    
77.7    
78.1    
78.4    
78.8    
79.1    
79.5    
79.8    
80.1    
80.5    
80.8    
81.2    
81.5    
81.8    
82.2    
82.5    
82.9    
83.2    
83.6    
83.9    
84.2    
84.6    
84.9    
85.3    
85.6    
86.0    
86.3    
86.6    
87.0    
87.3    
87.7    
88.0    
88.4    
88.7    
89.0    
89.4    
89.7    
90.1    
90.4    
90.8    
91.1    
91.4    
91.8    
92.1    
92.5    
92.8    
93.2    
93.5    
93.8    
94.2    
94.5    
94.9    
95.2    
95.5    
95.9    
96.2    
96.6    
96.9    
97.3    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 15 predictions from path traversal
Error with prediction: snap lend_intergenic: 34539, rend_intergenic: 30028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 10 predictions persist after filtering for low support