-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_10033039-10217638

-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 Augustus_model.g30508.t1
Valid prediction for snap_scaffold_19-snap.1925-T1
Valid prediction for snap_scaffold_19-snap.1915-T1
Valid prediction for HiQ_model.g30509.t1
Valid prediction for GeneMark_model.79790_t
Valid prediction for snap_scaffold_19-snap.1918-T1
Valid prediction for CodingQuarry_transcript_25721-T1
Valid prediction for GlimmerHMM_glimmerT_45730-T1
Valid prediction for GlimmerHMM_glimmerT_45746-T1
Couldn't classify 32883, 32993
Sorry, prediction pasa_asmbl_22416.p1 fails validation.
(CAT)	 GC	32883-32993	GT	AAG
(GTT)	 AG	33716-33798	GT	AGG
(TTG)	 AG	33891-33986	GT	ATG
(GAG)	 AG	34174-34274	GT	ATG
(GTT)	 AG	34509-34609	GT	TGG
(GAA)	 AG	34738-34857	GT	AGG
(TTA)	 AG	35006-35166	GT	AAG
(TGA)	 AG	35285-35443	GT	AAG
(GAC)	 AG	35550-35839	GT	GAG
(AAA)	 AG	36146-36255	GT	AGG
(GTG)	 AG	36444-36543	GT	CGG
(TGA)	 AG	36800-36884	GT	AGG
(GTT)	 AG	39144-39243	AG	GAA
-recovered pasa_asmbl_22416.p1, terminal, 39144, 39243
-recovered pasa_asmbl_22416.p1, internal, 33716, 33798
-recovered pasa_asmbl_22416.p1, internal, 33891, 33986
-recovered pasa_asmbl_22416.p1, internal, 34174, 34274
-recovered pasa_asmbl_22416.p1, internal, 34509, 34609
-recovered pasa_asmbl_22416.p1, internal, 34738, 34857
-recovered pasa_asmbl_22416.p1, internal, 35006, 35166
-recovered pasa_asmbl_22416.p1, internal, 35285, 35443
-recovered pasa_asmbl_22416.p1, internal, 35550, 35839
-recovered pasa_asmbl_22416.p1, internal, 36146, 36255
-recovered pasa_asmbl_22416.p1, internal, 36444, 36543
-recovered pasa_asmbl_22416.p1, internal, 36800, 36884
Valid prediction for GeneMark_model.79802_t
Valid prediction for GeneMark_model.79794_t
Valid prediction for Augustus_model.g30510.t1
Valid prediction for GeneMark_model.79796_t
Valid prediction for snap_scaffold_19-snap.1940-T1
Valid prediction for GeneMark_model.79785_t
Valid prediction for GeneMark_model.79797_t
Valid prediction for snap_scaffold_19-snap.1927-T1
Valid prediction for GeneMark_model.79792_t
Valid prediction for snap_scaffold_19-snap.1926-T1
Valid prediction for GlimmerHMM_glimmerT_45731-T1
Valid prediction for GlimmerHMM_glimmerT_45741-T1
Valid prediction for GlimmerHMM_glimmerT_45727-T1
Valid prediction for GeneMark_model.79782_t
Valid prediction for GlimmerHMM_glimmerT_45738-T1
Valid prediction for GeneMark_model.79807_t
Valid prediction for HiQ_model.g30506.t1
Valid prediction for snap_scaffold_19-snap.1941-T1
Valid prediction for Augustus_model.g30513.t1
Valid prediction for GeneMark_model.79787_t
Valid prediction for Augustus_model.g30507.t1
Valid prediction for snap_scaffold_19-snap.1932-T1
Valid prediction for GeneMark_model.79793_t
Valid prediction for GlimmerHMM_glimmerT_45735-T1
Valid prediction for snap_scaffold_19-snap.1917-T1
Couldn't classify 177546, 177637
Sorry, prediction pasa_asmbl_22428.p1 fails validation.
(ATG)	 TA	174218-174308	GT	AGG
(CTG)	 AG	174447-174770	GT	TGG
(GCG)	 AG	175189-175518	GT	TGG
(TGC)	 AG	176824-177108	GT	TAG
(TGG)	 AG	177546-177637	TG	TCT
-recovered pasa_asmbl_22428.p1, initial, 174218, 174308
-recovered pasa_asmbl_22428.p1, internal, 174447, 174770
-recovered pasa_asmbl_22428.p1, internal, 175189, 175518
-recovered pasa_asmbl_22428.p1, internal, 176824, 177108
Valid prediction for Augustus_model.g30516.t1
Valid prediction for pasa_asmbl_22421.p1
Valid prediction for GlimmerHMM_glimmerT_45736-T1
Valid prediction for GeneMark_model.79805_t
Valid prediction for snap_scaffold_19-snap.1924-T1
Valid prediction for GlimmerHMM_glimmerT_45739-T1
Valid prediction for snap_scaffold_19-snap.1921-T1
Valid prediction for GlimmerHMM_glimmerT_45728-T1
Valid prediction for snap_scaffold_19-snap.1923-T1
Valid prediction for snap_scaffold_19-snap.1931-T1
Valid prediction for snap_scaffold_19-snap.1929-T1
Valid prediction for CodingQuarry_transcript_25720-T1
Valid prediction for GeneMark_model.79781_t
Valid prediction for GlimmerHMM_glimmerT_45744-T1
Valid prediction for GeneMark_model.79800_t
Valid prediction for GeneMark_model.79795_t
Valid prediction for GlimmerHMM_glimmerT_45742-T1
Valid prediction for snap_scaffold_19-snap.1930-T1
Valid prediction for snap_scaffold_19-snap.1922-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.1938-T1
Valid prediction for GlimmerHMM_glimmerT_45737-T1
Valid prediction for GlimmerHMM_glimmerT_45749-T1
Valid prediction for Augustus_model.g30514.t1
Valid prediction for snap_scaffold_19-snap.1933-T1
Valid prediction for GlimmerHMM_glimmerT_45733-T1
Valid prediction for GlimmerHMM_glimmerT_45747-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 Augustus_model.g30515.t1
Valid prediction for GeneMark_model.79789_t
Valid prediction for Augustus_model.g30511.t1
Valid prediction for HiQ_model.g30512.t1
Valid prediction for GeneMark_model.79791_t
Valid prediction for snap_scaffold_19-snap.1920-T1
Valid prediction for GeneMark_model.79784_t
Valid prediction for pasa_asmbl_21553.p1
Valid prediction for GeneMark_model.79804_t
Valid prediction for GlimmerHMM_glimmerT_45726-T1
Valid prediction for snap_scaffold_19-snap.1939-T1
Valid prediction for snap_scaffold_19-snap.1937-T1
Valid prediction for GeneMark_model.79803_t
Valid prediction for GlimmerHMM_glimmerT_45740-T1
Valid prediction for GeneMark_model.79808_t
Valid prediction for snap_scaffold_19-snap.1919-T1
Valid prediction for GeneMark_model.79786_t
Valid prediction for Augustus_model.g30505.t1
Valid prediction for GlimmerHMM_glimmerT_45729-T1
Valid prediction for GlimmerHMM_glimmerT_45743-T1
Valid prediction for GeneMark_model.79779_t
Valid prediction for snap_scaffold_19-snap.1912-T1
Valid prediction for snap_scaffold_19-snap.1934-T1
Valid prediction for snap_scaffold_19-snap.1928-T1
Valid prediction for GlimmerHMM_glimmerT_45732-T1
Valid prediction for snap_scaffold_19-snap.1936-T1
Valid prediction for snap_scaffold_19-snap.1911-T1
Valid prediction for snap_scaffold_19-snap.1916-T1
Valid prediction for GlimmerHMM_glimmerT_45734-T1
Valid prediction for snap_scaffold_19-snap.1935-T1
Valid prediction for snap_scaffold_19-snap.1914-T1
Valid prediction for GeneMark_model.79801_t
Valid prediction for CodingQuarry_transcript_25725-T1
Valid prediction for GlimmerHMM_glimmerT_45745-T1
Valid prediction for GeneMark_model.79780_t
Valid prediction for GlimmerHMM_glimmerT_45748-T1
Valid prediction for GeneMark_model.79806_t
Valid prediction for GeneMark_model.79783_t
Valid prediction for GeneMark_model.79788_t
Valid prediction for snap_scaffold_19-snap.1913-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 92158, rend_intergenic: 90174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184600
-exon list size: 364


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.5    
2.7    
3.0    
3.3    
3.6    
3.8    
4.1    
4.4    
4.6    
4.9    
5.2    
5.5    
5.7    
6.0    
6.3    
6.6    
6.8    
7.1    
7.4    
7.7    
7.9    
8.2    
8.5    
8.7    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.7    
13.9    
14.2    
14.5    
14.8    
15.0    
15.3    
15.6    
15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.0    
21.3    
21.6    
21.9    
22.1    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.9    
72.1    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.1    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
93.7    
94.0    
94.3    
94.5    
94.8    
95.1    
95.4    
95.6    
95.9    
96.2    
96.4    
96.7    
97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 92158, rend_intergenic: 90174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 1 - 16867
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-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 - 15563
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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