-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_1110663-1418188

-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_16-snap.196-T1
Valid prediction for snap_scaffold_16-snap.195-T1
Valid prediction for GeneMark_model.66075_t
Valid prediction for HiQ_model.g25932.t1
Valid prediction for HiQ_model.g25917.t1
Valid prediction for GeneMark_model.66054_t
Valid prediction for GlimmerHMM_glimmerT_38635-T1
Valid prediction for snap_scaffold_16-snap.197-T1
Valid prediction for GlimmerHMM_glimmerT_38630-T1
Valid prediction for snap_scaffold_16-snap.199-T1
Valid prediction for snap_scaffold_16-snap.200-T1
Valid prediction for GlimmerHMM_glimmerT_38609-T1
Valid prediction for GlimmerHMM_glimmerT_38632-T1
Valid prediction for GlimmerHMM_glimmerT_38634-T1
Valid prediction for snap_scaffold_16-snap.205-T1
Valid prediction for Augustus_model.g25929.t1
Valid prediction for snap_scaffold_16-snap.213-T1
Valid prediction for GeneMark_model.66053_t
Valid prediction for GlimmerHMM_glimmerT_38615-T1
Valid prediction for snap_scaffold_16-snap.194-T1
Valid prediction for Augustus_model.g25920.t1
Valid prediction for snap_scaffold_16-snap.192-T1
Couldn't classify 276792, 277131
Sorry, prediction pasa_asmbl_16863.p1 fails validation.
(TTT)	 CC	276792-277131	GT	AGG
(GTG)	 AG	279198-279634	TA	AAT
-recovered pasa_asmbl_16863.p1, terminal, 279198, 279634
Valid prediction for pasa_asmbl_16861.p1
Valid prediction for GeneMark_model.66079_t
Valid prediction for GlimmerHMM_glimmerT_38619-T1
Valid prediction for GlimmerHMM_glimmerT_38608-T1
Valid prediction for GeneMark_model.66064_t
Valid prediction for snap_scaffold_16-snap.216-T1
Valid prediction for GlimmerHMM_glimmerT_38610-T1
Couldn't classify 46574, 46751
Sorry, prediction pasa_asmbl_16858.p1 fails validation.
(GTA)	 CA	46574-46751	GT	AAG
(CCA)	 AG	47361-47623	GT	AGG
(CTG)	 AG	47728-48030	GT	AGG
(ATG)	 AG	48237-49328	CG	AAC
-recovered pasa_asmbl_16858.p1, terminal, 48237, 49328
-recovered pasa_asmbl_16858.p1, internal, 47361, 47623
-recovered pasa_asmbl_16858.p1, internal, 47728, 48030
Valid prediction for GlimmerHMM_glimmerT_38623-T1
Valid prediction for GeneMark_model.66058_t
Valid prediction for GlimmerHMM_glimmerT_38639-T1
Valid prediction for snap_scaffold_16-snap.218-T1
Valid prediction for GlimmerHMM_glimmerT_38633-T1
Valid prediction for GeneMark_model.66056_t
Valid prediction for snap_scaffold_16-snap.202-T1
Valid prediction for GlimmerHMM_glimmerT_38631-T1
Valid prediction for GlimmerHMM_glimmerT_38628-T1
Valid prediction for GlimmerHMM_glimmerT_38637-T1
Valid prediction for snap_scaffold_16-snap.191-T1
Valid prediction for snap_scaffold_16-snap.190-T1
Valid prediction for Augustus_model.g25913.t1
Valid prediction for GlimmerHMM_glimmerT_38636-T1
Valid prediction for GlimmerHMM_glimmerT_38617-T1
Valid prediction for snap_scaffold_16-snap.219-T1
Valid prediction for snap_scaffold_16-snap.198-T1
Valid prediction for snap_scaffold_16-snap.214-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38621-T1
Valid prediction for Augustus_model.g25915.t1
Valid prediction for Augustus_model.g25919.t1
Valid prediction for GlimmerHMM_glimmerT_38613-T1
Valid prediction for HiQ_model.g25921.t1
Valid prediction for Augustus_model.g25914.t1
Valid prediction for GeneMark_model.66055_t
Valid prediction for snap_scaffold_16-snap.215-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_16-snap.207-T1
Valid prediction for snap_scaffold_16-snap.210-T1
Valid prediction for HiQ_model.g25931.t1
Valid prediction for GlimmerHMM_glimmerT_38626-T1
Valid prediction for Augustus_model.g25925.t1
Valid prediction for snap_scaffold_16-snap.209-T1
Valid prediction for GeneMark_model.66070_t
Valid prediction for GeneMark_model.66071_t
Valid prediction for GlimmerHMM_glimmerT_38622-T1
Valid prediction for Augustus_model.g25912.t1
Valid prediction for pasa_asmbl_16110.p1
Valid prediction for snap_scaffold_16-snap.217-T1
Valid prediction for GeneMark_model.66061_t
Valid prediction for snap_scaffold_16-snap.201-T1
Valid prediction for GeneMark_model.66069_t
Valid prediction for GlimmerHMM_glimmerT_38611-T1
Valid prediction for snap_scaffold_16-snap.211-T1
Valid prediction for Augustus_model.g25927.t1
Valid prediction for GeneMark_model.66051_t
Valid prediction for GeneMark_model.66067_t
Valid prediction for Augustus_model.g25930.t1
Valid prediction for GlimmerHMM_glimmerT_38638-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g25923.t1
Valid prediction for GeneMark_model.66074_t
Valid prediction for GeneMark_model.66057_t
Valid prediction for GlimmerHMM_glimmerT_38627-T1
Valid prediction for GlimmerHMM_glimmerT_38616-T1
Valid prediction for GlimmerHMM_glimmerT_38612-T1
Valid prediction for GeneMark_model.66073_t
Valid prediction for GeneMark_model.66068_t
Valid prediction for CodingQuarry_transcript_19860-T1
Valid prediction for Augustus_model.g25918.t1
Valid prediction for HiQ_model.g25922.t1
Valid prediction for pasa_asmbl_16101.p1
Valid prediction for Augustus_model.g25926.t1
Valid prediction for GlimmerHMM_glimmerT_38614-T1
Valid prediction for GlimmerHMM_glimmerT_38629-T1
Valid prediction for snap_scaffold_16-snap.208-T1
Valid prediction for Augustus_model.g25916.t1
Valid prediction for GeneMark_model.66059_t
Valid prediction for GeneMark_model.66072_t
Valid prediction for CodingQuarry_transcript_19859-T1
Valid prediction for Augustus_model.g25924.t1
Couldn't classify 153737, 153823
Sorry, prediction pasa_asmbl_16763.p1 fails validation.
(GCG)	 AG	153737-153823	GT	TGG
(ATG)	 AG	154182-154266	GT	CTG
(ATC)	 AG	154641-154828	AG	AAA
-recovered pasa_asmbl_16763.p1, initial, 154182, 154266
-recovered pasa_asmbl_16763.p1, terminal, 154641, 154828
-recovered pasa_asmbl_16763.p1, internal, 153737, 153823
-recovered pasa_asmbl_16763.p1, internal, 154182, 154266
Valid prediction for GlimmerHMM_glimmerT_38640-T1
Valid prediction for GlimmerHMM_glimmerT_38624-T1
Valid prediction for snap_scaffold_16-snap.203-T1
Valid prediction for GeneMark_model.66063_t
Valid prediction for CodingQuarry_transcript_19861-T1
Valid prediction for GlimmerHMM_glimmerT_38620-T1
Valid prediction for snap_scaffold_16-snap.212-T1
Valid prediction for Augustus_model.g25928.t1
Valid prediction for GeneMark_model.66052_t
Valid prediction for GeneMark_model.66065_t
Valid prediction for GlimmerHMM_glimmerT_38618-T1
Valid prediction for snap_scaffold_16-snap.189-T1
Valid prediction for GeneMark_model.66077_t
Valid prediction for snap_scaffold_16-snap.193-T1
Valid prediction for GlimmerHMM_glimmerT_38625-T1
Valid prediction for GeneMark_model.66078_t
Valid prediction for snap_scaffold_16-snap.204-T1
Valid prediction for GeneMark_model.66066_t
Valid prediction for snap_scaffold_16-snap.206-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42802, rend_intergenic: 41649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 307526
-exon list size: 286


building trellis

0.3    
0.7    
1.0    
1.4    
1.7    
2.1    
2.4    
2.8    
3.1    
3.5    
3.8    
4.2    
4.5    
4.9    
5.2    
5.6    
5.9    
6.2    
6.6    
6.9    
7.3    
7.6    
8.0    
8.3    
8.7    
9.0    
9.4    
9.7    
10.1    
10.4    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.8    
13.2    
13.5    
13.9    
14.2    
14.6    
14.9    
15.3    
15.6    
16.0    
16.3    
16.7    
17.0    
17.4    
17.7    
18.1    
18.4    
18.8    
19.1    
19.4    
19.8    
20.1    
20.5    
20.8    
21.2    
21.5    
21.9    
22.2    
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    
27.8    
28.1    
28.5    
28.8    
29.2    
29.5    
29.9    
30.2    
30.6    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.7    
35.1    
35.4    
35.8    
36.1    
36.5    
36.8    
37.2    
37.5    
37.8    
38.2    
38.5    
38.9    
39.2    
39.6    
39.9    
40.3    
40.6    
41.0    
41.3    
41.7    
42.0    
42.4    
42.7    
43.1    
43.4    
43.8    
44.1    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.5    
46.9    
47.2    
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    
52.8    
53.1    
53.5    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
55.9    
56.2    
56.6    
56.9    
57.3    
57.6    
58.0    
58.3    
58.7    
59.0    
59.4    
59.7    
60.1    
60.4    
60.8    
61.1    
61.5    
61.8    
62.2    
62.5    
62.8    
63.2    
63.5    
63.9    
64.2    
64.6    
64.9    
65.3    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.4    
69.8    
70.1    
70.5    
70.8    
71.2    
71.5    
71.9    
72.2    
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    
77.8    
78.1    
78.5    
78.8    
79.2    
79.5    
79.9    
80.2    
80.6    
80.9    
81.2    
81.6    
81.9    
82.3    
82.6    
83.0    
83.3    
83.7    
84.0    
84.4    
84.7    
85.1    
85.4    
85.8    
86.1    
86.5    
86.8    
87.2    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.6    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.0    
92.4    
92.7    
93.1    
93.4    
93.8    
94.1    
94.4    
94.8    
95.1    
95.5    
95.8    
96.2    
96.5    
96.9    
97.2    
97.6    
97.9    
98.3    
98.6    
99.0    
99.3    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 42802, rend_intergenic: 41649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 279635 - 307526
-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
	-no exons in range 279635 - 291004

-building DP trellis

-building trellis in range 291054 - 307526
-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