-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_11402506-11688280

-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 GlimmerHMM_glimmerT_30727-T1
Valid prediction for snap_scaffold_12-snap.2156-T1
Valid prediction for GeneMark_model.53062_t
Valid prediction for Augustus_model.g20490.t1
Valid prediction for GeneMark_model.53051_t
Valid prediction for snap_scaffold_12-snap.2158-T1
Valid prediction for GeneMark_model.53050_t
Valid prediction for GlimmerHMM_glimmerT_30735-T1
Valid prediction for snap_scaffold_12-snap.2163-T1
Valid prediction for GeneMark_model.53036_t
Valid prediction for Augustus_model.g20485.t1
Valid prediction for Augustus_model.g20493.t1
Valid prediction for GlimmerHMM_glimmerT_30728-T1
Valid prediction for GeneMark_model.53025_t
Valid prediction for CodingQuarry_transcript_10364-T1
Valid prediction for GeneMark_model.53041_t
Valid prediction for Augustus_model.g20492.t1
Valid prediction for snap_scaffold_12-snap.2149-T1
Valid prediction for GlimmerHMM_glimmerT_30726-T1
Valid prediction for snap_scaffold_12-snap.2144-T1
Valid prediction for GlimmerHMM_glimmerT_30752-T1
Valid prediction for snap_scaffold_12-snap.2166-T1
Valid prediction for GeneMark_model.53032_t
Valid prediction for Augustus_model.g20489.t1
Valid prediction for HiQ_model.g20496.t1
Valid prediction for GlimmerHMM_glimmerT_30736-T1
Valid prediction for Augustus_model.g20486.t1
Valid prediction for snap_scaffold_12-snap.2176-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g20503.t1
Valid prediction for pasa_asmbl_8930.p1
Valid prediction for Augustus_model.g20494.t1
Valid prediction for GeneMark_model.53042_t
Valid prediction for GeneMark_model.53046_t
Valid prediction for GlimmerHMM_glimmerT_30730-T1
Valid prediction for GeneMark_model.53044_t
Valid prediction for snap_scaffold_12-snap.2151-T1
Valid prediction for GlimmerHMM_glimmerT_30731-T1
Valid prediction for snap_scaffold_12-snap.2147-T1
Valid prediction for GeneMark_model.53029_t
Valid prediction for GeneMark_model.53048_t
Valid prediction for snap_scaffold_12-snap.2177-T1
Valid prediction for GlimmerHMM_glimmerT_30741-T1
Valid prediction for Augustus_model.g20491.t1
Valid prediction for GeneMark_model.53039_t
Valid prediction for GeneMark_model.53035_t
Valid prediction for GlimmerHMM_glimmerT_30734-T1
Valid prediction for snap_scaffold_12-snap.2161-T1
Valid prediction for Augustus_model.g20487.t1
Valid prediction for GlimmerHMM_glimmerT_30737-T1
Valid prediction for GlimmerHMM_glimmerT_30721-T1
Valid prediction for snap_scaffold_12-snap.2150-T1
Valid prediction for GlimmerHMM_glimmerT_30720-T1
Valid prediction for GlimmerHMM_glimmerT_30723-T1
Valid prediction for GeneMark_model.53024_t
Valid prediction for GeneMark_model.53059_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 GeneMark_model.53053_t
Couldn't classify 30976, 31116
Sorry, prediction pasa_asmbl_8346.p1 fails validation.
(GCG)	 AA	30976-31116	GT	AGG
(GTG)	 AG	31272-31393	GT	AGG
(GAG)	 AG	31483-31552	GT	AGG
(GCC)	 AG	31829-31933	GT	AAG
(GGA)	 AG	32123-32185	GT	GGG
(TGG)	 AG	32295-32365	GT	AGG
(CTC)	 AG	32527-32633	GT	AGG
(AGA)	 AG	32876-32932	GT	CTG
(GTA)	 AG	33063-33157	GT	AGG
(GAG)	 AG	33617-33687	GT	AGG
(GGA)	 AG	34275-34425	TG	GAT
-recovered pasa_asmbl_8346.p1, terminal, 34275, 34425
-recovered pasa_asmbl_8346.p1, internal, 31272, 31393
-recovered pasa_asmbl_8346.p1, internal, 31483, 31552
-recovered pasa_asmbl_8346.p1, internal, 31829, 31933
-recovered pasa_asmbl_8346.p1, internal, 32123, 32185
-recovered pasa_asmbl_8346.p1, internal, 32295, 32365
-recovered pasa_asmbl_8346.p1, internal, 32527, 32633
-recovered pasa_asmbl_8346.p1, internal, 32876, 32932
-recovered pasa_asmbl_8346.p1, internal, 33063, 33157
-recovered pasa_asmbl_8346.p1, internal, 33617, 33687
Valid prediction for snap_scaffold_12-snap.2165-T1
Valid prediction for Augustus_model.g20484.t1
Valid prediction for GeneMark_model.53037_t
Valid prediction for snap_scaffold_12-snap.2152-T1
Couldn't classify 66239, 66347
Couldn't classify 67261, 67466
Sorry, prediction pasa_asmbl_7951.p1 fails validation.
(TCA)	 TG	66239-66347	GT	TGG
(GTC)	 AG	66664-66744	GT	TGG
(ACT)	 AG	67261-67466	CT	AGC
-recovered pasa_asmbl_7951.p1, internal, 66664, 66744
Valid prediction for GeneMark_model.53028_t
Valid prediction for snap_scaffold_12-snap.2145-T1
Valid prediction for snap_scaffold_12-snap.2154-T1
Valid prediction for GlimmerHMM_glimmerT_30744-T1
Valid prediction for GlimmerHMM_glimmerT_30742-T1
Valid prediction for GeneMark_model.53040_t
Valid prediction for snap_scaffold_12-snap.2174-T1
Valid prediction for GlimmerHMM_glimmerT_30745-T1
Valid prediction for pasa_asmbl_7949.p1
Valid prediction for GeneMark_model.53043_t
Valid prediction for Augustus_model.g20499.t1
Valid prediction for GeneMark_model.53061_t
Valid prediction for GlimmerHMM_glimmerT_30733-T1
Valid prediction for GlimmerHMM_glimmerT_30724-T1
Valid prediction for GlimmerHMM_glimmerT_30748-T1
Valid prediction for snap_scaffold_12-snap.2155-T1
Valid prediction for Augustus_model.g20502.t1
Valid prediction for Augustus_model.g20500.t1
Valid prediction for GeneMark_model.53027_t
Couldn't classify 69288, 69393
Sorry, prediction pasa_asmbl_7950.p1 fails validation.
(AAC)	 AC	69288-69393	GT	CGG
(AAA)	 AG	71434-71573	GT	AGG
(GCC)	 AG	71891-72031	GG	AAG
-recovered pasa_asmbl_7950.p1, terminal, 71891, 72031
-recovered pasa_asmbl_7950.p1, internal, 71434, 71573
Valid prediction for GeneMark_model.53026_t
Valid prediction for GeneMark_model.53038_t
Valid prediction for GlimmerHMM_glimmerT_30747-T1
Valid prediction for GlimmerHMM_glimmerT_30743-T1
Valid prediction for GlimmerHMM_glimmerT_30750-T1
Valid prediction for GeneMark_model.53056_t
Valid prediction for snap_scaffold_12-snap.2164-T1
Valid prediction for HiQ_model.g20495.t1
Valid prediction for GeneMark_model.53055_t
Valid prediction for Augustus_model.g20483.t1
Valid prediction for GlimmerHMM_glimmerT_30722-T1
Valid prediction for GlimmerHMM_glimmerT_30738-T1
Valid prediction for snap_scaffold_12-snap.2157-T1
Valid prediction for GlimmerHMM_glimmerT_30740-T1
Valid prediction for GlimmerHMM_glimmerT_30739-T1
Valid prediction for GeneMark_model.53047_t
Valid prediction for GeneMark_model.53031_t
Valid prediction for CodingQuarry_transcript_10363-T1
Valid prediction for GlimmerHMM_glimmerT_30732-T1
Valid prediction for snap_scaffold_12-snap.2173-T1
Valid prediction for snap_scaffold_12-snap.2160-T1
Valid prediction for GlimmerHMM_glimmerT_30746-T1
Valid prediction for GlimmerHMM_glimmerT_30729-T1
Valid prediction for GlimmerHMM_glimmerT_30749-T1
Valid prediction for GeneMark_model.53057_t
Valid prediction for Augustus_model.g20488.t1
Valid prediction for GeneMark_model.53052_t
Valid prediction for GeneMark_model.53034_t
Valid prediction for GeneMark_model.53033_t
Valid prediction for snap_scaffold_12-snap.2159-T1
Valid prediction for GeneMark_model.53058_t
Valid prediction for snap_scaffold_12-snap.2162-T1
Valid prediction for GlimmerHMM_glimmerT_30725-T1
Valid prediction for Augustus_model.g20501.t1
Valid prediction for GeneMark_model.53030_t
Valid prediction for GeneMark_model.53054_t
Valid prediction for snap_scaffold_12-snap.2168-T1
Valid prediction for snap_scaffold_12-snap.2146-T1
Valid prediction for snap_scaffold_12-snap.2170-T1
Valid prediction for Augustus_model.g20498.t1
Valid prediction for snap_scaffold_12-snap.2169-T1
Valid prediction for GeneMark_model.53049_t
Valid prediction for Augustus_model.g20497.t1
Valid prediction for snap_scaffold_12-snap.2172-T1
Valid prediction for GlimmerHMM_glimmerT_30751-T1
Valid prediction for snap_scaffold_12-snap.2148-T1
Valid prediction for GeneMark_model.53045_t
Valid prediction for snap_scaffold_12-snap.2171-T1
Valid prediction for snap_scaffold_12-snap.2153-T1
Valid prediction for snap_scaffold_12-snap.2175-T1
Valid prediction for snap_scaffold_12-snap.2167-T1
Valid prediction for GeneMark_model.53060_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25469, rend_intergenic: 18176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128410, rend_intergenic: 126463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151529, rend_intergenic: 149596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161999, rend_intergenic: 161501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164472, rend_intergenic: 163174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180258, rend_intergenic: 167981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 40504, rend_intergenic: 40501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 285775
-exon list size: 484


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.6    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.1    
9.3    
9.5    
9.7    
9.9    
10.1    
10.3    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.3    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.3    
23.5    
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    
26.5    
26.7    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.4    
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    
51.6    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.1    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.3    
73.5    
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    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 25469, rend_intergenic: 18176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128410, rend_intergenic: 126463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151529, rend_intergenic: 149596  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161999, rend_intergenic: 161501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164472, rend_intergenic: 163174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180258, rend_intergenic: 167981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 40504, rend_intergenic: 40501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15751
-exon list size: 29


building trellis

3.2    
6.5    
9.7    
12.9    
16.1    
19.4    
22.6    
25.8    
29.0    
32.3    
35.5    
38.7    
41.9    
45.2    
48.4    
51.6    
54.8    
58.1    
61.3    
64.5    
67.7    
71.0    
74.2    
77.4    
80.6    
83.9    
87.1    
90.3    
93.5    
96.8    
-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 - 13588
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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 - 10627
-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
GOT 5prime partial gene.

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