-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_19791927-19972339

-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_3-snap.3946-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.14200_t
Valid prediction for GeneMark_model.14186_t
Valid prediction for GeneMark_model.14170_t
Valid prediction for snap_scaffold_3-snap.3957-T1
Valid prediction for GeneMark_model.14162_t
Valid prediction for snap_scaffold_3-snap.3949-T1
Valid prediction for pasa_asmbl_40736.p1
Valid prediction for GeneMark_model.14166_t
Valid prediction for GlimmerHMM_glimmerT_8736-T1
Valid prediction for snap_scaffold_3-snap.3938-T1
Valid prediction for GeneMark_model.14194_t
Valid prediction for snap_scaffold_3-snap.3947-T1
Valid prediction for GlimmerHMM_glimmerT_8733-T1
Valid prediction for snap_scaffold_3-snap.3948-T1
Valid prediction for GlimmerHMM_glimmerT_8724-T1
Valid prediction for GeneMark_model.14190_t
Valid prediction for GlimmerHMM_glimmerT_8726-T1
Valid prediction for GeneMark_model.14192_t
Valid prediction for snap_scaffold_3-snap.3937-T1
Valid prediction for snap_scaffold_3-snap.3952-T1
Valid prediction for GlimmerHMM_glimmerT_8737-T1
Valid prediction for GeneMark_model.14183_t
Valid prediction for snap_scaffold_3-snap.3939-T1
Valid prediction for snap_scaffold_3-snap.3935-T1
Valid prediction for GeneMark_model.14199_t
Valid prediction for GeneMark_model.14168_t
Valid prediction for snap_scaffold_3-snap.3954-T1
Valid prediction for snap_scaffold_3-snap.3941-T1
Valid prediction for snap_scaffold_3-snap.3950-T1
Valid prediction for GeneMark_model.14175_t
Valid prediction for snap_scaffold_3-snap.3944-T1
Valid prediction for snap_scaffold_3-snap.3955-T1
Valid prediction for GeneMark_model.14173_t
Valid prediction for GlimmerHMM_glimmerT_8720-T1
Valid prediction for GeneMark_model.14178_t
Valid prediction for GeneMark_model.14164_t
Valid prediction for snap_scaffold_3-snap.3942-T1
Valid prediction for GeneMark_model.14177_t
Valid prediction for GeneMark_model.14172_t
Valid prediction for GlimmerHMM_glimmerT_8718-T1
Valid prediction for GlimmerHMM_glimmerT_8731-T1
Valid prediction for GlimmerHMM_glimmerT_8719-T1
Valid prediction for GeneMark_model.14197_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 GlimmerHMM_glimmerT_8728-T1
Valid prediction for snap_scaffold_3-snap.3936-T1
Valid prediction for snap_scaffold_3-snap.3943-T1
Valid prediction for GlimmerHMM_glimmerT_8735-T1
Valid prediction for GeneMark_model.14191_t
Valid prediction for GlimmerHMM_glimmerT_8732-T1
Valid prediction for GeneMark_model.14184_t
Valid prediction for snap_scaffold_3-snap.3951-T1
Valid prediction for snap_scaffold_3-snap.3945-T1
Valid prediction for GeneMark_model.14171_t
Couldn't classify 123816, 123865
Couldn't classify 128753, 129061
Sorry, prediction pasa_asmbl_39611.p1 fails validation.
(CCT)	 AC	123816-123865	GT	AGG
(AAC)	 AG	126001-126094	GT	AGG
(GTG)	 AG	126197-126271	GT	TGG
(GTG)	 AG	127060-127170	GT	ACG
(AAG)	 AG	127604-127753	GT	ACG
(ATG)	 AG	128420-128521	GT	GGG
(GAA)	 AG	128753-129061	AG	GCA
-recovered pasa_asmbl_39611.p1, initial, 128420, 128521
-recovered pasa_asmbl_39611.p1, internal, 126001, 126094
-recovered pasa_asmbl_39611.p1, internal, 126197, 126271
-recovered pasa_asmbl_39611.p1, internal, 127060, 127170
-recovered pasa_asmbl_39611.p1, internal, 127604, 127753
-recovered pasa_asmbl_39611.p1, internal, 128420, 128521
Couldn't classify 70331, 70803
Couldn't classify 71249, 71632
Sorry, prediction pasa_asmbl_39624.p1 fails validation.
(CTA)	 TC	70331-70803	GT	AGG
(AAA)	 AG	70899-70932	GT	AGG
(GCT)	 AG	71249-71632	GA	CTG
-recovered pasa_asmbl_39624.p1, internal, 70899, 70932
Valid prediction for GeneMark_model.14180_t
Valid prediction for GeneMark_model.14167_t
Valid prediction for GlimmerHMM_glimmerT_8729-T1
Valid prediction for GeneMark_model.14182_t
Valid prediction for CodingQuarry_transcript_46379-T1
Valid prediction for GlimmerHMM_glimmerT_8721-T1
Valid prediction for GlimmerHMM_glimmerT_8723-T1
Valid prediction for snap_scaffold_3-snap.3956-T1
Valid prediction for GeneMark_model.14181_t
Couldn't classify 143635, 143745
Sorry, prediction pasa_asmbl_39608.p1 fails validation.
(ATG)	 GG	135261-135347	GT	AAG
(GAC)	 AG	135626-135828	GT	CTG
(GTT)	 AG	138040-138274	GT	CGG
(CAA)	 AG	138573-138641	GT	AAG
(ATC)	 AG	140051-140131	GT	TGG
(CTA)	 AG	140231-140360	GT	TGG
(TGT)	 AG	141007-141170	GT	AGG
(GAT)	 AG	141271-141372	GT	GGG
(CAA)	 AG	141729-141809	GT	AGG
(TGT)	 AG	143635-143745	GA	ACG
-recovered pasa_asmbl_39608.p1, initial, 135261, 135347
-recovered pasa_asmbl_39608.p1, internal, 135626, 135828
-recovered pasa_asmbl_39608.p1, internal, 138040, 138274
-recovered pasa_asmbl_39608.p1, internal, 138573, 138641
-recovered pasa_asmbl_39608.p1, internal, 140051, 140131
-recovered pasa_asmbl_39608.p1, internal, 140231, 140360
-recovered pasa_asmbl_39608.p1, internal, 141007, 141170
-recovered pasa_asmbl_39608.p1, internal, 141271, 141372
-recovered pasa_asmbl_39608.p1, internal, 141729, 141809
Valid prediction for GlimmerHMM_glimmerT_8730-T1
Valid prediction for GlimmerHMM_glimmerT_8722-T1
Valid prediction for GeneMark_model.14185_t
Valid prediction for GeneMark_model.14165_t
Valid prediction for snap_scaffold_3-snap.3940-T1
Valid prediction for GeneMark_model.14196_t
Valid prediction for GlimmerHMM_glimmerT_8725-T1
Valid prediction for GeneMark_model.14187_t
Valid prediction for pasa_asmbl_39621.p2
Valid prediction for GeneMark_model.14163_t
Valid prediction for GlimmerHMM_glimmerT_8727-T1
Valid prediction for CodingQuarry_transcript_46380-T1
Valid prediction for GeneMark_model.14176_t
Couldn't classify 71825, 72085
Sorry, prediction pasa_asmbl_39622.p1 fails validation.
(CTA)	 AC	71825-72085	GT	CGG
(TTC)	 AG	72993-73116	GT	GGG
(GAG)	 AG	74335-74578	GT	AGG
(AGA)	 AG	74744-74839	GT	AGG
(TGG)	 AG	76709-76802	GT	TGG
(GGA)	 AG	76902-76957	GT	AGG
(GCC)	 AG	77270-77412	GT	AGG
(GCT)	 AG	78079-78273	GT	AGG
(GCT)	 AG	79616-79773	GT	AGG
(GAG)	 AG	80365-80488	GT	CTG
(TGC)	 AG	80682-80979	GT	AGG
(AAT)	 AG	81471-81678	GT	AGG
(GTG)	 AG	81879-82015	GT	AGG
(GCT)	 AG	82388-82511	GT	AGG
(GCA)	 AG	82706-83179	GT	AGG
(TGT)	 AG	83385-83576	GT	AGG
(GTT)	 AG	83880-83984	GG	GAG
-recovered pasa_asmbl_39622.p1, terminal, 83880, 83984
-recovered pasa_asmbl_39622.p1, internal, 72993, 73116
-recovered pasa_asmbl_39622.p1, internal, 74335, 74578
-recovered pasa_asmbl_39622.p1, internal, 74744, 74839
-recovered pasa_asmbl_39622.p1, internal, 76709, 76802
-recovered pasa_asmbl_39622.p1, internal, 76902, 76957
-recovered pasa_asmbl_39622.p1, internal, 77270, 77412
-recovered pasa_asmbl_39622.p1, internal, 78079, 78273
-recovered pasa_asmbl_39622.p1, internal, 79616, 79773
-recovered pasa_asmbl_39622.p1, internal, 80365, 80488
-recovered pasa_asmbl_39622.p1, internal, 80682, 80979
-recovered pasa_asmbl_39622.p1, internal, 81471, 81678
-recovered pasa_asmbl_39622.p1, internal, 81879, 82015
-recovered pasa_asmbl_39622.p1, internal, 82388, 82511
-recovered pasa_asmbl_39622.p1, internal, 82706, 83179
-recovered pasa_asmbl_39622.p1, internal, 83385, 83576
Valid prediction for GeneMark_model.14188_t
Valid prediction for GeneMark_model.14174_t
Valid prediction for GlimmerHMM_glimmerT_8717-T1
Valid prediction for GeneMark_model.14169_t
Valid prediction for GeneMark_model.14179_t
Valid prediction for GlimmerHMM_glimmerT_8734-T1
Valid prediction for GeneMark_model.14195_t
Valid prediction for snap_scaffold_3-snap.3953-T1
Valid prediction for GeneMark_model.14189_t
Valid prediction for GeneMark_model.14193_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26863, rend_intergenic: 14381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46945, rend_intergenic: 38572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71455, rend_intergenic: 51360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80753, rend_intergenic: 72779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124494, rend_intergenic: 96461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131501, rend_intergenic: 125501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142379, rend_intergenic: 133842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160609, rend_intergenic: 147927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180413
-exon list size: 598


building trellis

0.2    
0.3    
0.5    
0.7    
0.8    
1.0    
1.2    
1.3    
1.5    
1.7    
1.8    
2.0    
2.2    
2.3    
2.5    
2.7    
2.8    
3.0    
3.2    
3.3    
3.5    
3.7    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.8    
5.0    
5.2    
5.3    
5.5    
5.7    
5.8    
6.0    
6.2    
6.3    
6.5    
6.7    
6.8    
7.0    
7.2    
7.3    
7.5    
7.7    
7.8    
8.0    
8.2    
8.3    
8.5    
8.7    
8.8    
9.0    
9.2    
9.3    
9.5    
9.7    
9.8    
10.0    
10.2    
10.3    
10.5    
10.7    
10.8    
11.0    
11.2    
11.3    
11.5    
11.7    
11.8    
12.0    
12.2    
12.3    
12.5    
12.7    
12.8    
13.0    
13.2    
13.3    
13.5    
13.7    
13.8    
14.0    
14.2    
14.3    
14.5    
14.7    
14.8    
15.0    
15.2    
15.3    
15.5    
15.7    
15.8    
16.0    
16.2    
16.3    
16.5    
16.7    
16.8    
17.0    
17.2    
17.3    
17.5    
17.7    
17.8    
18.0    
18.2    
18.3    
18.5    
18.7    
18.8    
19.0    
19.2    
19.3    
19.5    
19.7    
19.8    
20.0    
20.2    
20.3    
20.5    
20.7    
20.8    
21.0    
21.2    
21.3    
21.5    
21.7    
21.8    
22.0    
22.2    
22.3    
22.5    
22.7    
22.8    
23.0    
23.2    
23.3    
23.5    
23.7    
23.8    
24.0    
24.2    
24.3    
24.5    
24.7    
24.8    
25.0    
25.2    
25.3    
25.5    
25.7    
25.8    
26.0    
26.2    
26.3    
26.5    
26.7    
26.8    
27.0    
27.2    
27.3    
27.5    
27.7    
27.8    
28.0    
28.2    
28.3    
28.5    
28.7    
28.8    
29.0    
29.2    
29.3    
29.5    
29.7    
29.8    
30.0    
30.2    
30.3    
30.5    
30.7    
30.8    
31.0    
31.2    
31.3    
31.5    
31.7    
31.8    
32.0    
32.2    
32.3    
32.5    
32.7    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.8    
34.0    
34.2    
34.3    
34.5    
34.7    
34.8    
35.0    
35.2    
35.3    
35.5    
35.7    
35.8    
36.0    
36.2    
36.3    
36.5    
36.7    
36.8    
37.0    
37.2    
37.3    
37.5    
37.7    
37.8    
38.0    
38.2    
38.3    
38.5    
38.7    
38.8    
39.0    
39.2    
39.3    
39.5    
39.7    
39.8    
40.0    
40.2    
40.3    
40.5    
40.7    
40.8    
41.0    
41.2    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.8    
44.0    
44.2    
44.3    
44.5    
44.7    
44.8    
45.0    
45.2    
45.3    
45.5    
45.7    
45.8    
46.0    
46.2    
46.3    
46.5    
46.7    
46.8    
47.0    
47.2    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.3    
48.5    
48.7    
48.8    
49.0    
49.2    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.8    
51.0    
51.2    
51.3    
51.5    
51.7    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
52.8    
53.0    
53.2    
53.3    
53.5    
53.7    
53.8    
54.0    
54.2    
54.3    
54.5    
54.7    
54.8    
55.0    
55.2    
55.3    
55.5    
55.7    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.3    
61.5    
61.7    
61.8    
62.0    
62.2    
62.3    
62.5    
62.7    
62.8    
63.0    
63.2    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.8    
80.0    
80.2    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 15 predictions from path traversal
Error with prediction: snap lend_intergenic: 26863, rend_intergenic: 14381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46945, rend_intergenic: 38572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71455, rend_intergenic: 51360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80753, rend_intergenic: 72779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124494, rend_intergenic: 96461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131501, rend_intergenic: 125501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142379, rend_intergenic: 133842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160609, rend_intergenic: 147927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11771
-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 1 - 10580
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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 169154 - 180413
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

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