-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_15607160-15723826

-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.61885_t
Valid prediction for GeneMark_model.61913_t
Valid prediction for snap_scaffold_14-snap.3280-T1
Valid prediction for GeneMark_model.61903_t
Valid prediction for Augustus_model.g24286.t1
Valid prediction for GeneMark_model.61895_t
Couldn't classify 55192, 55264
Sorry, prediction pasa_asmbl_12619.p1 fails validation.
(GCT)	 CT	55192-55264	GT	GGG
(GCC)	 AG	55820-55972	GT	TGG
(GAG)	 AG	56282-56575	GT	AGG
(GAA)	 AG	56659-56897	GA	GAG
-recovered pasa_asmbl_12619.p1, terminal, 56659, 56897
-recovered pasa_asmbl_12619.p1, internal, 55820, 55972
-recovered pasa_asmbl_12619.p1, internal, 56282, 56575
Valid prediction for GlimmerHMM_glimmerT_36074-T1
Valid prediction for Augustus_model.g24285.t1
Valid prediction for GeneMark_model.61920_t
Couldn't classify 31454, 31549
Sorry, prediction pasa_asmbl_12616.p1 fails validation.
(CCC)	 AG	31454-31549	GT	AGG
(GTG)	 AG	31638-31771	GT	TGG
(TTA)	 AG	32404-32554	CC	GAC
-recovered pasa_asmbl_12616.p1, terminal, 32404, 32554
-recovered pasa_asmbl_12616.p1, internal, 31454, 31549
-recovered pasa_asmbl_12616.p1, internal, 31638, 31771
Valid prediction for GeneMark_model.61896_t
Valid prediction for snap_scaffold_14-snap.3285-T1
Valid prediction for GlimmerHMM_glimmerT_36075-T1
Valid prediction for snap_scaffold_14-snap.3278-T1
Valid prediction for snap_scaffold_14-snap.3289-T1
Valid prediction for GlimmerHMM_glimmerT_36072-T1
Valid prediction for GeneMark_model.61897_t
Valid prediction for GlimmerHMM_glimmerT_36070-T1
Valid prediction for Augustus_model.g24288.t1
Valid prediction for GeneMark_model.61884_t
Valid prediction for GeneMark_model.61915_t
Couldn't classify 30515, 31102
Sorry, prediction pasa_asmbl_12615.p1 fails validation.
(ACA)	 TC	30515-31102	CA	CCC
Valid prediction for GeneMark_model.61901_t
Valid prediction for snap_scaffold_14-snap.3282-T1
Valid prediction for snap_scaffold_14-snap.3274-T1
Valid prediction for Augustus_model.g24279.t1
Valid prediction for GeneMark_model.61917_t
Valid prediction for GeneMark_model.61893_t
Valid prediction for GeneMark_model.61907_t
Valid prediction for GeneMark_model.61918_t
Valid prediction for GeneMark_model.61906_t
Valid prediction for Augustus_model.g24283.t1
Valid prediction for GeneMark_model.61899_t
Valid prediction for GeneMark_model.61909_t
Valid prediction for snap_scaffold_14-snap.3271-T1
Valid prediction for GeneMark_model.61911_t
Valid prediction for GeneMark_model.61905_t
Valid prediction for snap_scaffold_14-snap.3291-T1
Valid prediction for snap_scaffold_14-snap.3277-T1
Couldn't classify 54248, 54348
Sorry, prediction pasa_asmbl_12618.p1 fails validation.
(ATG)	 CG	49634-49726	GT	TGG
(GAT)	 AG	51504-51636	GT	TGG
(ACA)	 AG	51989-52121	GT	AGG
(CAT)	 AG	52837-53171	GT	AGG
(GAC)	 AG	54248-54348	GG	CGG
-recovered pasa_asmbl_12618.p1, initial, 49634, 49726
-recovered pasa_asmbl_12618.p1, internal, 51504, 51636
-recovered pasa_asmbl_12618.p1, internal, 51989, 52121
-recovered pasa_asmbl_12618.p1, internal, 52837, 53171
Valid prediction for snap_scaffold_14-snap.3293-T1
Valid prediction for GeneMark_model.61892_t
Valid prediction for GeneMark_model.61888_t
Valid prediction for snap_scaffold_14-snap.3294-T1
Valid prediction for HiQ_model.g24287.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 GeneMark_model.61900_t
Valid prediction for snap_scaffold_14-snap.3283-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_36069-T1
Valid prediction for GlimmerHMM_glimmerT_36078-T1
Valid prediction for pasa_asmbl_13716.p1
Valid prediction for CodingQuarry_transcript_15908-T1
Valid prediction for GeneMark_model.61898_t
Valid prediction for Augustus_model.g24292.t1
Valid prediction for snap_scaffold_14-snap.3297-T1
Valid prediction for GlimmerHMM_glimmerT_36073-T1
Valid prediction for snap_scaffold_14-snap.3288-T1
Valid prediction for GeneMark_model.61882_t
Valid prediction for GeneMark_model.61902_t
Valid prediction for snap_scaffold_14-snap.3273-T1
Valid prediction for GeneMark_model.61883_t
Valid prediction for GlimmerHMM_glimmerT_36068-T1
Valid prediction for GeneMark_model.61914_t
Valid prediction for snap_scaffold_14-snap.3290-T1
Valid prediction for GlimmerHMM_glimmerT_36076-T1
Valid prediction for Augustus_model.g24284.t1
Valid prediction for snap_scaffold_14-snap.3287-T1
Valid prediction for snap_scaffold_14-snap.3284-T1
Valid prediction for snap_scaffold_14-snap.3275-T1
Valid prediction for GlimmerHMM_glimmerT_36081-T1
Valid prediction for Augustus_model.g24289.t1
Valid prediction for GlimmerHMM_glimmerT_36080-T1
Valid prediction for GeneMark_model.61887_t
Valid prediction for snap_scaffold_14-snap.3281-T1
Valid prediction for GeneMark_model.61916_t
Valid prediction for GeneMark_model.61894_t
Valid prediction for GeneMark_model.61891_t
Valid prediction for Augustus_model.g24278.t1
Valid prediction for snap_scaffold_14-snap.3292-T1
Valid prediction for GeneMark_model.61919_t
Valid prediction for HiQ_model.g24282.t1
Valid prediction for snap_scaffold_14-snap.3286-T1
Couldn't classify 111216, 111241
Couldn't classify 112601, 112701
Sorry, prediction pasa_asmbl_13827.p1 fails validation.
(CCG)	 CA	111216-111241	GT	ACG
(GAG)	 AG	111787-112400	GT	GGG
(GGA)	 AG	112601-112701	GA	TGG
-recovered pasa_asmbl_13827.p1, internal, 111787, 112400
Valid prediction for GlimmerHMM_glimmerT_36071-T1
Valid prediction for HiQ_model.g24291.t1
Valid prediction for GlimmerHMM_glimmerT_36067-T1
Valid prediction for GeneMark_model.61912_t
Valid prediction for Augustus_model.g24293.t1
Valid prediction for GlimmerHMM_glimmerT_36079-T1
Valid prediction for GeneMark_model.61890_t
Valid prediction for GeneMark_model.61886_t
Valid prediction for pasa_asmbl_13720.p1
Valid prediction for snap_scaffold_14-snap.3279-T1
Valid prediction for CodingQuarry_transcript_15909-T1
Valid prediction for Augustus_model.g24294.t1
Valid prediction for Augustus_model.g24290.t1
Valid prediction for Augustus_model.g24281.t1
Valid prediction for snap_scaffold_14-snap.3296-T1
Valid prediction for GeneMark_model.61889_t
Valid prediction for GeneMark_model.61910_t
Valid prediction for snap_scaffold_14-snap.3272-T1
Couldn't classify 113555, 113680
Sorry, prediction pasa_asmbl_13714.p1 fails validation.
(AGC)	 GC	113555-113680	GT	AGG
(CCT)	 AG	113905-114043	GT	GGG
(ACT)	 AG	114210-114293	GT	AGG
(GTG)	 AG	114385-114569	AC	GAA
-recovered pasa_asmbl_13714.p1, terminal, 114385, 114569
-recovered pasa_asmbl_13714.p1, internal, 113905, 114043
-recovered pasa_asmbl_13714.p1, internal, 114210, 114293
Valid prediction for snap_scaffold_14-snap.3295-T1
Valid prediction for CodingQuarry_transcript_15906-T1
Valid prediction for CodingQuarry_transcript_15907-T1
Valid prediction for Augustus_model.g24280.t1
Valid prediction for snap_scaffold_14-snap.3276-T1
Valid prediction for GeneMark_model.61904_t
Valid prediction for GlimmerHMM_glimmerT_36077-T1
Valid prediction for GlimmerHMM_glimmerT_36082-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4042, rend_intergenic: 2099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45369, rend_intergenic: 43812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54338, rend_intergenic: 52009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81854, rend_intergenic: 78691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87340, rend_intergenic: 86088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90025, rend_intergenic: 87415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102084, rend_intergenic: 91946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110024, rend_intergenic: 102277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 116667
-exon list size: 497


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.2    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
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    
9.0    
9.2    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
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    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.2    
18.4    
18.6    
18.8    
19.0    
19.2    
19.4    
19.6    
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    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
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    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
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    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
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    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
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    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
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    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
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    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
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    
80.4    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
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    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
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    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 4042, rend_intergenic: 2099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45369, rend_intergenic: 43812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54338, rend_intergenic: 52009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81854, rend_intergenic: 78691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87340, rend_intergenic: 86088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90025, rend_intergenic: 87415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102084, rend_intergenic: 91946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110024, rend_intergenic: 102277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support