-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_2457110-2633559

-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.g254.t1
Valid prediction for snap_scaffold_1-snap.403-T1
Valid prediction for GlimmerHMM_glimmerT_320-T1
Valid prediction for GlimmerHMM_glimmerT_313-T1
Valid prediction for Augustus_model.g259.t1
Valid prediction for GlimmerHMM_glimmerT_317-T1
Valid prediction for GlimmerHMM_glimmerT_327-T1
Valid prediction for Augustus_model.g262.t1
Valid prediction for Augustus_model.g256.t1
Valid prediction for GlimmerHMM_glimmerT_315-T1
Valid prediction for snap_scaffold_1-snap.428-T1
Valid prediction for Augustus_model.g253.t1
Valid prediction for Augustus_model.g258.t1
Valid prediction for snap_scaffold_1-snap.420-T1
Valid prediction for snap_scaffold_1-snap.398-T1
Valid prediction for Augustus_model.g268.t1
Valid prediction for CodingQuarry_transcript_2551-T1
Valid prediction for snap_scaffold_1-snap.413-T1
Valid prediction for Augustus_model.g255.t1
Valid prediction for GlimmerHMM_glimmerT_310-T1
Valid prediction for snap_scaffold_1-snap.417-T1
Valid prediction for snap_scaffold_1-snap.422-T1
Valid prediction for snap_scaffold_1-snap.396-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g267.t1
Valid prediction for snap_scaffold_1-snap.429-T1
Valid prediction for GlimmerHMM_glimmerT_324-T1
Valid prediction for GlimmerHMM_glimmerT_318-T1
Valid prediction for GlimmerHMM_glimmerT_316-T1
Valid prediction for GlimmerHMM_glimmerT_309-T1
Valid prediction for snap_scaffold_1-snap.402-T1
Couldn't classify 11377, 11498
Sorry, prediction pasa_asmbl_1541.p1 fails validation.
(GGC)	 TA	11377-11498	GT	AAG
(TGT)	 AG	14215-14326	GT	TGG
(GAG)	 AG	14606-14685	GT	AGG
(GGA)	 AG	14899-14962	GT	AGG
(GGT)	 AG	15116-15262	GT	AGG
(GAT)	 AG	15377-15410	GT	AGG
(ACT)	 AG	16477-16672	GT	TGG
(CTA)	 AG	18686-18812	GC	AGG
-recovered pasa_asmbl_1541.p1, terminal, 18686, 18812
-recovered pasa_asmbl_1541.p1, internal, 14215, 14326
-recovered pasa_asmbl_1541.p1, internal, 14606, 14685
-recovered pasa_asmbl_1541.p1, internal, 14899, 14962
-recovered pasa_asmbl_1541.p1, internal, 15116, 15262
-recovered pasa_asmbl_1541.p1, internal, 15377, 15410
-recovered pasa_asmbl_1541.p1, internal, 16477, 16672
-recovered pasa_asmbl_1541.p1, internal, 18686, 18812
Valid prediction for Augustus_model.g248.t1
Valid prediction for GlimmerHMM_glimmerT_330-T1
Valid prediction for GlimmerHMM_glimmerT_321-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g263.t1
Valid prediction for Augustus_model.g250.t1
Couldn't classify 40604, 40637
Couldn't classify 45480, 45626
Sorry, prediction pasa_asmbl_1543.p1 fails validation.
(ATT)	 TC	40604-40637	GT	AGG
(GCA)	 AG	40787-40923	GT	AGG
(GCG)	 AG	41130-41299	GT	CGG
(GGA)	 AG	42106-42262	GT	TGG
(ATG)	 AG	42369-42478	GT	AGG
(ACT)	 AG	42874-43075	GT	CGG
(GCG)	 AG	43186-43310	GT	AGG
(CTT)	 AG	43525-43642	GT	AGG
(TGT)	 AG	44253-44340	GT	TGG
(AGA)	 AG	44778-44884	GT	TGG
(CAA)	 AG	44974-45102	GT	TGG
(TTG)	 AG	45480-45626	GA	TGG
-recovered pasa_asmbl_1543.p1, initial, 42369, 42478
-recovered pasa_asmbl_1543.p1, internal, 40787, 40923
-recovered pasa_asmbl_1543.p1, internal, 41130, 41299
-recovered pasa_asmbl_1543.p1, internal, 42106, 42262
-recovered pasa_asmbl_1543.p1, internal, 42369, 42478
-recovered pasa_asmbl_1543.p1, internal, 42874, 43075
-recovered pasa_asmbl_1543.p1, internal, 43186, 43310
-recovered pasa_asmbl_1543.p1, internal, 43525, 43642
-recovered pasa_asmbl_1543.p1, internal, 44253, 44340
-recovered pasa_asmbl_1543.p1, internal, 44778, 44884
-recovered pasa_asmbl_1543.p1, internal, 44974, 45102
Valid prediction for snap_scaffold_1-snap.399-T1
Valid prediction for Augustus_model.g265.t1
Valid prediction for snap_scaffold_1-snap.427-T1
Valid prediction for snap_scaffold_1-snap.423-T1
Valid prediction for Augustus_model.g269.t1
Valid prediction for snap_scaffold_1-snap.406-T1
Valid prediction for Augustus_model.g249.t1
Valid prediction for snap_scaffold_1-snap.408-T1
Valid prediction for snap_scaffold_1-snap.411-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.397-T1
Valid prediction for snap_scaffold_1-snap.409-T1
Valid prediction for snap_scaffold_1-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_314-T1
Valid prediction for GlimmerHMM_glimmerT_331-T1
Valid prediction for snap_scaffold_1-snap.407-T1
Valid prediction for GlimmerHMM_glimmerT_319-T1
Valid prediction for GlimmerHMM_glimmerT_326-T1
Valid prediction for pasa_asmbl_1547.p1
Valid prediction for Augustus_model.g264.t1
Valid prediction for snap_scaffold_1-snap.421-T1
Valid prediction for snap_scaffold_1-snap.416-T1
Valid prediction for snap_scaffold_1-snap.426-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.g260.t1
Valid prediction for GlimmerHMM_glimmerT_322-T1
Valid prediction for GlimmerHMM_glimmerT_308-T1
Valid prediction for Augustus_model.g247.t1
Valid prediction for snap_scaffold_1-snap.400-T1
Valid prediction for snap_scaffold_1-snap.405-T1
Valid prediction for Augustus_model.g257.t1
Valid prediction for Augustus_model.g251.t1
Valid prediction for Augustus_model.g252.t1
Valid prediction for GlimmerHMM_glimmerT_325-T1
Valid prediction for Augustus_model.g266.t1
Valid prediction for snap_scaffold_1-snap.419-T1
Valid prediction for GlimmerHMM_glimmerT_332-T1
Valid prediction for Augustus_model.g261.t1
Valid prediction for GlimmerHMM_glimmerT_328-T1
Valid prediction for GlimmerHMM_glimmerT_311-T1
Valid prediction for GlimmerHMM_glimmerT_329-T1
Valid prediction for snap_scaffold_1-snap.401-T1
Valid prediction for snap_scaffold_1-snap.414-T1
Valid prediction for snap_scaffold_1-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_312-T1
Valid prediction for snap_scaffold_1-snap.404-T1
Valid prediction for snap_scaffold_1-snap.412-T1
Valid prediction for GlimmerHMM_glimmerT_307-T1
Valid prediction for snap_scaffold_1-snap.424-T1
Valid prediction for snap_scaffold_1-snap.418-T1
Valid prediction for snap_scaffold_1-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_323-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18812, rend_intergenic: 14177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33669, rend_intergenic: 31749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45555, rend_intergenic: 42137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69625, rend_intergenic: 63582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176450
-exon list size: 275


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.2    
2.5    
2.9    
3.2    
3.6    
4.0    
4.3    
4.7    
5.1    
5.4    
5.8    
6.1    
6.5    
6.9    
7.2    
7.6    
7.9    
8.3    
8.7    
9.0    
9.4    
9.7    
10.1    
10.5    
10.8    
11.2    
11.6    
11.9    
12.3    
12.6    
13.0    
13.4    
13.7    
14.1    
14.4    
14.8    
15.2    
15.5    
15.9    
16.2    
16.6    
17.0    
17.3    
17.7    
18.1    
18.4    
18.8    
19.1    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.7    
22.0    
22.4    
22.7    
23.1    
23.5    
23.8    
24.2    
24.5    
24.9    
25.3    
25.6    
26.0    
26.4    
26.7    
27.1    
27.4    
27.8    
28.2    
28.5    
28.9    
29.2    
29.6    
30.0    
30.3    
30.7    
31.0    
31.4    
31.8    
32.1    
32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.7    
35.0    
35.4    
35.7    
36.1    
36.5    
36.8    
37.2    
37.5    
37.9    
38.3    
38.6    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.2    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.6    
46.9    
47.3    
47.7    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.3    
52.7    
53.1    
53.4    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.8    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.4    
61.7    
62.1    
62.5    
62.8    
63.2    
63.5    
63.9    
64.3    
64.6    
65.0    
65.3    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.9    
68.2    
68.6    
69.0    
69.3    
69.7    
70.0    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.6    
72.9    
73.3    
73.6    
74.0    
74.4    
74.7    
75.1    
75.5    
75.8    
76.2    
76.5    
76.9    
77.3    
77.6    
78.0    
78.3    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.8    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.4    
87.7    
88.1    
88.4    
88.8    
89.2    
89.5    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.1    
92.4    
92.8    
93.1    
93.5    
93.9    
94.2    
94.6    
94.9    
95.3    
95.7    
96.0    
96.4    
96.8    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 18812, rend_intergenic: 14177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33669, rend_intergenic: 31749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45555, rend_intergenic: 42137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69625, rend_intergenic: 63582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 163875 - 176450
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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 163875 - 174334
-exon list size: 1


building trellis

33.3    
66.7    
-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