-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_4299350-4390921

-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.g19268.t1
Valid prediction for pasa_asmbl_7609.p1
Valid prediction for GlimmerHMM_glimmerT_29201-T1
Valid prediction for pasa_asmbl_7600.p1
Valid prediction for pasa_asmbl_7604.p1
Valid prediction for snap_scaffold_12-snap.882-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for pasa_asmbl_7603.p1
Valid prediction for GlimmerHMM_glimmerT_29204-T1
Valid prediction for snap_scaffold_12-snap.876-T1
Valid prediction for HiQ_model.g19271.t1
Valid prediction for snap_scaffold_12-snap.869-T1
Valid prediction for GlimmerHMM_glimmerT_29205-T1
Valid prediction for GlimmerHMM_glimmerT_29209-T1
Valid prediction for GlimmerHMM_glimmerT_29197-T1
Couldn't classify 39336, 39351
Couldn't classify 40211, 40317
Sorry, prediction pasa_asmbl_7602.p2 fails validation.
(TTC)	 GC	39336-39351	GT	AGG
(GGG)	 AG	39542-39698	GT	AGG
(GTG)	 AG	39791-39996	GT	AGG
(CTC)	 AG	40211-40317	AT	ACA
-recovered pasa_asmbl_7602.p2, internal, 39542, 39698
-recovered pasa_asmbl_7602.p2, internal, 39791, 39996
Valid prediction for snap_scaffold_12-snap.881-T1
Valid prediction for CodingQuarry_transcript_10175-T1
Valid prediction for pasa_asmbl_7597.p1
Valid prediction for GlimmerHMM_glimmerT_29206-T1
Valid prediction for GlimmerHMM_glimmerT_29212-T1
Valid prediction for Augustus_model.g19269.t1
Valid prediction for HiQ_model.g19275.t1
Valid prediction for snap_scaffold_12-snap.871-T1
Valid prediction for CodingQuarry_transcript_10181-T1
Valid prediction for snap_scaffold_12-snap.874-T1
Valid prediction for pasa_asmbl_7605.p1
Valid prediction for CodingQuarry_transcript_10179-T1
Valid prediction for snap_scaffold_12-snap.883-T1
Couldn't classify 6605, 6815
Sorry, prediction pasa_asmbl_7598.p1 fails validation.
(GTG)	 GT	6605-6815	GT	TGG
(GGC)	 AG	6941-7083	GT	AGG
(GTG)	 AG	7423-7626	GT	GGG
(AAC)	 AG	7805-7922	GT	AGG
(GTG)	 AG	8343-8445	GT	TGG
(TTA)	 AG	8877-9150	AG	AAA
-recovered pasa_asmbl_7598.p1, terminal, 8877, 9150
-recovered pasa_asmbl_7598.p1, internal, 6941, 7083
-recovered pasa_asmbl_7598.p1, internal, 7423, 7626
-recovered pasa_asmbl_7598.p1, internal, 7805, 7922
-recovered pasa_asmbl_7598.p1, internal, 8343, 8445
Valid prediction for snap_scaffold_12-snap.879-T1
Valid prediction for CodingQuarry_transcript_10177-T1
Valid prediction for Augustus_model.g19272.t1
Valid prediction for HiQ_model.g19270.t1
Valid prediction for snap_scaffold_12-snap.866-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.885-T1
Valid prediction for GlimmerHMM_glimmerT_29213-T1
Valid prediction for GlimmerHMM_glimmerT_29202-T1
Valid prediction for snap_scaffold_12-snap.878-T1
Valid prediction for Augustus_model.g19273.t1
Valid prediction for CodingQuarry_transcript_10178-T1
Valid prediction for HiQ_model.g19267.t1
Valid prediction for snap_scaffold_12-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_29203-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_12-snap.886-T1
Valid prediction for Augustus_model.g19279.t1
Valid prediction for snap_scaffold_12-snap.872-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.864-T1
Valid prediction for snap_scaffold_12-snap.865-T1
Valid prediction for snap_scaffold_12-snap.877-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g19266.t1
Valid prediction for GlimmerHMM_glimmerT_29198-T1
Valid prediction for pasa_asmbl_8390.p1
Valid prediction for CodingQuarry_transcript_10182-T1
Valid prediction for GlimmerHMM_glimmerT_29214-T1
Valid prediction for GlimmerHMM_glimmerT_29200-T1
Valid prediction for GlimmerHMM_glimmerT_29210-T1
Valid prediction for GlimmerHMM_glimmerT_29199-T1
Valid prediction for snap_scaffold_12-snap.875-T1
Valid prediction for CodingQuarry_transcript_10174-T1
Valid prediction for snap_scaffold_12-snap.884-T1
Valid prediction for Augustus_model.g19278.t1
Valid prediction for GlimmerHMM_glimmerT_29207-T1
Valid prediction for snap_scaffold_12-snap.868-T1
Valid prediction for snap_scaffold_12-snap.880-T1
Valid prediction for Augustus_model.g19277.t1
Valid prediction for HiQ_model.g19274.t1
Valid prediction for pasa_asmbl_8389.p1
Valid prediction for snap_scaffold_12-snap.867-T1
Valid prediction for CodingQuarry_transcript_10180-T1
Valid prediction for HiQ_model.g19265.t1
Valid prediction for GlimmerHMM_glimmerT_29211-T1
Valid prediction for snap_scaffold_12-snap.873-T1
Couldn't classify 14932, 14995
Sorry, prediction pasa_asmbl_8391.p1 fails validation.
(GCC)	 TG	14932-14995	GT	CGG
(GGT)	 AG	15164-15324	GT	AGG
(GCC)	 AG	15635-15724	GT	TGG
(CAC)	 AG	16004-16063	AT	AAA
-recovered pasa_asmbl_8391.p1, terminal, 16004, 16063
-recovered pasa_asmbl_8391.p1, internal, 15164, 15324
-recovered pasa_asmbl_8391.p1, internal, 15635, 15724
Valid prediction for Augustus_model.g19276.t1
Valid prediction for GlimmerHMM_glimmerT_29208-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 43436, rend_intergenic: 34162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51606, rend_intergenic: 49225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66527, rend_intergenic: 56020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81835, rend_intergenic: 81445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85823, rend_intergenic: 81968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88783, rend_intergenic: 85823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 91572
-exon list size: 268


building trellis

0.4    
0.7    
1.1    
1.5    
1.9    
2.2    
2.6    
3.0    
3.3    
3.7    
4.1    
4.4    
4.8    
5.2    
5.6    
5.9    
6.3    
6.7    
7.0    
7.4    
7.8    
8.1    
8.5    
8.9    
9.3    
9.6    
10.0    
10.4    
10.7    
11.1    
11.5    
11.9    
12.2    
12.6    
13.0    
13.3    
13.7    
14.1    
14.4    
14.8    
15.2    
15.6    
15.9    
16.3    
16.7    
17.0    
17.4    
17.8    
18.1    
18.5    
18.9    
19.3    
19.6    
20.0    
20.4    
20.7    
21.1    
21.5    
21.9    
22.2    
22.6    
23.0    
23.3    
23.7    
24.1    
24.4    
24.8    
25.2    
25.6    
25.9    
26.3    
26.7    
27.0    
27.4    
27.8    
28.1    
28.5    
28.9    
29.3    
29.6    
30.0    
30.4    
30.7    
31.1    
31.5    
31.9    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.4    
34.8    
35.2    
35.6    
35.9    
36.3    
36.7    
37.0    
37.4    
37.8    
38.1    
38.5    
38.9    
39.3    
39.6    
40.0    
40.4    
40.7    
41.1    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.1    
44.4    
44.8    
45.2    
45.6    
45.9    
46.3    
46.7    
47.0    
47.4    
47.8    
48.1    
48.5    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.9    
52.2    
52.6    
53.0    
53.3    
53.7    
54.1    
54.4    
54.8    
55.2    
55.6    
55.9    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.9    
59.3    
59.6    
60.0    
60.4    
60.7    
61.1    
61.5    
61.9    
62.2    
62.6    
63.0    
63.3    
63.7    
64.1    
64.4    
64.8    
65.2    
65.6    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.1    
68.5    
68.9    
69.3    
69.6    
70.0    
70.4    
70.7    
71.1    
71.5    
71.9    
72.2    
72.6    
73.0    
73.3    
73.7    
74.1    
74.4    
74.8    
75.2    
75.6    
75.9    
76.3    
76.7    
77.0    
77.4    
77.8    
78.1    
78.5    
78.9    
79.3    
79.6    
80.0    
80.4    
80.7    
81.1    
81.5    
81.9    
82.2    
82.6    
83.0    
83.3    
83.7    
84.1    
84.4    
84.8    
85.2    
85.6    
85.9    
86.3    
86.7    
87.0    
87.4    
87.8    
88.1    
88.5    
88.9    
89.3    
89.6    
90.0    
90.4    
90.7    
91.1    
91.5    
91.9    
92.2    
92.6    
93.0    
93.3    
93.7    
94.1    
94.4    
94.8    
95.2    
95.6    
95.9    
96.3    
96.7    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 43436, rend_intergenic: 34162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51606, rend_intergenic: 49225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66527, rend_intergenic: 56020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81835, rend_intergenic: 81445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85823, rend_intergenic: 81968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88783, rend_intergenic: 85823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support