-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_801434-912589

-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: +)Couldn't classify 52052, 52114
Sorry, prediction pasa_asmbl_21216.p1 fails validation.
(CCT)	 TC	52052-52114	GT	GGG
(ACG)	 AG	52402-52605	GT	GGG
(CTC)	 AG	53078-53197	AT	AGA
-recovered pasa_asmbl_21216.p1, terminal, 53078, 53197
-recovered pasa_asmbl_21216.p1, internal, 52402, 52605
Valid prediction for snap_scaffold_19-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_43530-T1
Valid prediction for GlimmerHMM_glimmerT_43540-T1
Valid prediction for snap_scaffold_19-snap.177-T1
Valid prediction for CodingQuarry_transcript_25581-T1
Valid prediction for GlimmerHMM_glimmerT_43539-T1
Valid prediction for GlimmerHMM_glimmerT_43543-T1
Valid prediction for snap_scaffold_19-snap.202-T1
Valid prediction for Augustus_model.g28927.t1
Valid prediction for snap_scaffold_19-snap.198-T1
Valid prediction for pasa_asmbl_21957.p1
Valid prediction for snap_scaffold_19-snap.179-T1
Valid prediction for GlimmerHMM_glimmerT_43531-T1
Valid prediction for CodingQuarry_transcript_25586-T1
Valid prediction for GlimmerHMM_glimmerT_43534-T1
Valid prediction for Augustus_model.g28935.t1
Valid prediction for CodingQuarry_transcript_25588-T1
Valid prediction for GlimmerHMM_glimmerT_43537-T1
Valid prediction for Augustus_model.g28928.t1
Valid prediction for Augustus_model.g28926.t1
Valid prediction for snap_scaffold_19-snap.184-T1
Valid prediction for snap_scaffold_19-snap.195-T1
Valid prediction for GlimmerHMM_glimmerT_43546-T1
Valid prediction for CodingQuarry_transcript_25589-T1
Valid prediction for Augustus_model.g28931.t1
Valid prediction for Augustus_model.g28933.t1
Valid prediction for snap_scaffold_19-snap.182-T1
Valid prediction for snap_scaffold_19-snap.204-T1
Valid prediction for GlimmerHMM_glimmerT_43532-T1
Valid prediction for snap_scaffold_19-snap.188-T1
Valid prediction for snap_scaffold_19-snap.205-T1
Valid prediction for GlimmerHMM_glimmerT_43545-T1
Couldn't classify 34612, 34708
Sorry, prediction pasa_asmbl_21215.p1 fails validation.
(ATG)	 TC	27116-27143	GT	AGG
(AGA)	 AG	27490-27686	GT	TGG
(GCC)	 AG	28055-28291	GT	AGG
(CTC)	 AG	29146-29195	GT	AGG
(GTA)	 AG	29565-29700	GT	CGG
(ATA)	 AG	30264-30434	GT	AGG
(GAG)	 AG	31118-31322	GT	CGG
(GTG)	 AG	32037-32200	GT	AGG
(GAC)	 AG	32289-32439	GT	TGG
(CCA)	 AG	32749-32933	GT	AGG
(GTG)	 AG	33945-34147	GT	AAG
(ACC)	 AG	34612-34708	GT	AGG
-recovered pasa_asmbl_21215.p1, initial, 27116, 27143
-recovered pasa_asmbl_21215.p1, internal, 27490, 27686
-recovered pasa_asmbl_21215.p1, internal, 28055, 28291
-recovered pasa_asmbl_21215.p1, internal, 29146, 29195
-recovered pasa_asmbl_21215.p1, internal, 29565, 29700
-recovered pasa_asmbl_21215.p1, internal, 30264, 30434
-recovered pasa_asmbl_21215.p1, internal, 31118, 31322
-recovered pasa_asmbl_21215.p1, internal, 32037, 32200
-recovered pasa_asmbl_21215.p1, internal, 32289, 32439
-recovered pasa_asmbl_21215.p1, internal, 32749, 32933
-recovered pasa_asmbl_21215.p1, internal, 33945, 34147
-recovered pasa_asmbl_21215.p1, internal, 34612, 34708
Valid prediction for snap_scaffold_19-snap.186-T1
Valid prediction for Augustus_model.g28934.t1
Valid prediction for GlimmerHMM_glimmerT_43544-T1
Valid prediction for Augustus_model.g28932.t1
Valid prediction for snap_scaffold_19-snap.190-T1
Valid prediction for CodingQuarry_transcript_25582-T1
Valid prediction for GlimmerHMM_glimmerT_43533-T1
Valid prediction for CodingQuarry_transcript_25587-T1
Valid prediction for pasa_asmbl_21220.p1
Valid prediction for GlimmerHMM_glimmerT_43541-T1
Valid prediction for snap_scaffold_19-snap.194-T1
Valid prediction for CodingQuarry_transcript_25583-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_19-snap.185-T1
Valid prediction for snap_scaffold_19-snap.178-T1
Valid prediction for HiQ_model.g28929.t1
Valid prediction for snap_scaffold_19-snap.196-T1
Valid prediction for snap_scaffold_19-snap.192-T1
Valid prediction for CodingQuarry_transcript_25585-T1
Valid prediction for snap_scaffold_19-snap.197-T1
Valid prediction for snap_scaffold_19-snap.201-T1
Valid prediction for snap_scaffold_19-snap.200-T1
Valid prediction for snap_scaffold_19-snap.193-T1
Valid prediction for snap_scaffold_19-snap.189-T1
Valid prediction for pasa_asmbl_22006.p1
Valid prediction for snap_scaffold_19-snap.181-T1
Valid prediction for snap_scaffold_19-snap.180-T1
Valid prediction for CodingQuarry_transcript_25584-T1
Valid prediction for snap_scaffold_19-snap.187-T1
Valid prediction for GlimmerHMM_glimmerT_43536-T1
Valid prediction for snap_scaffold_19-snap.203-T1
Valid prediction for GlimmerHMM_glimmerT_43538-T1
Valid prediction for GlimmerHMM_glimmerT_43535-T1
Valid prediction for snap_scaffold_19-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_43542-T1
Valid prediction for snap_scaffold_19-snap.183-T1
Valid prediction for Augustus_model.g28930.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9841, rend_intergenic: 5661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19440, rend_intergenic: 13468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34777, rend_intergenic: 29520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38419, rend_intergenic: 36061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53197, rend_intergenic: 47845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66768, rend_intergenic: 61915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77264, rend_intergenic: 68284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86966, rend_intergenic: 85383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101440, rend_intergenic: 90781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103563, rend_intergenic: 102370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108786, rend_intergenic: 104438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 111156
-exon list size: 280


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.1    
2.5    
2.8    
3.2    
3.5    
3.9    
4.3    
4.6    
5.0    
5.3    
5.7    
6.0    
6.4    
6.7    
7.1    
7.4    
7.8    
8.2    
8.5    
8.9    
9.2    
9.6    
9.9    
10.3    
10.6    
11.0    
11.3    
11.7    
12.1    
12.4    
12.8    
13.1    
13.5    
13.8    
14.2    
14.5    
14.9    
15.2    
15.6    
16.0    
16.3    
16.7    
17.0    
17.4    
17.7    
18.1    
18.4    
18.8    
19.1    
19.5    
19.9    
20.2    
20.6    
20.9    
21.3    
21.6    
22.0    
22.3    
22.7    
23.0    
23.4    
23.8    
24.1    
24.5    
24.8    
25.2    
25.5    
25.9    
26.2    
26.6    
27.0    
27.3    
27.7    
28.0    
28.4    
28.7    
29.1    
29.4    
29.8    
30.1    
30.5    
30.9    
31.2    
31.6    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.0    
34.4    
34.8    
35.1    
35.5    
35.8    
36.2    
36.5    
36.9    
37.2    
37.6    
37.9    
38.3    
38.7    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.1    
41.5    
41.8    
42.2    
42.6    
42.9    
43.3    
43.6    
44.0    
44.3    
44.7    
45.0    
45.4    
45.7    
46.1    
46.5    
46.8    
47.2    
47.5    
47.9    
48.2    
48.6    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.4    
51.8    
52.1    
52.5    
52.8    
53.2    
53.5    
53.9    
54.3    
54.6    
55.0    
55.3    
55.7    
56.0    
56.4    
56.7    
57.1    
57.4    
57.8    
58.2    
58.5    
58.9    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.3    
61.7    
62.1    
62.4    
62.8    
63.1    
63.5    
63.8    
64.2    
64.5    
64.9    
65.2    
65.6    
66.0    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.4    
68.8    
69.1    
69.5    
69.9    
70.2    
70.6    
70.9    
71.3    
71.6    
72.0    
72.3    
72.7    
73.0    
73.4    
73.8    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.2    
76.6    
77.0    
77.3    
77.7    
78.0    
78.4    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.6    
83.0    
83.3    
83.7    
84.0    
84.4    
84.8    
85.1    
85.5    
85.8    
86.2    
86.5    
86.9    
87.2    
87.6    
87.9    
88.3    
88.7    
89.0    
89.4    
89.7    
90.1    
90.4    
90.8    
91.1    
91.5    
91.8    
92.2    
92.6    
92.9    
93.3    
93.6    
94.0    
94.3    
94.7    
95.0    
95.4    
95.7    
96.1    
96.5    
96.8    
97.2    
97.5    
97.9    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 9841, rend_intergenic: 5661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19440, rend_intergenic: 13468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34777, rend_intergenic: 29520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38419, rend_intergenic: 36061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53197, rend_intergenic: 47845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66768, rend_intergenic: 61915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77264, rend_intergenic: 68284  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86966, rend_intergenic: 85383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101440, rend_intergenic: 90781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103563, rend_intergenic: 102370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108786, rend_intergenic: 104438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support