-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_1458228-1730681

-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 112458, 113033
Sorry, prediction pasa_asmbl_45132.p1 fails validation.
(AAG)	 AT	112458-113033	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_11486-T1
Valid prediction for snap_scaffold_5-snap.331-T1
Valid prediction for GlimmerHMM_glimmerT_11477-T1
Valid prediction for snap_scaffold_5-snap.312-T1
Valid prediction for GlimmerHMM_glimmerT_11491-T1
Valid prediction for GlimmerHMM_glimmerT_11494-T1
Valid prediction for snap_scaffold_5-snap.315-T1
Valid prediction for snap_scaffold_5-snap.304-T1
Valid prediction for snap_scaffold_5-snap.324-T1
Valid prediction for Augustus_model.g7509.t1
Valid prediction for Augustus_model.g7521.t1
Valid prediction for GlimmerHMM_glimmerT_11483-T1
Valid prediction for snap_scaffold_5-snap.317-T1
Valid prediction for HiQ_model.g7519.t1
Valid prediction for snap_scaffold_5-snap.332-T1
Valid prediction for GlimmerHMM_glimmerT_11490-T1
Couldn't classify 171402, 171488
Sorry, prediction pasa_asmbl_45136.p1 fails validation.
(ATC)	 AG	171402-171488	GT	TGG
(GCT)	 AG	172575-172644	GT	AGG
(ACC)	 AG	173317-173409	GT	AGG
(GTG)	 AG	173704-173888	TG	AAT
-recovered pasa_asmbl_45136.p1, terminal, 173704, 173888
-recovered pasa_asmbl_45136.p1, internal, 171402, 171488
-recovered pasa_asmbl_45136.p1, internal, 172575, 172644
-recovered pasa_asmbl_45136.p1, internal, 173317, 173409
Valid prediction for Augustus_model.g7508.t1
Valid prediction for snap_scaffold_5-snap.314-T1
Valid prediction for snap_scaffold_5-snap.298-T1
Valid prediction for Augustus_model.g7516.t1
Valid prediction for GlimmerHMM_glimmerT_11478-T1
Valid prediction for GlimmerHMM_glimmerT_11479-T1
Valid prediction for GlimmerHMM_glimmerT_11495-T1
Valid prediction for snap_scaffold_5-snap.316-T1
Valid prediction for Augustus_model.g7518.t1
Valid prediction for snap_scaffold_5-snap.333-T1
Valid prediction for Augustus_model.g7506.t1
Valid prediction for GlimmerHMM_glimmerT_11492-T1
Valid prediction for snap_scaffold_5-snap.330-T1
Valid prediction for snap_scaffold_5-snap.319-T1
Valid prediction for Augustus_model.g7514.t1
Couldn't classify 116719, 116785
Couldn't classify 116897, 117213
Sorry, prediction pasa_asmbl_45134.p1 fails validation.
(GGA)	 TA	116719-116785	GT	CGG
(GAA)	 AG	116897-117213	AA	AGA
Valid prediction for GlimmerHMM_glimmerT_11487-T1
Couldn't classify 25767, 26040
Couldn't classify 26321, 26454
Sorry, prediction pasa_asmbl_46396.p1 fails validation.
(TCC)	 GA	25767-26040	GT	TGG
(ATG)	 AG	26321-26454	TG	ATT
Valid prediction for CodingQuarry_transcript_51987-T1
Valid prediction for snap_scaffold_5-snap.326-T1
Valid prediction for snap_scaffold_5-snap.318-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.335-T1
Valid prediction for snap_scaffold_5-snap.305-T1
Valid prediction for GlimmerHMM_glimmerT_11497-T1
Valid prediction for snap_scaffold_5-snap.339-T1
Valid prediction for snap_scaffold_5-snap.328-T1
Valid prediction for snap_scaffold_5-snap.306-T1
Couldn't classify 241006, 241151
Sorry, prediction pasa_asmbl_45142.p1 fails validation.
(ATG)	 TC	236089-236379	GT	AGG
(CAC)	 AG	238449-238556	GT	CTG
(GCT)	 AG	239047-239263	GT	TGG
(GCC)	 AG	239583-239729	GT	AGG
(ATG)	 AG	241006-241151	TA	GGT
-recovered pasa_asmbl_45142.p1, initial, 236089, 236379
-recovered pasa_asmbl_45142.p1, internal, 238449, 238556
-recovered pasa_asmbl_45142.p1, internal, 239047, 239263
-recovered pasa_asmbl_45142.p1, internal, 239583, 239729
Valid prediction for Augustus_model.g7498.t1
Valid prediction for Augustus_model.g7507.t1
Couldn't classify 247004, 247118
Sorry, prediction pasa_asmbl_45144.p1 fails validation.
(CCC)	 AT	247004-247118	GT	TGG
(GGG)	 AG	248114-248397	GT	AGG
(GTG)	 AG	248699-248872	GT	AAG
-recovered pasa_asmbl_45144.p1, terminal, 248699, 248872
-recovered pasa_asmbl_45144.p1, internal, 248114, 248397
-recovered pasa_asmbl_45144.p1, internal, 248699, 248872
Valid prediction for snap_scaffold_5-snap.302-T1
Valid prediction for Augustus_model.g7517.t1
Valid prediction for GlimmerHMM_glimmerT_11498-T1
Valid prediction for GlimmerHMM_glimmerT_11482-T1
Valid prediction for Augustus_model.g7515.t1
Valid prediction for snap_scaffold_5-snap.342-T1
Valid prediction for snap_scaffold_5-snap.308-T1
Valid prediction for snap_scaffold_5-snap.322-T1
Valid prediction for snap_scaffold_5-snap.329-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_5-snap.309-T1
Valid prediction for snap_scaffold_5-snap.334-T1
Valid prediction for Augustus_model.g7522.t1
Valid prediction for snap_scaffold_5-snap.340-T1
Valid prediction for snap_scaffold_5-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_11496-T1
Couldn't classify 209664, 209730
Couldn't classify 209841, 210070
Sorry, prediction pasa_asmbl_43857.p1 fails validation.
(GGA)	 TA	209664-209730	GT	CGG
(GAA)	 AG	209841-210070	AA	GCA
Valid prediction for snap_scaffold_5-snap.311-T1
Valid prediction for snap_scaffold_5-snap.301-T1
Valid prediction for snap_scaffold_5-snap.307-T1
Couldn't classify 102273, 102621
Couldn't classify 102760, 103013
Sorry, prediction pasa_asmbl_43864.p1 fails validation.
(GAA)	 TA	102273-102621	GT	AGG
(CTG)	 AG	102760-103013	GA	GAG
Valid prediction for Augustus_model.g7500.t1
Valid prediction for GlimmerHMM_glimmerT_11476-T1
Valid prediction for GlimmerHMM_glimmerT_11481-T1
Valid prediction for Augustus_model.g7512.t1
Valid prediction for snap_scaffold_5-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_11484-T1
Valid prediction for Augustus_model.g7511.t1
Couldn't classify 181936, 182095
Sorry, prediction pasa_asmbl_43861.p1 fails validation.
(CTT)	 AA	181936-182095	GT	AGG
(GTC)	 AG	182159-182319	TG	GAT
-recovered pasa_asmbl_43861.p1, terminal, 182159, 182319
Valid prediction for snap_scaffold_5-snap.336-T1
Valid prediction for GlimmerHMM_glimmerT_11493-T1
Valid prediction for Augustus_model.g7502.t1
Valid prediction for GlimmerHMM_glimmerT_11485-T1
Valid prediction for snap_scaffold_5-snap.341-T1
Valid prediction for Augustus_model.g7503.t1
Valid prediction for GlimmerHMM_glimmerT_11480-T1
Valid prediction for snap_scaffold_5-snap.327-T1
Valid prediction for snap_scaffold_5-snap.303-T1
Valid prediction for snap_scaffold_5-snap.300-T1
Valid prediction for snap_scaffold_5-snap.343-T1
Valid prediction for GlimmerHMM_glimmerT_11489-T1
Valid prediction for Augustus_model.g7497.t1
Valid prediction for snap_scaffold_5-snap.299-T1
Valid prediction for snap_scaffold_5-snap.313-T1
Valid prediction for GlimmerHMM_glimmerT_11488-T1
Valid prediction for snap_scaffold_5-snap.338-T1
Valid prediction for Augustus_model.g7520.t1
Valid prediction for snap_scaffold_5-snap.337-T1
Valid prediction for snap_scaffold_5-snap.320-T1
Valid prediction for pasa_asmbl_43852.p1
Valid prediction for snap_scaffold_5-snap.323-T1
Valid prediction for pasa_asmbl_43851.p2
Valid prediction for snap_scaffold_5-snap.321-T1
Valid prediction for Augustus_model.g7504.t1
Valid prediction for Augustus_model.g7513.t1
Valid prediction for Augustus_model.g7505.t1
Valid prediction for Augustus_model.g7499.t1
Valid prediction for Augustus_model.g7510.t1
Valid prediction for Augustus_model.g7501.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9468, rend_intergenic: 7478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18977, rend_intergenic: 17812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19129, rend_intergenic: 18979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23987, rend_intergenic: 19228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147134, rend_intergenic: 144894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147426, rend_intergenic: 147327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151940, rend_intergenic: 147520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174799, rend_intergenic: 171391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237501, rend_intergenic: 236215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241716, rend_intergenic: 237813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248872, rend_intergenic: 242436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261190, rend_intergenic: 256752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266070, rend_intergenic: 263312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 272454
-exon list size: 304


building trellis

0.3    
0.7    
1.0    
1.3    
1.6    
2.0    
2.3    
2.6    
2.9    
3.3    
3.6    
3.9    
4.2    
4.6    
4.9    
5.2    
5.6    
5.9    
6.2    
6.5    
6.9    
7.2    
7.5    
7.8    
8.2    
8.5    
8.8    
9.2    
9.5    
9.8    
10.1    
10.5    
10.8    
11.1    
11.4    
11.8    
12.1    
12.4    
12.7    
13.1    
13.4    
13.7    
14.1    
14.4    
14.7    
15.0    
15.4    
15.7    
16.0    
16.3    
16.7    
17.0    
17.3    
17.6    
18.0    
18.3    
18.6    
19.0    
19.3    
19.6    
19.9    
20.3    
20.6    
20.9    
21.2    
21.6    
21.9    
22.2    
22.5    
22.9    
23.2    
23.5    
23.9    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.1    
26.5    
26.8    
27.1    
27.5    
27.8    
28.1    
28.4    
28.8    
29.1    
29.4    
29.7    
30.1    
30.4    
30.7    
31.0    
31.4    
31.7    
32.0    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
35.0    
35.3    
35.6    
35.9    
36.3    
36.6    
36.9    
37.3    
37.6    
37.9    
38.2    
38.6    
38.9    
39.2    
39.5    
39.9    
40.2    
40.5    
40.8    
41.2    
41.5    
41.8    
42.2    
42.5    
42.8    
43.1    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.8    
46.1    
46.4    
46.7    
47.1    
47.4    
47.7    
48.0    
48.4    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.6    
52.0    
52.3    
52.6    
52.9    
53.3    
53.6    
53.9    
54.2    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.9    
57.2    
57.5    
57.8    
58.2    
58.5    
58.8    
59.2    
59.5    
59.8    
60.1    
60.5    
60.8    
61.1    
61.4    
61.8    
62.1    
62.4    
62.7    
63.1    
63.4    
63.7    
64.1    
64.4    
64.7    
65.0    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
68.0    
68.3    
68.6    
69.0    
69.3    
69.6    
69.9    
70.3    
70.6    
70.9    
71.2    
71.6    
71.9    
72.2    
72.5    
72.9    
73.2    
73.5    
73.9    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.1    
76.5    
76.8    
77.1    
77.5    
77.8    
78.1    
78.4    
78.8    
79.1    
79.4    
79.7    
80.1    
80.4    
80.7    
81.0    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.7    
84.0    
84.3    
84.6    
85.0    
85.3    
85.6    
85.9    
86.3    
86.6    
86.9    
87.3    
87.6    
87.9    
88.2    
88.6    
88.9    
89.2    
89.5    
89.9    
90.2    
90.5    
90.8    
91.2    
91.5    
91.8    
92.2    
92.5    
92.8    
93.1    
93.5    
93.8    
94.1    
94.4    
94.8    
95.1    
95.4    
95.8    
96.1    
96.4    
96.7    
97.1    
97.4    
97.7    
98.0    
98.4    
98.7    
99.0    
99.3    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 9468, rend_intergenic: 7478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18977, rend_intergenic: 17812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19129, rend_intergenic: 18979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23987, rend_intergenic: 19228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147134, rend_intergenic: 144894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147426, rend_intergenic: 147327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151940, rend_intergenic: 147520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174799, rend_intergenic: 171391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237501, rend_intergenic: 236215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 241716, rend_intergenic: 237813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 248872, rend_intergenic: 242436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261190, rend_intergenic: 256752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266070, rend_intergenic: 263312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support