-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_12556343-12706870

-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.g15390.t1
Valid prediction for snap_scaffold_9-snap.2497-T1
Valid prediction for CodingQuarry_transcript_62380-T1
Valid prediction for snap_scaffold_9-snap.2480-T1
Valid prediction for snap_scaffold_9-snap.2492-T1
Valid prediction for snap_scaffold_9-snap.2495-T1
Valid prediction for Augustus_model.g15385.t1
Valid prediction for Augustus_model.g15384.t1
Valid prediction for CodingQuarry_transcript_62379-T1
Valid prediction for GlimmerHMM_glimmerT_23076-T1
Valid prediction for snap_scaffold_9-snap.2502-T1
Valid prediction for GlimmerHMM_glimmerT_23080-T1
Valid prediction for GlimmerHMM_glimmerT_23082-T1
Valid prediction for pasa_asmbl_54459.p1
Valid prediction for snap_scaffold_9-snap.2500-T1
Valid prediction for HiQ_model.g15391.t1
Valid prediction for Augustus_model.g15383.t1
Valid prediction for pasa_asmbl_54446.p1
Valid prediction for GlimmerHMM_glimmerT_23073-T1
Valid prediction for GlimmerHMM_glimmerT_23081-T1
Valid prediction for HiQ_model.g15395.t1
Valid prediction for snap_scaffold_9-snap.2478-T1
Valid prediction for Augustus_model.g15393.t1
Valid prediction for GlimmerHMM_glimmerT_23079-T1
Valid prediction for snap_scaffold_9-snap.2488-T1
Valid prediction for Augustus_model.g15392.t1
Couldn't classify 90832, 91023
Sorry, prediction pasa_asmbl_54458.p2 fails validation.
(CAG)	 CT	90832-91023	GT	AGG
(GTT)	 AG	91170-91436	AG	AGA
-recovered pasa_asmbl_54458.p2, terminal, 91170, 91436
Valid prediction for CodingQuarry_transcript_62381-T1
Couldn't classify 9353, 9398
Sorry, prediction pasa_asmbl_54441.p1 fails validation.
(CTT)	 AT	9353-9398	GT	AGG
(TGT)	 AG	9504-9814	TA	GAT
-recovered pasa_asmbl_54441.p1, terminal, 9504, 9814
Valid prediction for snap_scaffold_9-snap.2482-T1
Valid prediction for GlimmerHMM_glimmerT_23067-T1
Valid prediction for snap_scaffold_9-snap.2484-T1
Valid prediction for CodingQuarry_transcript_62377-T1
Valid prediction for GlimmerHMM_glimmerT_23066-T1
Valid prediction for snap_scaffold_9-snap.2477-T1
Valid prediction for CodingQuarry_transcript_62378-T1
Valid prediction for snap_scaffold_9-snap.2489-T1
Valid prediction for GlimmerHMM_glimmerT_23077-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_9-snap.2501-T1
Valid prediction for GlimmerHMM_glimmerT_23074-T1
Valid prediction for GlimmerHMM_glimmerT_23072-T1
Valid prediction for snap_scaffold_9-snap.2499-T1
Valid prediction for snap_scaffold_9-snap.2491-T1
Valid prediction for snap_scaffold_9-snap.2487-T1
Couldn't classify 84884, 84979
Sorry, prediction pasa_asmbl_55399.p1 fails validation.
(GAG)	 AG	84884-84979	GT	AGG
(GTG)	 AG	85110-85328	GT	AGG
(GGC)	 AG	86279-86396	GT	GGG
(AGA)	 AG	86567-86681	GT	AAG
(GAG)	 AG	86860-86923	GT	TGG
(GAT)	 AG	87148-87177	CT	AAC
-recovered pasa_asmbl_55399.p1, terminal, 87148, 87177
-recovered pasa_asmbl_55399.p1, internal, 84884, 84979
-recovered pasa_asmbl_55399.p1, internal, 85110, 85328
-recovered pasa_asmbl_55399.p1, internal, 86279, 86396
-recovered pasa_asmbl_55399.p1, internal, 86567, 86681
-recovered pasa_asmbl_55399.p1, internal, 86860, 86923
Valid prediction for Augustus_model.g15394.t1
Valid prediction for GlimmerHMM_glimmerT_23075-T1
Valid prediction for Augustus_model.g15389.t1
Valid prediction for snap_scaffold_9-snap.2490-T1
Valid prediction for snap_scaffold_9-snap.2481-T1
Valid prediction for pasa_asmbl_55402.p1
Valid prediction for snap_scaffold_9-snap.2498-T1
Valid prediction for snap_scaffold_9-snap.2486-T1
Couldn't classify 91096, 91182
Couldn't classify 91882, 91998
Sorry, prediction pasa_asmbl_55397.p1 fails validation.
(CAT)	 CG	91096-91182	GT	CGG
(TTG)	 AG	91280-91387	GT	AGG
(AAT)	 AG	91631-91684	GT	TGG
(GAT)	 AG	91882-91998	TC	CCT
-recovered pasa_asmbl_55397.p1, internal, 91280, 91387
-recovered pasa_asmbl_55397.p1, internal, 91631, 91684
Couldn't classify 101072, 101929
Sorry, prediction pasa_asmbl_55395.p1 fails validation.
(ATG)	 CC	101072-101929	CT	TGC
Valid prediction for GlimmerHMM_glimmerT_23065-T1
Valid prediction for HiQ_model.g15396.t1
Valid prediction for Augustus_model.g15386.t1
Valid prediction for snap_scaffold_9-snap.2483-T1
Valid prediction for GlimmerHMM_glimmerT_23078-T1
Valid prediction for CodingQuarry_transcript_62382-T1
Valid prediction for snap_scaffold_9-snap.2485-T1
Valid prediction for snap_scaffold_9-snap.2476-T1
Valid prediction for GlimmerHMM_glimmerT_23070-T1
Valid prediction for GlimmerHMM_glimmerT_23071-T1
Valid prediction for Augustus_model.g15388.t1
Valid prediction for GlimmerHMM_glimmerT_23084-T1
Valid prediction for snap_scaffold_9-snap.2479-T1
Valid prediction for GlimmerHMM_glimmerT_23083-T1
Valid prediction for snap_scaffold_9-snap.2493-T1
Valid prediction for GlimmerHMM_glimmerT_23086-T1
Valid prediction for snap_scaffold_9-snap.2496-T1
Valid prediction for GlimmerHMM_glimmerT_23069-T1
Valid prediction for GlimmerHMM_glimmerT_23068-T1
Valid prediction for Augustus_model.g15387.t1
Valid prediction for GlimmerHMM_glimmerT_23085-T1
Valid prediction for snap_scaffold_9-snap.2494-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22270, rend_intergenic: 18996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39254, rend_intergenic: 33353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76814, rend_intergenic: 66396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80298, rend_intergenic: 77637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89679, rend_intergenic: 85394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98293, rend_intergenic: 94997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114667, rend_intergenic: 100130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120230, rend_intergenic: 117726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143129, rend_intergenic: 137201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146117, rend_intergenic: 143335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150528
-exon list size: 242


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.5    
2.9    
3.3    
3.7    
4.1    
4.5    
4.9    
5.3    
5.7    
6.1    
6.6    
7.0    
7.4    
7.8    
8.2    
8.6    
9.0    
9.4    
9.8    
10.2    
10.7    
11.1    
11.5    
11.9    
12.3    
12.7    
13.1    
13.5    
13.9    
14.3    
14.8    
15.2    
15.6    
16.0    
16.4    
16.8    
17.2    
17.6    
18.0    
18.4    
18.9    
19.3    
19.7    
20.1    
20.5    
20.9    
21.3    
21.7    
22.1    
22.5    
23.0    
23.4    
23.8    
24.2    
24.6    
25.0    
25.4    
25.8    
26.2    
26.6    
27.0    
27.5    
27.9    
28.3    
28.7    
29.1    
29.5    
29.9    
30.3    
30.7    
31.1    
31.6    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.8    
35.2    
35.7    
36.1    
36.5    
36.9    
37.3    
37.7    
38.1    
38.5    
38.9    
39.3    
39.8    
40.2    
40.6    
41.0    
41.4    
41.8    
42.2    
42.6    
43.0    
43.4    
43.9    
44.3    
44.7    
45.1    
45.5    
45.9    
46.3    
46.7    
47.1    
47.5    
48.0    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
52.0    
52.5    
52.9    
53.3    
53.7    
54.1    
54.5    
54.9    
55.3    
55.7    
56.1    
56.6    
57.0    
57.4    
57.8    
58.2    
58.6    
59.0    
59.4    
59.8    
60.2    
60.7    
61.1    
61.5    
61.9    
62.3    
62.7    
63.1    
63.5    
63.9    
64.3    
64.8    
65.2    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.4    
68.9    
69.3    
69.7    
70.1    
70.5    
70.9    
71.3    
71.7    
72.1    
72.5    
73.0    
73.4    
73.8    
74.2    
74.6    
75.0    
75.4    
75.8    
76.2    
76.6    
77.0    
77.5    
77.9    
78.3    
78.7    
79.1    
79.5    
79.9    
80.3    
80.7    
81.1    
81.6    
82.0    
82.4    
82.8    
83.2    
83.6    
84.0    
84.4    
84.8    
85.2    
85.7    
86.1    
86.5    
86.9    
87.3    
87.7    
88.1    
88.5    
88.9    
89.3    
89.8    
90.2    
90.6    
91.0    
91.4    
91.8    
92.2    
92.6    
93.0    
93.4    
93.9    
94.3    
94.7    
95.1    
95.5    
95.9    
96.3    
96.7    
97.1    
97.5    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 22270, rend_intergenic: 18996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39254, rend_intergenic: 33353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76814, rend_intergenic: 66396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80298, rend_intergenic: 77637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89679, rend_intergenic: 85394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98293, rend_intergenic: 94997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114667, rend_intergenic: 100130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120230, rend_intergenic: 117726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143129, rend_intergenic: 137201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146117, rend_intergenic: 143335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support