-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_2976238-3146206

-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 CodingQuarry_transcript_10145-T1
Valid prediction for GlimmerHMM_glimmerT_29040-T1
Valid prediction for snap_scaffold_12-snap.614-T1
Valid prediction for GlimmerHMM_glimmerT_29022-T1
Valid prediction for snap_scaffold_12-snap.604-T1
Couldn't classify 119961, 120056
Couldn't classify 121109, 121281
Sorry, prediction pasa_asmbl_7540.p2 fails validation.
(CAG)	 CT	119961-120056	GT	AGG
(GTG)	 AG	120344-120437	GT	CAG
(TTC)	 AG	120655-120885	GT	AGG
(ACA)	 AG	121109-121281	GA	GTG
-recovered pasa_asmbl_7540.p2, internal, 120344, 120437
-recovered pasa_asmbl_7540.p2, internal, 120655, 120885
Valid prediction for GlimmerHMM_glimmerT_29032-T1
Valid prediction for CodingQuarry_transcript_10146-T1
Valid prediction for GlimmerHMM_glimmerT_29026-T1
Valid prediction for Augustus_model.g19152.t1
Valid prediction for CodingQuarry_transcript_10144-T1
Valid prediction for snap_scaffold_12-snap.627-T1
Valid prediction for GlimmerHMM_glimmerT_29030-T1
Valid prediction for GlimmerHMM_glimmerT_29039-T1
Valid prediction for snap_scaffold_12-snap.599-T1
Valid prediction for Augustus_model.g19157.t1
Valid prediction for pasa_asmbl_7534.p2
Valid prediction for snap_scaffold_12-snap.615-T1
Valid prediction for snap_scaffold_12-snap.596-T1
Valid prediction for GlimmerHMM_glimmerT_29033-T1
Valid prediction for GlimmerHMM_glimmerT_29042-T1
Valid prediction for Augustus_model.g19159.t1
Valid prediction for Augustus_model.g19154.t1
Valid prediction for snap_scaffold_12-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_29043-T1
Valid prediction for GlimmerHMM_glimmerT_29035-T1
Valid prediction for snap_scaffold_12-snap.619-T1
Valid prediction for GlimmerHMM_glimmerT_29020-T1
Valid prediction for snap_scaffold_12-snap.601-T1
Valid prediction for snap_scaffold_12-snap.593-T1
Valid prediction for snap_scaffold_12-snap.623-T1
Valid prediction for Augustus_model.g19150.t1
Valid prediction for GlimmerHMM_glimmerT_29044-T1
Valid prediction for snap_scaffold_12-snap.617-T1
Valid prediction for GlimmerHMM_glimmerT_29046-T1
Couldn't classify 122894, 123010
Couldn't classify 127032, 127087
Sorry, prediction pasa_asmbl_7541.p1 fails validation.
(GGG)	 CA	122894-123010	GT	AGG
(ATG)	 AG	123145-123218	GT	TGG
(TCG)	 AG	123590-123668	GT	AGG
(TTG)	 AG	123904-123983	GT	AAG
(AGA)	 AG	124109-124246	GT	AAG
(GTA)	 AG	124503-124588	GT	AGG
(TGA)	 AG	124892-125040	GC	AGG
(GAC)	 AG	125278-125401	GT	TGG
(GAG)	 AG	125809-125906	GT	AGG
(GCG)	 AG	126440-126641	GT	AGG
(ATA)	 AG	127032-127087	GC	ACG
-recovered pasa_asmbl_7541.p1, initial, 123145, 123218
-recovered pasa_asmbl_7541.p1, internal, 123145, 123218
-recovered pasa_asmbl_7541.p1, internal, 123590, 123668
-recovered pasa_asmbl_7541.p1, internal, 123904, 123983
-recovered pasa_asmbl_7541.p1, internal, 124109, 124246
-recovered pasa_asmbl_7541.p1, internal, 124503, 124588
-recovered pasa_asmbl_7541.p1, internal, 124892, 125040
-recovered pasa_asmbl_7541.p1, internal, 125278, 125401
-recovered pasa_asmbl_7541.p1, internal, 125809, 125906
-recovered pasa_asmbl_7541.p1, internal, 126440, 126641
-recovered pasa_asmbl_7541.p1, internal, 127032, 127087
Valid prediction for GlimmerHMM_glimmerT_29023-T1
Valid prediction for GlimmerHMM_glimmerT_29038-T1
Valid prediction for GlimmerHMM_glimmerT_29034-T1
Valid prediction for snap_scaffold_12-snap.609-T1
Valid prediction for snap_scaffold_12-snap.621-T1
Valid prediction for snap_scaffold_12-snap.594-T1
Valid prediction for CodingQuarry_transcript_10148-T1
Valid prediction for snap_scaffold_12-snap.603-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_29036-T1
Valid prediction for Augustus_model.g19162.t1
Valid prediction for CodingQuarry_transcript_10149-T1
Valid prediction for snap_scaffold_12-snap.602-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 GlimmerHMM_glimmerT_29037-T1
Valid prediction for snap_scaffold_12-snap.610-T1
Valid prediction for snap_scaffold_12-snap.626-T1
Valid prediction for GlimmerHMM_glimmerT_29025-T1
Couldn't classify 156944, 157363
Sorry, prediction pasa_asmbl_8344.p1 fails validation.
(ATG)	 AC	156944-157363	AA	CCA
Valid prediction for snap_scaffold_12-snap.608-T1
Valid prediction for Augustus_model.g19155.t1
Valid prediction for snap_scaffold_12-snap.612-T1
Valid prediction for snap_scaffold_12-snap.597-T1
Valid prediction for Augustus_model.g19156.t1
Valid prediction for snap_scaffold_12-snap.622-T1
Valid prediction for GlimmerHMM_glimmerT_29031-T1
Valid prediction for snap_scaffold_12-snap.605-T1
Couldn't classify 111509, 111730
Couldn't classify 112343, 112426
Sorry, prediction pasa_asmbl_9174.p1 fails validation.
(TTC)	 GG	111509-111730	GT	AGG
(ACG)	 AG	112343-112426	TT	GCT
Valid prediction for GlimmerHMM_glimmerT_29024-T1
Valid prediction for snap_scaffold_12-snap.606-T1
Valid prediction for snap_scaffold_12-snap.598-T1
Valid prediction for snap_scaffold_12-snap.616-T1
Valid prediction for snap_scaffold_12-snap.613-T1
Valid prediction for GlimmerHMM_glimmerT_29021-T1
Valid prediction for GlimmerHMM_glimmerT_29028-T1
Valid prediction for snap_scaffold_12-snap.620-T1
Valid prediction for Augustus_model.g19158.t1
Valid prediction for snap_scaffold_12-snap.595-T1
Valid prediction for GlimmerHMM_glimmerT_29041-T1
Valid prediction for snap_scaffold_12-snap.618-T1
Valid prediction for snap_scaffold_12-snap.607-T1
Valid prediction for snap_scaffold_12-snap.611-T1
Valid prediction for GlimmerHMM_glimmerT_29029-T1
Valid prediction for GlimmerHMM_glimmerT_29045-T1
Valid prediction for snap_scaffold_12-snap.600-T1
Valid prediction for snap_scaffold_12-snap.625-T1
Valid prediction for Augustus_model.g19161.t1
Valid prediction for GlimmerHMM_glimmerT_29027-T1
Valid prediction for Augustus_model.g19160.t1
Couldn't classify 124102, 124164
Sorry, prediction pasa_asmbl_8348.p1 fails validation.
(GTC)	 AG	124102-124164	GT	AGG
(TGC)	 AG	124434-124540	GT	AGG
(TAT)	 AG	124849-124990	GT	AGG
(GTG)	 AG	125181-125315	GT	TGG
(GAC)	 AG	126813-126916	GT	AGG
(CAT)	 AG	127153-127245	GT	AGG
(GTT)	 AG	127549-127792	GT	AGG
(GTG)	 AG	128164-128322	GA	GAG
-recovered pasa_asmbl_8348.p1, terminal, 128164, 128322
-recovered pasa_asmbl_8348.p1, internal, 124102, 124164
-recovered pasa_asmbl_8348.p1, internal, 124434, 124540
-recovered pasa_asmbl_8348.p1, internal, 124849, 124990
-recovered pasa_asmbl_8348.p1, internal, 125181, 125315
-recovered pasa_asmbl_8348.p1, internal, 126813, 126916
-recovered pasa_asmbl_8348.p1, internal, 127153, 127245
-recovered pasa_asmbl_8348.p1, internal, 127549, 127792
Couldn't classify 157484, 157892
Couldn't classify 158640, 158695
Sorry, prediction pasa_asmbl_8343.p1 fails validation.
(TGC)	 AG	157484-157892	GT	AGG
(GTG)	 AG	158046-158129	GT	AGG
(GTG)	 AG	158640-158695	GT	AGG
-recovered pasa_asmbl_8343.p1, internal, 157484, 157892
-recovered pasa_asmbl_8343.p1, internal, 158046, 158129
-recovered pasa_asmbl_8343.p1, internal, 158640, 158695
Valid prediction for pasa_asmbl_8346.p1
Valid prediction for HiQ_model.g19151.t1
Valid prediction for Augustus_model.g19153.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 64528, rend_intergenic: 42256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99594, rend_intergenic: 85280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127231, rend_intergenic: 118790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130058, rend_intergenic: 128170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136428, rend_intergenic: 135362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139534, rend_intergenic: 139488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142141, rend_intergenic: 140129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146817, rend_intergenic: 142155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151146, rend_intergenic: 150050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169969
-exon list size: 372


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.7    
4.0    
4.3    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.7    
7.0    
7.2    
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7.8    
8.0    
8.3    
8.6    
8.8    
9.1    
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9.6    
9.9    
10.2    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.8    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
21.9    
22.2    
22.5    
22.7    
23.0    
23.3    
23.5    
23.8    
24.1    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
25.9    
26.2    
26.5    
26.7    
27.0    
27.3    
27.5    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.2    
41.4    
41.7    
42.0    
42.2    
42.5    
42.8    
43.0    
43.3    
43.6    
43.9    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.1    
56.4    
56.7    
57.0    
57.2    
57.5    
57.8    
58.0    
58.3    
58.6    
58.8    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.5    
72.7    
73.0    
73.3    
73.5    
73.8    
74.1    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
75.9    
76.2    
76.5    
76.7    
77.0    
77.3    
77.5    
77.8    
78.1    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.7    
96.0    
96.3    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 64528, rend_intergenic: 42256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99594, rend_intergenic: 85280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127231, rend_intergenic: 118790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130058, rend_intergenic: 128170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136428, rend_intergenic: 135362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139534, rend_intergenic: 139488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142141, rend_intergenic: 140129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146817, rend_intergenic: 142155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151146, rend_intergenic: 150050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support