-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_5084836-5232878

-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 GlimmerHMM_glimmerT_14624-T1
Valid prediction for Augustus_model.g9691.t1
Valid prediction for GlimmerHMM_glimmerT_14617-T1
Valid prediction for GlimmerHMM_glimmerT_14605-T1
Valid prediction for pasa_asmbl_46916.p2
Valid prediction for snap_scaffold_6-snap.1202-T1
Valid prediction for snap_scaffold_6-snap.1210-T1
Valid prediction for CodingQuarry_transcript_55044-T1
Valid prediction for Augustus_model.g9677.t1
Valid prediction for GlimmerHMM_glimmerT_14608-T1
Valid prediction for snap_scaffold_6-snap.1193-T1
Valid prediction for snap_scaffold_6-snap.1217-T1
Valid prediction for snap_scaffold_6-snap.1219-T1
Valid prediction for GlimmerHMM_glimmerT_14611-T1
Valid prediction for CodingQuarry_transcript_55041-T1
Valid prediction for pasa_asmbl_46924.p1
Valid prediction for snap_scaffold_6-snap.1227-T1
Valid prediction for GlimmerHMM_glimmerT_14613-T1
Valid prediction for snap_scaffold_6-snap.1209-T1
Valid prediction for GlimmerHMM_glimmerT_14615-T1
Valid prediction for snap_scaffold_6-snap.1197-T1
Valid prediction for snap_scaffold_6-snap.1224-T1
Valid prediction for HiQ_model.g9689.t1
Valid prediction for GlimmerHMM_glimmerT_14625-T1
Valid prediction for snap_scaffold_6-snap.1194-T1
Valid prediction for snap_scaffold_6-snap.1206-T1
Valid prediction for snap_scaffold_6-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_14606-T1
Valid prediction for snap_scaffold_6-snap.1200-T1
Valid prediction for snap_scaffold_6-snap.1222-T1
Valid prediction for GlimmerHMM_glimmerT_14623-T1
Valid prediction for Augustus_model.g9685.t1
Valid prediction for snap_scaffold_6-snap.1196-T1
Valid prediction for CodingQuarry_transcript_55040-T1
Valid prediction for Augustus_model.g9686.t1
Valid prediction for snap_scaffold_6-snap.1215-T1
Valid prediction for GlimmerHMM_glimmerT_14618-T1
Valid prediction for snap_scaffold_6-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_14619-T1
Valid prediction for snap_scaffold_6-snap.1212-T1
Valid prediction for Augustus_model.g9680.t1
Valid prediction for snap_scaffold_6-snap.1226-T1
Valid prediction for snap_scaffold_6-snap.1203-T1
Valid prediction for snap_scaffold_6-snap.1214-T1
Valid prediction for CodingQuarry_transcript_55045-T1
Couldn't classify 105877, 105877
Sorry, prediction CodingQuarry_transcript_55042-T1 fails validation.
(AGT)	 AG	105877-105877	GT	GAG
(TGA)	 AG	106466-106568	GT	AAG
(GTA)	 AG	106962-107125	GT	CCG
(CTT)	 AG	107296-107387	GT	AGG
(AAA)	 AG	107492-107704	CA	AGC
-recovered CodingQuarry_transcript_55042-T1, terminal, 107492, 107704
-recovered CodingQuarry_transcript_55042-T1, internal, 105877, 105877
-recovered CodingQuarry_transcript_55042-T1, internal, 106466, 106568
-recovered CodingQuarry_transcript_55042-T1, internal, 106962, 107125
-recovered CodingQuarry_transcript_55042-T1, internal, 107296, 107387
Valid prediction for Augustus_model.g9678.t1
Couldn't classify 105877, 105877
Sorry, prediction pasa_asmbl_46920.p1 fails validation.
(AGT)	 AG	105877-105877	GT	GAG
(TGA)	 AG	106466-106568	GT	AAG
(GTA)	 AG	106962-107125	GT	CCG
(CTT)	 AG	107296-107387	GT	AGG
(AAA)	 AG	107492-107654	GT	AGG
(AGG)	 AG	108902-109086	GT	AGG
(GTG)	 AG	110190-110281	GC	AGG
(ATT)	 AG	110516-110544	GT	AGG
(ACA)	 AG	110670-110795	GT	GTG
(GCC)	 AG	112202-112380	GT	AGG
(CAC)	 AG	112540-112635	GT	AGG
(TTG)	 AG	112753-112834	GT	CGG
(ACT)	 AG	112941-113021	GT	GGG
(TTG)	 AG	113145-113229	GT	AGG
(ATA)	 AG	113514-113574	CC	AGC
-recovered pasa_asmbl_46920.p1, terminal, 113514, 113574
-recovered pasa_asmbl_46920.p1, internal, 105877, 105877
-recovered pasa_asmbl_46920.p1, internal, 106466, 106568
-recovered pasa_asmbl_46920.p1, internal, 106962, 107125
-recovered pasa_asmbl_46920.p1, internal, 107296, 107387
-recovered pasa_asmbl_46920.p1, internal, 107492, 107654
-recovered pasa_asmbl_46920.p1, internal, 108902, 109086
-recovered pasa_asmbl_46920.p1, internal, 110190, 110281
-recovered pasa_asmbl_46920.p1, internal, 110516, 110544
-recovered pasa_asmbl_46920.p1, internal, 110670, 110795
-recovered pasa_asmbl_46920.p1, internal, 112202, 112380
-recovered pasa_asmbl_46920.p1, internal, 112540, 112635
-recovered pasa_asmbl_46920.p1, internal, 112753, 112834
-recovered pasa_asmbl_46920.p1, internal, 112941, 113021
-recovered pasa_asmbl_46920.p1, internal, 113145, 113229

-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 Augustus_model.g9682.t1
Valid prediction for snap_scaffold_6-snap.1211-T1
Valid prediction for snap_scaffold_6-snap.1216-T1
Valid prediction for snap_scaffold_6-snap.1228-T1
Valid prediction for GlimmerHMM_glimmerT_14604-T1
Valid prediction for snap_scaffold_6-snap.1201-T1
Valid prediction for GlimmerHMM_glimmerT_14609-T1
Valid prediction for snap_scaffold_6-snap.1213-T1
Valid prediction for Augustus_model.g9675.t1
Valid prediction for pasa_asmbl_48403.p1
Valid prediction for CodingQuarry_transcript_55039-T1
Valid prediction for Augustus_model.g9683.t1
Valid prediction for GlimmerHMM_glimmerT_14614-T1
Valid prediction for snap_scaffold_6-snap.1225-T1
Valid prediction for snap_scaffold_6-snap.1198-T1
Valid prediction for snap_scaffold_6-snap.1223-T1
Valid prediction for Augustus_model.g9676.t1
Valid prediction for snap_scaffold_6-snap.1230-T1
Valid prediction for snap_scaffold_6-snap.1204-T1
Valid prediction for snap_scaffold_6-snap.1205-T1
Valid prediction for snap_scaffold_6-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_14621-T1
Valid prediction for GlimmerHMM_glimmerT_14616-T1
Valid prediction for snap_scaffold_6-snap.1220-T1
Valid prediction for GlimmerHMM_glimmerT_14626-T1
Valid prediction for GlimmerHMM_glimmerT_14612-T1
Valid prediction for snap_scaffold_6-snap.1199-T1
Valid prediction for Augustus_model.g9684.t1
Valid prediction for GlimmerHMM_glimmerT_14627-T1
Valid prediction for snap_scaffold_6-snap.1195-T1
Valid prediction for Augustus_model.g9690.t1
Valid prediction for GlimmerHMM_glimmerT_14610-T1
Valid prediction for Augustus_model.g9687.t1
Valid prediction for snap_scaffold_6-snap.1207-T1
Valid prediction for GlimmerHMM_glimmerT_14607-T1
Valid prediction for GlimmerHMM_glimmerT_14620-T1
Valid prediction for Augustus_model.g9679.t1
Valid prediction for snap_scaffold_6-snap.1192-T1
Valid prediction for Augustus_model.g9681.t1
Valid prediction for Augustus_model.g9688.t1
Valid prediction for snap_scaffold_6-snap.1208-T1
Couldn't classify 26647, 26791
Couldn't classify 27333, 27553
Sorry, prediction pasa_asmbl_48408.p1 fails validation.
(CTG)	 CA	26647-26791	GT	TGG
(GCT)	 AG	26981-27220	GT	AGG
(ACA)	 AG	27333-27553	GT	CGG
-recovered pasa_asmbl_48408.p1, internal, 26981, 27220
-recovered pasa_asmbl_48408.p1, internal, 27333, 27553
Valid prediction for GlimmerHMM_glimmerT_14622-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12055, rend_intergenic: 3752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21314, rend_intergenic: 20471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28141, rend_intergenic: 23878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33736, rend_intergenic: 32270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35522, rend_intergenic: 33753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41978, rend_intergenic: 36913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45777, rend_intergenic: 44488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59441, rend_intergenic: 57515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72176, rend_intergenic: 69660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76730, rend_intergenic: 74481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110303, rend_intergenic: 107439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112361, rend_intergenic: 110519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129812, rend_intergenic: 128360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136345, rend_intergenic: 134102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138646, rend_intergenic: 136575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 148043
-exon list size: 322


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.4    
16.7    
17.0    
17.3    
17.6    
17.9    
18.2    
18.5    
18.8    
19.1    
19.4    
19.8    
20.1    
20.4    
20.7    
21.0    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.1    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
26.5    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.6    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.3    
33.6    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.2    
43.5    
43.8    
44.1    
44.4    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.6    
55.9    
56.2    
56.5    
56.8    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.4    
66.7    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.4    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.9    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.6    
80.9    
81.2    
81.5    
81.8    
82.1    
82.4    
82.7    
83.0    
83.3    
83.6    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 12055, rend_intergenic: 3752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21314, rend_intergenic: 20471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28141, rend_intergenic: 23878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33736, rend_intergenic: 32270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35522, rend_intergenic: 33753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41978, rend_intergenic: 36913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45777, rend_intergenic: 44488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59441, rend_intergenic: 57515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72176, rend_intergenic: 69660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76730, rend_intergenic: 74481  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110303, rend_intergenic: 107439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112361, rend_intergenic: 110519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129812, rend_intergenic: 128360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136345, rend_intergenic: 134102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138646, rend_intergenic: 136575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 129813 - 148043
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 134118 - 148043
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support