-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_5606174-5900373

-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_38387-T1
Valid prediction for GlimmerHMM_glimmerT_38397-T1
Valid prediction for GlimmerHMM_glimmerT_38390-T1
Valid prediction for GlimmerHMM_glimmerT_38392-T1
Valid prediction for GlimmerHMM_glimmerT_38408-T1
Valid prediction for snap_scaffold_16-snap.1118-T1
Couldn't classify 31008, 31358
Sorry, prediction pasa_asmbl_17131.p1 fails validation.
(CTG)	 TG	31008-31358	CT	CCC
Valid prediction for GlimmerHMM_glimmerT_38382-T1
Valid prediction for snap_scaffold_16-snap.1125-T1
Valid prediction for Augustus_model.g25623.t1
Valid prediction for GlimmerHMM_glimmerT_38404-T1
Valid prediction for CodingQuarry_transcript_19974-T1
Couldn't classify 190713, 191058
Sorry, prediction pasa_asmbl_16230.p1 fails validation.
(ATG)	 TT	188633-188651	GT	AGG
(ACG)	 AG	189639-189720	GT	AGG
(TGA)	 AG	189967-190015	GT	AAG
(AAT)	 AG	190410-190483	GT	AGG
(CGG)	 AG	190713-191058	TC	GCT
-recovered pasa_asmbl_16230.p1, initial, 188633, 188651
-recovered pasa_asmbl_16230.p1, internal, 189639, 189720
-recovered pasa_asmbl_16230.p1, internal, 189967, 190015
-recovered pasa_asmbl_16230.p1, internal, 190410, 190483
Valid prediction for snap_scaffold_16-snap.1098-T1
Valid prediction for snap_scaffold_16-snap.1115-T1
Valid prediction for snap_scaffold_16-snap.1097-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1102-T1
Valid prediction for Augustus_model.g25621.t1
Valid prediction for snap_scaffold_16-snap.1113-T1
Valid prediction for snap_scaffold_16-snap.1119-T1
Valid prediction for CodingQuarry_transcript_19975-T1
Valid prediction for GlimmerHMM_glimmerT_38380-T1
Valid prediction for HiQ_model.g25615.t1
Valid prediction for Augustus_model.g25622.t1
Valid prediction for Augustus_model.g25626.t1
Valid prediction for snap_scaffold_16-snap.1130-T1
Valid prediction for GlimmerHMM_glimmerT_38396-T1
Valid prediction for GlimmerHMM_glimmerT_38398-T1
Valid prediction for Augustus_model.g25630.t1
Valid prediction for GlimmerHMM_glimmerT_38389-T1
Valid prediction for GlimmerHMM_glimmerT_38400-T1
Valid prediction for snap_scaffold_16-snap.1122-T1
Valid prediction for pasa_asmbl_16223.p1
Valid prediction for GlimmerHMM_glimmerT_38395-T1
Valid prediction for CodingQuarry_transcript_19973-T1
Valid prediction for GlimmerHMM_glimmerT_38399-T1
Valid prediction for snap_scaffold_16-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_38386-T1
Valid prediction for snap_scaffold_16-snap.1129-T1
Valid prediction for snap_scaffold_16-snap.1114-T1
Couldn't classify 196254, 196399
Sorry, prediction pasa_asmbl_16231.p1 fails validation.
(ATG)	 TT	188633-188651	GT	AGG
(ACG)	 AG	189639-189720	GT	AGG
(TGA)	 AG	189967-190015	GT	AAG
(AAT)	 AG	190410-190483	GT	AGG
(CGG)	 AG	190713-191004	GT	AAG
(GTT)	 AG	193044-193172	GT	AGG
(GTT)	 AG	193409-193577	GT	AGG
(AAC)	 AG	193776-194002	GT	AGG
(CAG)	 AG	194831-195182	GT	AGG
(TGC)	 AG	196254-196399	CC	TCC
-recovered pasa_asmbl_16231.p1, initial, 188633, 188651
add_exon() Sorry, pasa_asmbl_16231.p1 193409-193577-terminal-3 is invalid.
-recovered pasa_asmbl_16231.p1, terminal, 193409, 193577
-recovered pasa_asmbl_16231.p1, internal, 189639, 189720
-recovered pasa_asmbl_16231.p1, internal, 189967, 190015
-recovered pasa_asmbl_16231.p1, internal, 190410, 190483
-recovered pasa_asmbl_16231.p1, internal, 190713, 191004
-recovered pasa_asmbl_16231.p1, internal, 193044, 193172
-recovered pasa_asmbl_16231.p1, internal, 193409, 193577
-recovered pasa_asmbl_16231.p1, internal, 193776, 194002
-recovered pasa_asmbl_16231.p1, internal, 194831, 195182
Valid prediction for snap_scaffold_16-snap.1095-T1
Valid prediction for snap_scaffold_16-snap.1131-T1
Valid prediction for HiQ_model.g25625.t1
Couldn't classify 202232, 202576
Sorry, prediction pasa_asmbl_16232.p1 fails validation.
(CAA)	 GC	202232-202576	GT	GGG
(GGA)	 AG	204479-204655	GT	GGG
(GTG)	 AG	205546-205752	GT	AGG
(ATG)	 AG	206097-206185	GT	AGG
(GCA)	 AG	206644-206692	GG	GAG
-recovered pasa_asmbl_16232.p1, initial, 206097, 206185
-recovered pasa_asmbl_16232.p1, terminal, 206644, 206692
-recovered pasa_asmbl_16232.p1, internal, 204479, 204655
-recovered pasa_asmbl_16232.p1, internal, 205546, 205752
-recovered pasa_asmbl_16232.p1, internal, 206097, 206185
Valid prediction for snap_scaffold_16-snap.1109-T1
Valid prediction for pasa_asmbl_16221.p1
Valid prediction for snap_scaffold_16-snap.1117-T1
Valid prediction for CodingQuarry_transcript_19972-T1
Valid prediction for Augustus_model.g25624.t1
Valid prediction for GlimmerHMM_glimmerT_38391-T1
Valid prediction for GlimmerHMM_glimmerT_38393-T1
Valid prediction for snap_scaffold_16-snap.1110-T1
Valid prediction for snap_scaffold_16-snap.1112-T1
Valid prediction for HiQ_model.g25627.t1
Valid prediction for snap_scaffold_16-snap.1107-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_16-snap.1100-T1
Valid prediction for snap_scaffold_16-snap.1120-T1
Valid prediction for snap_scaffold_16-snap.1124-T1
Valid prediction for snap_scaffold_16-snap.1104-T1
Valid prediction for Augustus_model.g25618.t1
Valid prediction for snap_scaffold_16-snap.1105-T1
Valid prediction for snap_scaffold_16-snap.1108-T1
Valid prediction for Augustus_model.g25629.t1
Valid prediction for GlimmerHMM_glimmerT_38401-T1
Valid prediction for HiQ_model.g25616.t1
Valid prediction for Augustus_model.g25632.t1
Couldn't classify 271658, 271990
Couldn't classify 272236, 272316
Sorry, prediction pasa_asmbl_17130.p1 fails validation.
(CCG)	 CC	271658-271990	GT	AGG
(GTT)	 AG	272236-272316	AG	GAA
Valid prediction for GlimmerHMM_glimmerT_38384-T1
Valid prediction for GlimmerHMM_glimmerT_38388-T1
Valid prediction for Augustus_model.g25620.t1
Valid prediction for snap_scaffold_16-snap.1094-T1
Valid prediction for snap_scaffold_16-snap.1126-T1
Valid prediction for GlimmerHMM_glimmerT_38385-T1
Valid prediction for GlimmerHMM_glimmerT_38405-T1
Valid prediction for Augustus_model.g25628.t1
Valid prediction for GlimmerHMM_glimmerT_38381-T1
Valid prediction for snap_scaffold_16-snap.1103-T1
Valid prediction for snap_scaffold_16-snap.1099-T1
Valid prediction for snap_scaffold_16-snap.1101-T1
Valid prediction for GlimmerHMM_glimmerT_38394-T1
Valid prediction for snap_scaffold_16-snap.1121-T1
Valid prediction for snap_scaffold_16-snap.1096-T1
Valid prediction for Augustus_model.g25631.t1
Valid prediction for GlimmerHMM_glimmerT_38383-T1
Valid prediction for Augustus_model.g25617.t1
Valid prediction for snap_scaffold_16-snap.1116-T1
Valid prediction for GlimmerHMM_glimmerT_38409-T1
Valid prediction for snap_scaffold_16-snap.1123-T1
Valid prediction for snap_scaffold_16-snap.1127-T1
Valid prediction for GlimmerHMM_glimmerT_38406-T1
Valid prediction for Augustus_model.g25619.t1
Valid prediction for GlimmerHMM_glimmerT_38402-T1
Valid prediction for GlimmerHMM_glimmerT_38403-T1
Valid prediction for snap_scaffold_16-snap.1106-T1
Valid prediction for GlimmerHMM_glimmerT_38407-T1
Valid prediction for Augustus_model.g25614.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22765, rend_intergenic: 17702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37045, rend_intergenic: 28112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78703, rend_intergenic: 74930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 269103, rend_intergenic: 263799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 41074, rend_intergenic: 41071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 294200
-exon list size: 307


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.6    
3.9    
4.2    
4.5    
4.9    
5.2    
5.5    
5.8    
6.1    
6.5    
6.8    
7.1    
7.4    
7.8    
8.1    
8.4    
8.7    
9.1    
9.4    
9.7    
10.0    
10.4    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.9    
16.2    
16.5    
16.8    
17.2    
17.5    
17.8    
18.1    
18.4    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.4    
21.7    
22.0    
22.3    
22.7    
23.0    
23.3    
23.6    
23.9    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.9    
27.2    
27.5    
27.8    
28.2    
28.5    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.7    
31.1    
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    
36.2    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.2    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.4    
43.7    
44.0    
44.3    
44.7    
45.0    
45.3    
45.6    
46.0    
46.3    
46.6    
46.9    
47.2    
47.6    
47.9    
48.2    
48.5    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.5    
51.8    
52.1    
52.4    
52.8    
53.1    
53.4    
53.7    
54.0    
54.4    
54.7    
55.0    
55.3    
55.7    
56.0    
56.3    
56.6    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.8    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.8    
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    
68.9    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.2    
72.5    
72.8    
73.1    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.1    
76.4    
76.7    
77.0    
77.3    
77.7    
78.0    
78.3    
78.6    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.6    
81.9    
82.2    
82.5    
82.8    
83.2    
83.5    
83.8    
84.1    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.6    
90.0    
90.3    
90.6    
90.9    
91.3    
91.6    
91.9    
92.2    
92.6    
92.9    
93.2    
93.5    
93.9    
94.2    
94.5    
94.8    
95.1    
95.5    
95.8    
96.1    
96.4    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 22765, rend_intergenic: 17702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37045, rend_intergenic: 28112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78703, rend_intergenic: 74930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 269103, rend_intergenic: 263799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 41074, rend_intergenic: 41071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support