-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_6036066-6188135

-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_34176-T1
Valid prediction for Augustus_model.g33049.t1
Valid prediction for CodingQuarry_transcript_34177-T1
Valid prediction for GlimmerHMM_glimmerT_49558-T1
Valid prediction for GlimmerHMM_glimmerT_49546-T1
Valid prediction for GlimmerHMM_glimmerT_49537-T1
Valid prediction for pasa_asmbl_30096.p1
Valid prediction for snap_scaffold_22-snap.1148-T1
Valid prediction for snap_scaffold_22-snap.1154-T1
Valid prediction for snap_scaffold_22-snap.1181-T1
Valid prediction for snap_scaffold_22-snap.1157-T1
Valid prediction for CodingQuarry_transcript_34171-T1
Valid prediction for GlimmerHMM_glimmerT_49545-T1
Valid prediction for GlimmerHMM_glimmerT_49536-T1
Valid prediction for Augustus_model.g33044.t1
Couldn't classify 30963, 31264
Sorry, prediction pasa_asmbl_30091.p1 fails validation.
(ATG)	 GC	27158-27170	GT	TGG
(GCC)	 AG	27570-27790	GT	GGG
(GCA)	 AG	27952-28021	GT	GGG
(AGA)	 AG	28299-28438	GT	AGG
(GTC)	 AG	28773-28849	GT	GGG
(ACC)	 AG	28988-29055	GT	CAG
(ATG)	 AG	29256-29390	GT	GCG
(GTT)	 AG	29858-29989	GT	GGG
(GCT)	 AG	30089-30265	GT	CTG
(ACA)	 AG	30530-30754	GT	GGG
(GGA)	 AG	30963-31264	TA	CCT
-recovered pasa_asmbl_30091.p1, initial, 27158, 27170
add_exon() Sorry, pasa_asmbl_30091.p1 29256-29390-initial-1 is invalid.
-recovered pasa_asmbl_30091.p1, initial, 29256, 29390
-recovered pasa_asmbl_30091.p1, internal, 27570, 27790
-recovered pasa_asmbl_30091.p1, internal, 27952, 28021
-recovered pasa_asmbl_30091.p1, internal, 28299, 28438
-recovered pasa_asmbl_30091.p1, internal, 28773, 28849
-recovered pasa_asmbl_30091.p1, internal, 28988, 29055
-recovered pasa_asmbl_30091.p1, internal, 29256, 29390
-recovered pasa_asmbl_30091.p1, internal, 29858, 29989
-recovered pasa_asmbl_30091.p1, internal, 30089, 30265
-recovered pasa_asmbl_30091.p1, internal, 30530, 30754
Valid prediction for pasa_asmbl_30093.p1
Valid prediction for HiQ_model.g33037.t1
Valid prediction for snap_scaffold_22-snap.1150-T1
Valid prediction for GlimmerHMM_glimmerT_49550-T1
Valid prediction for GlimmerHMM_glimmerT_49551-T1
Valid prediction for CodingQuarry_transcript_34174-T1
Valid prediction for GlimmerHMM_glimmerT_49554-T1
Valid prediction for snap_scaffold_22-snap.1182-T1
Valid prediction for HiQ_model.g33055.t1
Valid prediction for GlimmerHMM_glimmerT_49541-T1
Valid prediction for snap_scaffold_22-snap.1171-T1
Valid prediction for Augustus_model.g33033.t1
Valid prediction for GlimmerHMM_glimmerT_49535-T1
Valid prediction for snap_scaffold_22-snap.1177-T1
Valid prediction for snap_scaffold_22-snap.1174-T1
Valid prediction for CodingQuarry_transcript_34180-T1
Valid prediction for snap_scaffold_22-snap.1167-T1
Valid prediction for snap_scaffold_22-snap.1169-T1
Valid prediction for snap_scaffold_22-snap.1161-T1
Valid prediction for Augustus_model.g33047.t1
Valid prediction for CodingQuarry_transcript_34172-T1
Valid prediction for Augustus_model.g33041.t1
Valid prediction for GlimmerHMM_glimmerT_49539-T1
Valid prediction for snap_scaffold_22-snap.1151-T1
Valid prediction for snap_scaffold_22-snap.1165-T1
Valid prediction for HiQ_model.g33035.t1
Valid prediction for pasa_asmbl_30094.p2
Valid prediction for snap_scaffold_22-snap.1162-T1
Valid prediction for snap_scaffold_22-snap.1152-T1
Couldn't classify 17430, 17644
Sorry, prediction pasa_asmbl_30530.p1 fails validation.
(AGC)	 AG	17430-17644	GT	GGG
(CTA)	 AG	19665-19785	CA	GAC
-recovered pasa_asmbl_30530.p1, terminal, 19665, 19785
-recovered pasa_asmbl_30530.p1, internal, 17430, 17644
Valid prediction for HiQ_model.g33043.t1
Valid prediction for Augustus_model.g33034.t1
Valid prediction for snap_scaffold_22-snap.1173-T1
Valid prediction for Augustus_model.g33039.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_49538-T1
Valid prediction for snap_scaffold_22-snap.1144-T1
Valid prediction for snap_scaffold_22-snap.1156-T1
Valid prediction for GlimmerHMM_glimmerT_49543-T1
Valid prediction for Augustus_model.g33038.t1
Valid prediction for HiQ_model.g33042.t1
Valid prediction for Augustus_model.g33048.t1
Valid prediction for snap_scaffold_22-snap.1158-T1
Valid prediction for snap_scaffold_22-snap.1153-T1
Valid prediction for snap_scaffold_22-snap.1147-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49542-T1
Valid prediction for CodingQuarry_transcript_34179-T1
Couldn't classify 77493, 78879
Sorry, prediction pasa_asmbl_29307.p1 fails validation.
(CGC)	 CC	77493-78879	GT	CTG
(CAT)	 AG	79164-79352	GT	ACG
(CGT)	 AG	80556-80705	GT	ACG
(GAG)	 AG	82916-82966	GT	CGG
(CTG)	 AG	83558-83638	GT	TGG
(TTC)	 AG	83874-84508	AG	GAA
-recovered pasa_asmbl_29307.p1, terminal, 83874, 84508
-recovered pasa_asmbl_29307.p1, internal, 79164, 79352
-recovered pasa_asmbl_29307.p1, internal, 80556, 80705
-recovered pasa_asmbl_29307.p1, internal, 82916, 82966
-recovered pasa_asmbl_29307.p1, internal, 83558, 83638
Valid prediction for HiQ_model.g33050.t1
Valid prediction for GlimmerHMM_glimmerT_49549-T1
Valid prediction for HiQ_model.g33040.t1
Valid prediction for CodingQuarry_transcript_34173-T1
Valid prediction for snap_scaffold_22-snap.1164-T1
Valid prediction for GlimmerHMM_glimmerT_49548-T1
Valid prediction for GlimmerHMM_glimmerT_49557-T1
Valid prediction for snap_scaffold_22-snap.1179-T1
Valid prediction for GlimmerHMM_glimmerT_49547-T1
Valid prediction for GlimmerHMM_glimmerT_49534-T1
Valid prediction for snap_scaffold_22-snap.1168-T1
Valid prediction for snap_scaffold_22-snap.1175-T1
Valid prediction for Augustus_model.g33054.t1
Couldn't classify 31404, 31456
Sorry, prediction pasa_asmbl_29310.p1 fails validation.
(GGC)	 AG	31404-31456	GT	AAG
(TTG)	 AG	32484-32577	GT	AGG
(GTG)	 AG	32748-32834	GT	TGG
(TTC)	 AG	34197-34345	GT	ATG
(CTG)	 AG	34611-34704	GT	TGG
(TCA)	 AG	34960-35076	GT	AGG
(ACC)	 AG	35318-35488	GT	AGG
(ACA)	 AG	35638-35716	GT	AGG
(GCA)	 AG	36113-36273	GT	AGG
(GGC)	 AG	36873-36959	GT	AGG
(GAA)	 AG	38622-38844	GT	TGG
(GCA)	 AG	38935-39114	GT	AGG
(TCT)	 AG	39212-39415	GT	GGG
(ACG)	 AG	39572-39679	GT	CGG
(TGA)	 AG	39907-39995	GT	AGG
(GAA)	 AG	40073-40183	AG	AGA
add_exon() Sorry, pasa_asmbl_29310.p1 35638-35716-terminal-3 is invalid.
-recovered pasa_asmbl_29310.p1, terminal, 35638, 35716
-recovered pasa_asmbl_29310.p1, terminal, 40073, 40183
-recovered pasa_asmbl_29310.p1, internal, 31404, 31456
-recovered pasa_asmbl_29310.p1, internal, 32484, 32577
-recovered pasa_asmbl_29310.p1, internal, 32748, 32834
-recovered pasa_asmbl_29310.p1, internal, 34197, 34345
-recovered pasa_asmbl_29310.p1, internal, 34611, 34704
-recovered pasa_asmbl_29310.p1, internal, 34960, 35076
-recovered pasa_asmbl_29310.p1, internal, 35318, 35488
-recovered pasa_asmbl_29310.p1, internal, 35638, 35716
-recovered pasa_asmbl_29310.p1, internal, 36113, 36273
-recovered pasa_asmbl_29310.p1, internal, 36873, 36959
-recovered pasa_asmbl_29310.p1, internal, 38622, 38844
-recovered pasa_asmbl_29310.p1, internal, 38935, 39114
-recovered pasa_asmbl_29310.p1, internal, 39212, 39415
-recovered pasa_asmbl_29310.p1, internal, 39572, 39679
-recovered pasa_asmbl_29310.p1, internal, 39907, 39995
Valid prediction for Augustus_model.g33036.t1
Valid prediction for pasa_asmbl_29319.p1
Valid prediction for snap_scaffold_22-snap.1163-T1
Valid prediction for Augustus_model.g33051.t1
Valid prediction for snap_scaffold_22-snap.1145-T1
Valid prediction for Augustus_model.g33045.t1
Valid prediction for snap_scaffold_22-snap.1170-T1
Valid prediction for GlimmerHMM_glimmerT_49540-T1
Valid prediction for GlimmerHMM_glimmerT_49552-T1
Valid prediction for snap_scaffold_22-snap.1172-T1
Valid prediction for snap_scaffold_22-snap.1166-T1
Valid prediction for pasa_asmbl_29308.p1
Valid prediction for GlimmerHMM_glimmerT_49556-T1
Valid prediction for CodingQuarry_transcript_34178-T1
Valid prediction for GlimmerHMM_glimmerT_49544-T1
Valid prediction for snap_scaffold_22-snap.1180-T1
Valid prediction for Augustus_model.g33032.t1
Valid prediction for Augustus_model.g33046.t1
Valid prediction for snap_scaffold_22-snap.1149-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49553-T1
Valid prediction for snap_scaffold_22-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_49533-T1
Valid prediction for snap_scaffold_22-snap.1160-T1
Valid prediction for snap_scaffold_22-snap.1159-T1
Couldn't classify 141881, 142525
Sorry, prediction pasa_asmbl_29304.p1 fails validation.
(ACC)	 AA	141881-142525	GG	GAG
Valid prediction for Augustus_model.g33053.t1
Valid prediction for snap_scaffold_22-snap.1155-T1
Valid prediction for snap_scaffold_22-snap.1178-T1
Valid prediction for snap_scaffold_22-snap.1176-T1
Valid prediction for Augustus_model.g33052.t1
Valid prediction for GlimmerHMM_glimmerT_49555-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32255, rend_intergenic: 22551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52172, rend_intergenic: 49157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60613, rend_intergenic: 56918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62159, rend_intergenic: 61028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70541, rend_intergenic: 62765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79006, rend_intergenic: 72070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91812, rend_intergenic: 87079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95801, rend_intergenic: 92095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112151, rend_intergenic: 111888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123723, rend_intergenic: 114519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147831, rend_intergenic: 142810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 152070
-exon list size: 390


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.5    
13.8    
14.0    
14.3    
14.5    
14.8    
15.1    
15.3    
15.6    
15.8    
16.1    
16.3    
16.6    
16.8    
17.1    
17.3    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
23.0    
23.2    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.5    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.5    
76.8    
77.0    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.7    
82.9    
83.2    
83.4    
83.7    
83.9    
84.2    
84.4    
84.7    
84.9    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 32255, rend_intergenic: 22551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52172, rend_intergenic: 49157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60613, rend_intergenic: 56918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62159, rend_intergenic: 61028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70541, rend_intergenic: 62765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79006, rend_intergenic: 72070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91812, rend_intergenic: 87079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95801, rend_intergenic: 92095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112151, rend_intergenic: 111888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123723, rend_intergenic: 114519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147831, rend_intergenic: 142810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support