-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_6527076-6747971

-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 snap_scaffold_20-snap.1407-T1
Valid prediction for Augustus_model.g30637.t1
Valid prediction for GlimmerHMM_glimmerT_46169-T1
Valid prediction for HiQ_model.g30653.t1
Couldn't classify 201788, 202124
Couldn't classify 204485, 204558
Sorry, prediction pasa_asmbl_26673.p1 fails validation.
(TTC)	 AC	201788-202124	GT	AGG
(GCC)	 AG	204485-204558	CC	TCC
Valid prediction for snap_scaffold_20-snap.1415-T1
Valid prediction for Augustus_model.g30648.t1
Valid prediction for snap_scaffold_20-snap.1418-T1
Valid prediction for GlimmerHMM_glimmerT_46162-T1
Valid prediction for snap_scaffold_20-snap.1451-T1
Valid prediction for Augustus_model.g30638.t1
Valid prediction for Augustus_model.g30642.t1
Valid prediction for GlimmerHMM_glimmerT_46173-T1
Valid prediction for snap_scaffold_20-snap.1424-T1
Valid prediction for snap_scaffold_20-snap.1427-T1
Valid prediction for GlimmerHMM_glimmerT_46183-T1
Couldn't classify 194015, 194146
Couldn't classify 195570, 195600
Sorry, prediction pasa_asmbl_26671.p1 fails validation.
(GAG)	 AT	194015-194146	GT	AGG
(GTT)	 AG	194615-194728	GT	AAG
(GTT)	 AG	194826-194882	GT	CTG
(GTA)	 AG	195049-195197	GT	AGG
(GTG)	 AG	195570-195600	CA	AGC
-recovered pasa_asmbl_26671.p1, internal, 194615, 194728
-recovered pasa_asmbl_26671.p1, internal, 194826, 194882
-recovered pasa_asmbl_26671.p1, internal, 195049, 195197
Valid prediction for Augustus_model.g30634.t1
Valid prediction for GlimmerHMM_glimmerT_46191-T1
Valid prediction for snap_scaffold_20-snap.1442-T1
Valid prediction for snap_scaffold_20-snap.1421-T1
Couldn't classify 17479, 17636
Sorry, prediction pasa_asmbl_26662.p1 fails validation.
(GTG)	 TA	17479-17636	GT	TTG
(CAA)	 AG	17991-18125	GT	TGG
(GTA)	 AG	19011-19104	GT	AGG
(GTA)	 AG	21201-21275	TT	GAT
-recovered pasa_asmbl_26662.p1, terminal, 21201, 21275
-recovered pasa_asmbl_26662.p1, internal, 17991, 18125
-recovered pasa_asmbl_26662.p1, internal, 19011, 19104
Valid prediction for Augustus_model.g30632.t1
Valid prediction for GlimmerHMM_glimmerT_46182-T1
Valid prediction for snap_scaffold_20-snap.1419-T1
Couldn't classify 214530, 214624
Couldn't classify 215459, 215540
Couldn't classify 215987, 216095
Couldn't classify 216780, 217222
Sorry, prediction pasa_asmbl_27152.p1 fails validation.
(AAG)	 CC	214530-214624	GT	AGG
(GAC)	 AG	214735-214866	GT	AGG
(GCT)	 AG	215459-215540	AT	CCA
(CGC)	 AC	215987-216095	GT	AGG
(ATG)	 AG	216325-216618	GT	AGG
(GGA)	 AG	216780-217222	AC	GGA
add_exon() Sorry, pasa_asmbl_27152.p1 216325-216618-initial-1 is invalid.
-recovered pasa_asmbl_27152.p1, initial, 216325, 216618
-recovered pasa_asmbl_27152.p1, internal, 214735, 214866
-recovered pasa_asmbl_27152.p1, internal, 216325, 216618
Valid prediction for snap_scaffold_20-snap.1441-T1
Valid prediction for snap_scaffold_20-snap.1426-T1
Valid prediction for Augustus_model.g30643.t1
Valid prediction for snap_scaffold_20-snap.1450-T1
Valid prediction for Augustus_model.g30651.t1
Valid prediction for CodingQuarry_transcript_30534-T1
Valid prediction for GlimmerHMM_glimmerT_46177-T1
Valid prediction for Augustus_model.g30654.t1
Valid prediction for snap_scaffold_20-snap.1429-T1
Valid prediction for snap_scaffold_20-snap.1439-T1
Valid prediction for Augustus_model.g30635.t1
Valid prediction for GlimmerHMM_glimmerT_46190-T1
Valid prediction for snap_scaffold_20-snap.1413-T1
Valid prediction for GlimmerHMM_glimmerT_46176-T1
Valid prediction for GlimmerHMM_glimmerT_46175-T1
Valid prediction for GlimmerHMM_glimmerT_46188-T1
Valid prediction for snap_scaffold_20-snap.1436-T1
Valid prediction for GlimmerHMM_glimmerT_46172-T1
Couldn't classify 195787, 195889
Sorry, prediction pasa_asmbl_26672.p1 fails validation.
(AAC)	 CA	195787-195889	GT	GTG
(ACC)	 AG	196072-196272	GT	AGG
(ATT)	 AG	196494-196570	GT	AGG
(CTG)	 AG	196692-196815	GC	AGG
(AGC)	 AG	196949-197040	GT	GGG
(AGG)	 AG	197174-197239	GT	AGG
(ACT)	 AG	197368-197552	GT	AGG
(TCT)	 AG	197735-197860	GT	AGG
(TGT)	 AG	197970-198206	GT	CTG
(AAA)	 AG	198461-198539	GT	TCG
(CTC)	 AG	198676-198768	GT	AGG
(ATC)	 AG	198913-199020	GT	AGG
(GTG)	 AG	199243-199356	AC	AGA
-recovered pasa_asmbl_26672.p1, terminal, 199243, 199356
-recovered pasa_asmbl_26672.p1, internal, 196072, 196272
-recovered pasa_asmbl_26672.p1, internal, 196494, 196570
-recovered pasa_asmbl_26672.p1, internal, 196692, 196815
-recovered pasa_asmbl_26672.p1, internal, 196949, 197040
-recovered pasa_asmbl_26672.p1, internal, 197174, 197239
-recovered pasa_asmbl_26672.p1, internal, 197368, 197552
-recovered pasa_asmbl_26672.p1, internal, 197735, 197860
-recovered pasa_asmbl_26672.p1, internal, 197970, 198206
-recovered pasa_asmbl_26672.p1, internal, 198461, 198539
-recovered pasa_asmbl_26672.p1, internal, 198676, 198768
-recovered pasa_asmbl_26672.p1, internal, 198913, 199020
Valid prediction for GlimmerHMM_glimmerT_46185-T1
Valid prediction for snap_scaffold_20-snap.1423-T1
Couldn't classify 92329, 92404
Sorry, prediction pasa_asmbl_26666.p1 fails validation.
(GTG)	 CA	92329-92404	GT	AGG
(AGT)	 AG	94677-94817	GT	AGG
(GCC)	 AG	95029-95261	TG	GAT
-recovered pasa_asmbl_26666.p1, terminal, 95029, 95261
-recovered pasa_asmbl_26666.p1, internal, 94677, 94817
Couldn't classify 217553, 218577
Couldn't classify 220320, 220402
Sorry, prediction pasa_asmbl_26674.p1 fails validation.
(GAG)	 CG	217553-218577	GT	AGG
(GTA)	 AG	219380-219504	GT	AGG
(AGA)	 AG	219837-219965	GT	AGG
(AAA)	 AG	220320-220402	GT	CGG
-recovered pasa_asmbl_26674.p1, internal, 219380, 219504
-recovered pasa_asmbl_26674.p1, internal, 219837, 219965
-recovered pasa_asmbl_26674.p1, internal, 220320, 220402
Valid prediction for Augustus_model.g30641.t1
Valid prediction for GlimmerHMM_glimmerT_46189-T1
Valid prediction for Augustus_model.g30633.t1
Valid prediction for snap_scaffold_20-snap.1449-T1
Valid prediction for GlimmerHMM_glimmerT_46187-T1
Valid prediction for GlimmerHMM_glimmerT_46186-T1
Valid prediction for snap_scaffold_20-snap.1411-T1
Valid prediction for HiQ_model.g30652.t1
Valid prediction for GlimmerHMM_glimmerT_46167-T1
Valid prediction for snap_scaffold_20-snap.1433-T1
Valid prediction for snap_scaffold_20-snap.1417-T1
Valid prediction for GlimmerHMM_glimmerT_46164-T1
Valid prediction for GlimmerHMM_glimmerT_46165-T1
Valid prediction for snap_scaffold_20-snap.1446-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_20-snap.1416-T1
Valid prediction for Augustus_model.g30644.t1
Valid prediction for GlimmerHMM_glimmerT_46192-T1
Valid prediction for snap_scaffold_20-snap.1428-T1
Valid prediction for snap_scaffold_20-snap.1443-T1
Valid prediction for snap_scaffold_20-snap.1452-T1
Valid prediction for snap_scaffold_20-snap.1445-T1
Valid prediction for snap_scaffold_20-snap.1434-T1
Valid prediction for Augustus_model.g30655.t1
Valid prediction for pasa_asmbl_25840.p1
Valid prediction for Augustus_model.g30639.t1
Valid prediction for snap_scaffold_20-snap.1432-T1
Valid prediction for snap_scaffold_20-snap.1410-T1
Valid prediction for Augustus_model.g30636.t1
Couldn't classify 101232, 101382
Couldn't classify 107390, 107598
Sorry, prediction pasa_asmbl_25842.p1 fails validation.
(ACG)	 AG	101232-101382	GT	CGG
(GGC)	 AG	103296-103414	GT	AGG
(CTC)	 AG	104702-104847	GT	AAG
(CTA)	 AG	105115-105262	GT	AGG
(GTG)	 AG	106291-106474	GT	AGG
(GTA)	 AG	107390-107598	TG	TCT
-recovered pasa_asmbl_25842.p1, internal, 101232, 101382
-recovered pasa_asmbl_25842.p1, internal, 103296, 103414
-recovered pasa_asmbl_25842.p1, internal, 104702, 104847
-recovered pasa_asmbl_25842.p1, internal, 105115, 105262
-recovered pasa_asmbl_25842.p1, internal, 106291, 106474
Valid prediction for snap_scaffold_20-snap.1447-T1
Valid prediction for CodingQuarry_transcript_30535-T1
Valid prediction for GlimmerHMM_glimmerT_46170-T1
Valid prediction for GlimmerHMM_glimmerT_46163-T1
Valid prediction for Augustus_model.g30645.t1
Valid prediction for GlimmerHMM_glimmerT_46178-T1
Valid prediction for GlimmerHMM_glimmerT_46180-T1
Valid prediction for snap_scaffold_20-snap.1422-T1
Valid prediction for snap_scaffold_20-snap.1435-T1
Valid prediction for snap_scaffold_20-snap.1437-T1
Valid prediction for GlimmerHMM_glimmerT_46168-T1
Valid prediction for GlimmerHMM_glimmerT_46184-T1
Valid prediction for Augustus_model.g30650.t1
Valid prediction for GlimmerHMM_glimmerT_46166-T1
Valid prediction for GlimmerHMM_glimmerT_46179-T1
Valid prediction for snap_scaffold_20-snap.1420-T1
Valid prediction for pasa_asmbl_25847.p2
Valid prediction for snap_scaffold_20-snap.1438-T1
Valid prediction for CodingQuarry_transcript_30536-T1
Valid prediction for snap_scaffold_20-snap.1425-T1
Valid prediction for snap_scaffold_20-snap.1440-T1
Valid prediction for snap_scaffold_20-snap.1431-T1
Valid prediction for GlimmerHMM_glimmerT_46181-T1
Valid prediction for snap_scaffold_20-snap.1414-T1
Valid prediction for GlimmerHMM_glimmerT_46174-T1
Valid prediction for snap_scaffold_20-snap.1412-T1
Valid prediction for HiQ_model.g30647.t1
Valid prediction for pasa_asmbl_25848.p1
Valid prediction for HiQ_model.g30646.t1
Valid prediction for snap_scaffold_20-snap.1448-T1
Valid prediction for GlimmerHMM_glimmerT_46171-T1
Valid prediction for snap_scaffold_20-snap.1430-T1
Valid prediction for Augustus_model.g30640.t1
Valid prediction for snap_scaffold_20-snap.1444-T1
Valid prediction for Augustus_model.g30649.t1
Valid prediction for snap_scaffold_20-snap.1408-T1
Valid prediction for snap_scaffold_20-snap.1409-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20660, rend_intergenic: 16482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30253, rend_intergenic: 23827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43760, rend_intergenic: 33000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52105, rend_intergenic: 50906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86702, rend_intergenic: 84338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130408, rend_intergenic: 117387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147571, rend_intergenic: 144819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157049, rend_intergenic: 151196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169472, rend_intergenic: 158102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188118, rend_intergenic: 182147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208818, rend_intergenic: 207402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220896
-exon list size: 431


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.8    
2.1    
2.3    
2.5    
2.8    
3.0    
3.2    
3.5    
3.7    
3.9    
4.2    
4.4    
4.6    
4.8    
5.1    
5.3    
5.5    
5.8    
6.0    
6.2    
6.5    
6.7    
6.9    
7.2    
7.4    
7.6    
7.9    
8.1    
8.3    
8.5    
8.8    
9.0    
9.2    
9.5    
9.7    
9.9    
10.2    
10.4    
10.6    
10.9    
11.1    
11.3    
11.5    
11.8    
12.0    
12.2    
12.5    
12.7    
12.9    
13.2    
13.4    
13.6    
13.9    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.5    
15.7    
15.9    
16.2    
16.4    
16.6    
16.9    
17.1    
17.3    
17.6    
17.8    
18.0    
18.2    
18.5    
18.7    
18.9    
19.2    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.0    
21.2    
21.5    
21.7    
21.9    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
33.9    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.3    
36.5    
36.7    
37.0    
37.2    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.3    
47.6    
47.8    
48.0    
48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
49.7    
49.9    
50.1    
50.3    
50.6    
50.8    
51.0    
51.3    
51.5    
51.7    
52.0    
52.2    
52.4    
52.7    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
58.0    
58.2    
58.4    
58.7    
58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
60.7    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.8    
63.0    
63.3    
63.5    
63.7    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.1    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.4    
68.6    
68.8    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.4    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.1    
92.4    
92.6    
92.8    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 20660, rend_intergenic: 16482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30253, rend_intergenic: 23827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43760, rend_intergenic: 33000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52105, rend_intergenic: 50906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86702, rend_intergenic: 84338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130408, rend_intergenic: 117387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147571, rend_intergenic: 144819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157049, rend_intergenic: 151196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169472, rend_intergenic: 158102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188118, rend_intergenic: 182147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208818, rend_intergenic: 207402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 210709 - 220896
-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 1 predictions persist after filtering for low support