-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_6972344-7156211

-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_27338-T1
Valid prediction for CodingQuarry_transcript_8111-T1
Valid prediction for GlimmerHMM_glimmerT_27322-T1
Valid prediction for GlimmerHMM_glimmerT_27334-T1
Valid prediction for GlimmerHMM_glimmerT_27341-T1
Valid prediction for snap_scaffold_11-snap.1641-T1
Valid prediction for snap_scaffold_11-snap.1662-T1
Valid prediction for Augustus_model.g18094.t1
Valid prediction for snap_scaffold_11-snap.1655-T1
Valid prediction for Augustus_model.g18091.t1
Valid prediction for snap_scaffold_11-snap.1637-T1
Valid prediction for CodingQuarry_transcript_8112-T1
Valid prediction for CodingQuarry_transcript_8113-T1
Valid prediction for snap_scaffold_11-snap.1651-T1
Valid prediction for GlimmerHMM_glimmerT_27339-T1
Couldn't classify 109045, 109157
Couldn't classify 114248, 114278
Sorry, prediction pasa_asmbl_5655.p1 fails validation.
(GGA)	 GG	109045-109157	GT	CCG
(GCC)	 AG	109445-109639	GT	AAG
(GTG)	 AG	110174-110415	GT	TGG
(AGA)	 AG	110558-110680	GT	AGG
(ACG)	 AG	110815-110893	GT	GAG
(CCT)	 AG	111000-111120	GT	AGG
(GTC)	 AG	111600-111709	GT	AGG
(GGA)	 AG	112031-112120	GT	AGG
(AGG)	 AG	112479-112554	GT	AGG
(ATG)	 AG	112691-112896	GT	TGG
(TTG)	 AG	113128-113257	GT	AGG
(GAT)	 AG	113335-113478	GC	AGG
(AGT)	 AG	113777-113943	GT	AGG
(GAG)	 AG	114248-114278	TG	TGT
-recovered pasa_asmbl_5655.p1, initial, 112691, 112896
-recovered pasa_asmbl_5655.p1, terminal, 110815, 110893
-recovered pasa_asmbl_5655.p1, internal, 109445, 109639
-recovered pasa_asmbl_5655.p1, internal, 110174, 110415
-recovered pasa_asmbl_5655.p1, internal, 110558, 110680
-recovered pasa_asmbl_5655.p1, internal, 110815, 110893
-recovered pasa_asmbl_5655.p1, internal, 111000, 111120
-recovered pasa_asmbl_5655.p1, internal, 111600, 111709
-recovered pasa_asmbl_5655.p1, internal, 112031, 112120
-recovered pasa_asmbl_5655.p1, internal, 112479, 112554
-recovered pasa_asmbl_5655.p1, internal, 112691, 112896
-recovered pasa_asmbl_5655.p1, internal, 113128, 113257
-recovered pasa_asmbl_5655.p1, internal, 113335, 113478
-recovered pasa_asmbl_5655.p1, internal, 113777, 113943
Valid prediction for HiQ_model.g18098.t1
Valid prediction for GlimmerHMM_glimmerT_27335-T1
Valid prediction for snap_scaffold_11-snap.1635-T1
Valid prediction for snap_scaffold_11-snap.1643-T1
Valid prediction for pasa_asmbl_5662.p1
Valid prediction for Augustus_model.g18096.t1
Valid prediction for snap_scaffold_11-snap.1631-T1
Valid prediction for snap_scaffold_11-snap.1657-T1
Valid prediction for HiQ_model.g18095.t1
Valid prediction for Augustus_model.g18093.t1
Valid prediction for CodingQuarry_transcript_8114-T1
Couldn't classify 108665, 108696
Sorry, prediction pasa_asmbl_5654.p1 fails validation.
(ATG)	 GA	107808-107885	GT	CGG
(AGT)	 AG	108390-108582	GT	AGG
(GGG)	 AG	108665-108696	GT	GTG
-recovered pasa_asmbl_5654.p1, initial, 107808, 107885
-recovered pasa_asmbl_5654.p1, internal, 108390, 108582
-recovered pasa_asmbl_5654.p1, internal, 108665, 108696
Valid prediction for Augustus_model.g18085.t1
Valid prediction for snap_scaffold_11-snap.1648-T1
Valid prediction for snap_scaffold_11-snap.1661-T1
Valid prediction for snap_scaffold_11-snap.1634-T1
Valid prediction for GlimmerHMM_glimmerT_27342-T1
Valid prediction for GlimmerHMM_glimmerT_27328-T1
Valid prediction for snap_scaffold_11-snap.1659-T1
Valid prediction for GlimmerHMM_glimmerT_27340-T1
Valid prediction for snap_scaffold_11-snap.1638-T1
Valid prediction for Augustus_model.g18084.t1
Couldn't classify 142355, 142771
Sorry, prediction pasa_asmbl_5661.p1 fails validation.
(CCC)	 GG	142355-142771	AC	AGA
Valid prediction for pasa_asmbl_5648.p1
Valid prediction for GlimmerHMM_glimmerT_27330-T1
Couldn't classify 114458, 114529
Sorry, prediction pasa_asmbl_5657.p1 fails validation.
(GAG)	 AG	114458-114529	GT	TTG
(GAC)	 AG	114665-114719	GT	GGG
(GCG)	 AG	114861-114997	GT	AGG
(GTG)	 AG	115280-115383	GT	AAG
(GGC)	 AG	115511-115660	GT	AGG
(GTT)	 AG	116348-116411	GT	CTG
(GTG)	 AG	116617-116695	GT	AGG
(CCC)	 AG	117337-117548	GT	AGG
(GAG)	 AG	117812-117919	GT	AGG
(TAC)	 AG	118052-118115	GT	GGG
(TAT)	 AG	118511-118692	GT	AGG
(TGT)	 AG	118783-118890	GT	TGG
(GAG)	 AG	119211-119306	CC	GAC
-recovered pasa_asmbl_5657.p1, terminal, 119211, 119306
-recovered pasa_asmbl_5657.p1, internal, 114458, 114529
-recovered pasa_asmbl_5657.p1, internal, 114665, 114719
-recovered pasa_asmbl_5657.p1, internal, 114861, 114997
-recovered pasa_asmbl_5657.p1, internal, 115280, 115383
-recovered pasa_asmbl_5657.p1, internal, 115511, 115660
-recovered pasa_asmbl_5657.p1, internal, 116348, 116411
-recovered pasa_asmbl_5657.p1, internal, 116617, 116695
-recovered pasa_asmbl_5657.p1, internal, 117337, 117548
-recovered pasa_asmbl_5657.p1, internal, 117812, 117919
-recovered pasa_asmbl_5657.p1, internal, 118052, 118115
-recovered pasa_asmbl_5657.p1, internal, 118511, 118692
-recovered pasa_asmbl_5657.p1, internal, 118783, 118890
Valid prediction for GlimmerHMM_glimmerT_27337-T1
Couldn't classify 143141, 143440
Sorry, prediction pasa_asmbl_6248.p1 fails validation.
(GAC)	 CA	143141-143440	GG	AAG
Valid prediction for snap_scaffold_11-snap.1628-T1
Valid prediction for Augustus_model.g18082.t1
Valid prediction for GlimmerHMM_glimmerT_27329-T1
Valid prediction for GlimmerHMM_glimmerT_27344-T1
Valid prediction for HiQ_model.g18092.t1
Valid prediction for GlimmerHMM_glimmerT_27332-T1
Valid prediction for snap_scaffold_11-snap.1658-T1
Valid prediction for snap_scaffold_11-snap.1645-T1
Valid prediction for HiQ_model.g18088.t1
Valid prediction for GlimmerHMM_glimmerT_27325-T1
Valid prediction for pasa_asmbl_5665.p1
Valid prediction for Augustus_model.g18086.t1
Valid prediction for snap_scaffold_11-snap.1629-T1
Valid prediction for snap_scaffold_11-snap.1650-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_11-snap.1644-T1
Valid prediction for GlimmerHMM_glimmerT_27323-T1
Valid prediction for snap_scaffold_11-snap.1660-T1
Valid prediction for snap_scaffold_11-snap.1640-T1
Valid prediction for snap_scaffold_11-snap.1646-T1
Valid prediction for GlimmerHMM_glimmerT_27333-T1
Valid prediction for Augustus_model.g18083.t1
Valid prediction for GlimmerHMM_glimmerT_27321-T1
Valid prediction for GlimmerHMM_glimmerT_27343-T1
Valid prediction for Augustus_model.g18089.t1
Couldn't classify 100676, 100777
Couldn't classify 101101, 101213
Sorry, prediction pasa_asmbl_7329.p1 fails validation.
(CGC)	 GG	100676-100777	GT	TGG
(GCC)	 AG	100883-100967	GT	AGG
(TGT)	 AG	101101-101213	GG	GGG
-recovered pasa_asmbl_7329.p1, internal, 100883, 100967
Valid prediction for snap_scaffold_11-snap.1630-T1
Valid prediction for snap_scaffold_11-snap.1652-T1
Valid prediction for GlimmerHMM_glimmerT_27324-T1
Valid prediction for GlimmerHMM_glimmerT_27336-T1
Valid prediction for snap_scaffold_11-snap.1653-T1
Valid prediction for Augustus_model.g18090.t1
Couldn't classify 96941, 96992
Couldn't classify 98664, 98763
Sorry, prediction pasa_asmbl_7378.p1 fails validation.
(TTC)	 CA	96941-96992	GT	AGG
(GAG)	 AG	97381-97518	GT	TGG
(ATG)	 AG	98005-98050	GT	AGG
(GAA)	 AG	98664-98763	GG	CCG
add_exon() Sorry, pasa_asmbl_7378.p1 98005-98050-initial-1 is invalid.
-recovered pasa_asmbl_7378.p1, initial, 98005, 98050
-recovered pasa_asmbl_7378.p1, internal, 97381, 97518
-recovered pasa_asmbl_7378.p1, internal, 98005, 98050
Valid prediction for GlimmerHMM_glimmerT_27331-T1
Valid prediction for Augustus_model.g18087.t1
Valid prediction for GlimmerHMM_glimmerT_27326-T1
Valid prediction for snap_scaffold_11-snap.1627-T1
Valid prediction for snap_scaffold_11-snap.1636-T1
Valid prediction for CodingQuarry_transcript_8109-T1
Valid prediction for snap_scaffold_11-snap.1654-T1
Valid prediction for snap_scaffold_11-snap.1649-T1
Valid prediction for CodingQuarry_transcript_8108-T1
Couldn't classify 113827, 113997
Couldn't classify 116416, 116565
Sorry, prediction pasa_asmbl_6756.p1 fails validation.
(GGT)	 GA	113827-113997	GT	AGG
(GAC)	 AG	115581-115883	GT	AGG
(AAT)	 AG	116416-116565	CA	GCC
-recovered pasa_asmbl_6756.p1, internal, 115581, 115883
Valid prediction for GlimmerHMM_glimmerT_27327-T1
Valid prediction for snap_scaffold_11-snap.1663-T1
Valid prediction for snap_scaffold_11-snap.1642-T1
Valid prediction for snap_scaffold_11-snap.1664-T1
Valid prediction for CodingQuarry_transcript_8110-T1
Valid prediction for snap_scaffold_11-snap.1647-T1
Couldn't classify 112546, 113511
Sorry, prediction pasa_asmbl_7304.p1 fails validation.
(AAG)	 TG	112546-113511	CA	TCC
Couldn't classify 116647, 116764
Sorry, prediction pasa_asmbl_6754.p1 fails validation.
(CGT)	 TC	116647-116764	GT	TAG
(ACA)	 AG	117067-117133	GT	CCG
(GCG)	 AG	118909-119051	GT	AGG
(TGG)	 AG	119279-119382	GT	TGG
(GGA)	 AG	120100-120175	GT	TGG
(GGT)	 AG	120832-120920	GT	TGG
(GTG)	 AG	121163-121306	GT	AGG
(AGC)	 AG	121706-121831	GT	ATG
(GCT)	 AG	122380-122552	GT	AGG
(AGT)	 AG	123374-123614	GG	GAG
-recovered pasa_asmbl_6754.p1, terminal, 123374, 123614
-recovered pasa_asmbl_6754.p1, internal, 117067, 117133
-recovered pasa_asmbl_6754.p1, internal, 118909, 119051
-recovered pasa_asmbl_6754.p1, internal, 119279, 119382
-recovered pasa_asmbl_6754.p1, internal, 120100, 120175
-recovered pasa_asmbl_6754.p1, internal, 120832, 120920
-recovered pasa_asmbl_6754.p1, internal, 121163, 121306
-recovered pasa_asmbl_6754.p1, internal, 121706, 121831
-recovered pasa_asmbl_6754.p1, internal, 122380, 122552
Valid prediction for snap_scaffold_11-snap.1632-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.1639-T1
Valid prediction for snap_scaffold_11-snap.1633-T1
Valid prediction for snap_scaffold_11-snap.1656-T1
Valid prediction for Augustus_model.g18097.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6366, rend_intergenic: 2936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28027, rend_intergenic: 12818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35136, rend_intergenic: 29547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51387, rend_intergenic: 47698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55439, rend_intergenic: 54464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58559, rend_intergenic: 57007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64917, rend_intergenic: 60255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101085, rend_intergenic: 98351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116817, rend_intergenic: 109499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119452, rend_intergenic: 117303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140565, rend_intergenic: 123988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161038, rend_intergenic: 155644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181970, rend_intergenic: 162855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183868
-exon list size: 479


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.5    
1.7    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
5.8    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.4    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.8    
20.0    
20.2    
20.4    
20.6    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.8    
57.0    
57.2    
57.4    
57.6    
57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
59.0    
59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.5    
60.7    
60.9    
61.1    
61.3    
61.5    
61.7    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.2    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 6366, rend_intergenic: 2936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28027, rend_intergenic: 12818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35136, rend_intergenic: 29547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51387, rend_intergenic: 47698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55439, rend_intergenic: 54464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58559, rend_intergenic: 57007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64917, rend_intergenic: 60255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101085, rend_intergenic: 98351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116817, rend_intergenic: 109499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119452, rend_intergenic: 117303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140565, rend_intergenic: 123988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161038, rend_intergenic: 155644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181970, rend_intergenic: 162855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support