-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_4893845-5081929

-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: +)Couldn't classify 102868, 102979
Couldn't classify 108251, 108441
Sorry, prediction pasa_asmbl_30054.p1 fails validation.
(TTC)	 AG	102868-102979	GT	AGG
(TCC)	 AG	103557-103668	GT	CGG
(AAT)	 AG	104861-104976	GT	ACG
(GTC)	 AG	105196-105373	GT	CGG
(GCT)	 AG	105553-105730	GT	AGG
(GTG)	 AG	106321-106482	GT	AGG
(GCA)	 AG	106975-107075	GT	AAG
(GAA)	 AG	107825-108063	GT	CTG
(CCT)	 AG	108251-108441	TG	GGT
-recovered pasa_asmbl_30054.p1, internal, 102868, 102979
-recovered pasa_asmbl_30054.p1, internal, 103557, 103668
-recovered pasa_asmbl_30054.p1, internal, 104861, 104976
-recovered pasa_asmbl_30054.p1, internal, 105196, 105373
-recovered pasa_asmbl_30054.p1, internal, 105553, 105730
-recovered pasa_asmbl_30054.p1, internal, 106321, 106482
-recovered pasa_asmbl_30054.p1, internal, 106975, 107075
-recovered pasa_asmbl_30054.p1, internal, 107825, 108063
Valid prediction for GlimmerHMM_glimmerT_49387-T1
Couldn't classify 47043, 47140
Couldn't classify 51220, 51234
Sorry, prediction pasa_asmbl_30049.p1 fails validation.
(AGA)	 AC	47043-47140	GT	AGG
(GTT)	 AG	48290-48455	GT	AGG
(AAC)	 AG	48756-48930	GT	CCG
(TGT)	 AG	49611-49748	GT	GTG
(TGG)	 AG	50252-50364	GT	TGG
(ATC)	 AG	50590-50730	GT	AAG
(GCC)	 AG	50908-51063	GT	AGG
(CTT)	 AG	51220-51234	GA	GAG
-recovered pasa_asmbl_30049.p1, internal, 48290, 48455
-recovered pasa_asmbl_30049.p1, internal, 48756, 48930
-recovered pasa_asmbl_30049.p1, internal, 49611, 49748
-recovered pasa_asmbl_30049.p1, internal, 50252, 50364
-recovered pasa_asmbl_30049.p1, internal, 50590, 50730
-recovered pasa_asmbl_30049.p1, internal, 50908, 51063
Valid prediction for GlimmerHMM_glimmerT_49376-T1
Valid prediction for GlimmerHMM_glimmerT_49382-T1
Valid prediction for snap_scaffold_22-snap.943-T1
Valid prediction for GlimmerHMM_glimmerT_49377-T1
Valid prediction for HiQ_model.g32954.t1
Valid prediction for GlimmerHMM_glimmerT_49381-T1
Valid prediction for GlimmerHMM_glimmerT_49392-T1
Valid prediction for GlimmerHMM_glimmerT_49393-T1
Valid prediction for snap_scaffold_22-snap.922-T1
Valid prediction for snap_scaffold_22-snap.932-T1
Valid prediction for GlimmerHMM_glimmerT_49385-T1
Valid prediction for GlimmerHMM_glimmerT_49394-T1
Valid prediction for GlimmerHMM_glimmerT_49383-T1
Valid prediction for snap_scaffold_22-snap.939-T1
Valid prediction for GlimmerHMM_glimmerT_49391-T1
Valid prediction for snap_scaffold_22-snap.940-T1
Valid prediction for CodingQuarry_transcript_34156-T1
Valid prediction for GlimmerHMM_glimmerT_49379-T1
Valid prediction for snap_scaffold_22-snap.928-T1
Couldn't classify 51256, 51323
Sorry, prediction pasa_asmbl_30050.p2 fails validation.
(ACA)	 TG	51256-51323	GT	AGG
(GTG)	 AG	52928-53261	CA	AAC
-recovered pasa_asmbl_30050.p2, terminal, 52928, 53261
Valid prediction for Augustus_model.g32961.t1
Valid prediction for GlimmerHMM_glimmerT_49398-T1
Valid prediction for GlimmerHMM_glimmerT_49399-T1
Valid prediction for snap_scaffold_22-snap.925-T1
Valid prediction for snap_scaffold_22-snap.938-T1
Valid prediction for snap_scaffold_22-snap.915-T1
Valid prediction for snap_scaffold_22-snap.914-T1
Valid prediction for Augustus_model.g32956.t1
Valid prediction for snap_scaffold_22-snap.929-T1
Valid prediction for snap_scaffold_22-snap.930-T1
Valid prediction for snap_scaffold_22-snap.931-T1
Couldn't classify 109400, 109726
Sorry, prediction pasa_asmbl_30055.p2 fails validation.
(CCC)	 CC	109400-109726	AC	AAA
Valid prediction for Augustus_model.g32957.t1
Valid prediction for GlimmerHMM_glimmerT_49400-T1
Valid prediction for GlimmerHMM_glimmerT_49386-T1
Valid prediction for snap_scaffold_22-snap.918-T1
Valid prediction for snap_scaffold_22-snap.919-T1
Valid prediction for snap_scaffold_22-snap.920-T1
Valid prediction for snap_scaffold_22-snap.936-T1
Valid prediction for snap_scaffold_22-snap.913-T1
Valid prediction for CodingQuarry_transcript_34157-T1
Valid prediction for GlimmerHMM_glimmerT_49396-T1
Valid prediction for GlimmerHMM_glimmerT_49395-T1
Valid prediction for GlimmerHMM_glimmerT_49389-T1
Valid prediction for GlimmerHMM_glimmerT_49402-T1
Valid prediction for snap_scaffold_22-snap.924-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_22-snap.944-T1
Valid prediction for GlimmerHMM_glimmerT_49388-T1
Valid prediction for snap_scaffold_22-snap.934-T1
Valid prediction for snap_scaffold_22-snap.937-T1
Valid prediction for snap_scaffold_22-snap.917-T1
Valid prediction for GlimmerHMM_glimmerT_49380-T1
Valid prediction for Augustus_model.g32953.t1
Valid prediction for snap_scaffold_22-snap.927-T1
Valid prediction for snap_scaffold_22-snap.942-T1
Valid prediction for snap_scaffold_22-snap.935-T1
Valid prediction for snap_scaffold_22-snap.923-T1
Valid prediction for GlimmerHMM_glimmerT_49403-T1
Valid prediction for snap_scaffold_22-snap.933-T1
Valid prediction for snap_scaffold_22-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_49397-T1
Valid prediction for GlimmerHMM_glimmerT_49384-T1
Valid prediction for GlimmerHMM_glimmerT_49390-T1
Valid prediction for snap_scaffold_22-snap.916-T1
Valid prediction for snap_scaffold_22-snap.941-T1
Valid prediction for Augustus_model.g32960.t1
Valid prediction for GlimmerHMM_glimmerT_49378-T1
Valid prediction for Augustus_model.g32955.t1
Valid prediction for Augustus_model.g32959.t1
Valid prediction for GlimmerHMM_glimmerT_49401-T1
Valid prediction for snap_scaffold_22-snap.921-T1
Valid prediction for Augustus_model.g32958.t1
Valid prediction for pasa_asmbl_30048.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 59860, rend_intergenic: 59857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42414, rend_intergenic: 30123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51414, rend_intergenic: 42606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76928, rend_intergenic: 75308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109726, rend_intergenic: 102405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117945, rend_intergenic: 114896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188085
-exon list size: 248


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.2    
3.6    
4.0    
4.4    
4.8    
5.2    
5.6    
6.0    
6.4    
6.8    
7.2    
7.6    
8.0    
8.4    
8.8    
9.2    
9.6    
10.0    
10.4    
10.8    
11.2    
11.6    
12.0    
12.4    
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13.2    
13.6    
14.0    
14.4    
14.8    
15.2    
15.6    
16.0    
16.4    
16.8    
17.2    
17.6    
18.0    
18.4    
18.8    
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20.0    
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21.6    
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26.0    
26.4    
26.8    
27.2    
27.6    
28.0    
28.4    
28.8    
29.2    
29.6    
30.0    
30.4    
30.8    
31.2    
31.6    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.8    
35.2    
35.6    
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37.6    
38.0    
38.4    
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39.2    
39.6    
40.0    
40.4    
40.8    
41.2    
41.6    
42.0    
42.4    
42.8    
43.2    
43.6    
44.0    
44.4    
44.8    
45.2    
45.6    
46.0    
46.4    
46.8    
47.2    
47.6    
48.0    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
52.0    
52.4    
52.8    
53.2    
53.6    
54.0    
54.4    
54.8    
55.2    
55.6    
56.0    
56.4    
56.8    
57.2    
57.6    
58.0    
58.4    
58.8    
59.2    
59.6    
60.0    
60.4    
60.8    
61.2    
61.6    
62.0    
62.4    
62.8    
63.2    
63.6    
64.0    
64.4    
64.8    
65.2    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.4    
68.8    
69.2    
69.6    
70.0    
70.4    
70.8    
71.2    
71.6    
72.0    
72.4    
72.8    
73.2    
73.6    
74.0    
74.4    
74.8    
75.2    
75.6    
76.0    
76.4    
76.8    
77.2    
77.6    
78.0    
78.4    
78.8    
79.2    
79.6    
80.0    
80.4    
80.8    
81.2    
81.6    
82.0    
82.4    
82.8    
83.2    
83.6    
84.0    
84.4    
84.8    
85.2    
85.6    
86.0    
86.4    
86.8    
87.2    
87.6    
88.0    
88.4    
88.8    
89.2    
89.6    
90.0    
90.4    
90.8    
91.2    
91.6    
92.0    
92.4    
92.8    
93.2    
93.6    
94.0    
94.4    
94.8    
95.2    
95.6    
96.0    
96.4    
96.8    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 26 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 59860, rend_intergenic: 59857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42414, rend_intergenic: 30123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51414, rend_intergenic: 42606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76928, rend_intergenic: 75308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109726, rend_intergenic: 102405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117945, rend_intergenic: 114896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 168386 - 188085
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 168386 - 182183
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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