-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_618997-840022

-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_51930-T1
Valid prediction for snap_scaffold_24-snap.180-T1
Valid prediction for GlimmerHMM_glimmerT_51921-T1
Valid prediction for snap_scaffold_24-snap.166-T1
Valid prediction for snap_scaffold_24-snap.187-T1
Couldn't classify 76429, 76501
Couldn't classify 79534, 79626
Sorry, prediction pasa_asmbl_32034.p1 fails validation.
(GAG)	 AC	76429-76501	GT	AGG
(GAG)	 AG	76970-77076	GT	AGG
(GAG)	 AG	78698-78883	GT	AGG
(AAC)	 AG	79301-79417	GT	AGG
(CAA)	 AG	79534-79626	AC	ACA
-recovered pasa_asmbl_32034.p1, internal, 76970, 77076
-recovered pasa_asmbl_32034.p1, internal, 78698, 78883
-recovered pasa_asmbl_32034.p1, internal, 79301, 79417
Valid prediction for snap_scaffold_24-snap.190-T1
Valid prediction for snap_scaffold_24-snap.194-T1
Valid prediction for CodingQuarry_transcript_37223-T1
Valid prediction for snap_scaffold_24-snap.173-T1
Valid prediction for snap_scaffold_24-snap.171-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_51917-T1
Valid prediction for GlimmerHMM_glimmerT_51918-T1
Couldn't classify 101158, 101190
Sorry, prediction pasa_asmbl_32041.p1 fails validation.
(CAA)	 AT	101158-101190	GT	TGG
(CTT)	 AG	101499-101566	GT	AGG
(CAT)	 AG	101936-101966	GT	AGG
(TAT)	 AG	102086-102145	GT	TGG
(CTG)	 AG	103305-103430	TG	GAT
-recovered pasa_asmbl_32041.p1, terminal, 103305, 103430
-recovered pasa_asmbl_32041.p1, internal, 101499, 101566
-recovered pasa_asmbl_32041.p1, internal, 101936, 101966
-recovered pasa_asmbl_32041.p1, internal, 102086, 102145
Valid prediction for Augustus_model.g34613.t1
Valid prediction for CodingQuarry_transcript_37220-T1
Valid prediction for GlimmerHMM_glimmerT_51906-T1
Valid prediction for snap_scaffold_24-snap.161-T1
Valid prediction for CodingQuarry_transcript_37219-T1
Valid prediction for Augustus_model.g34616.t1
Valid prediction for GlimmerHMM_glimmerT_51916-T1
Valid prediction for GlimmerHMM_glimmerT_51923-T1
Valid prediction for CodingQuarry_transcript_37224-T1
Valid prediction for GlimmerHMM_glimmerT_51910-T1
Valid prediction for snap_scaffold_24-snap.179-T1
Couldn't classify 49739, 49847
Couldn't classify 51581, 51691
Sorry, prediction pasa_asmbl_32032.p1 fails validation.
(GAG)	 CC	49739-49847	GT	GGG
(ATG)	 AG	50353-50478	GT	AGG
(AGG)	 AG	50896-50999	GT	TGG
(TCC)	 AG	51284-51397	GT	AGG
(GGT)	 AG	51581-51691	GC	CGG
-recovered pasa_asmbl_32032.p1, initial, 50353, 50478
-recovered pasa_asmbl_32032.p1, internal, 50353, 50478
-recovered pasa_asmbl_32032.p1, internal, 50896, 50999
-recovered pasa_asmbl_32032.p1, internal, 51284, 51397
-recovered pasa_asmbl_32032.p1, internal, 51581, 51691
Valid prediction for GlimmerHMM_glimmerT_51911-T1
Valid prediction for GlimmerHMM_glimmerT_51915-T1
Valid prediction for HiQ_model.g34610.t1
Valid prediction for snap_scaffold_24-snap.182-T1
Valid prediction for snap_scaffold_24-snap.155-T1
Valid prediction for snap_scaffold_24-snap.163-T1
Valid prediction for snap_scaffold_24-snap.191-T1
Valid prediction for snap_scaffold_24-snap.184-T1
Valid prediction for snap_scaffold_24-snap.177-T1
Valid prediction for Augustus_model.g34620.t1
Valid prediction for snap_scaffold_24-snap.181-T1
Valid prediction for snap_scaffold_24-snap.197-T1
Valid prediction for snap_scaffold_24-snap.193-T1
Valid prediction for snap_scaffold_24-snap.164-T1
Valid prediction for Augustus_model.g34614.t1
Valid prediction for snap_scaffold_24-snap.153-T1
Valid prediction for Augustus_model.g34611.t1
Valid prediction for snap_scaffold_24-snap.170-T1
Couldn't classify 89695, 89757
Couldn't classify 91762, 91897
Sorry, prediction pasa_asmbl_32036.p1 fails validation.
(TAC)	 GG	89695-89757	GT	AGG
(GCT)	 AG	91179-91314	GT	AGG
(AGC)	 AG	91463-91625	GT	CAG
(CGT)	 AG	91762-91897	AA	TGA
-recovered pasa_asmbl_32036.p1, internal, 91179, 91314
-recovered pasa_asmbl_32036.p1, internal, 91463, 91625
Couldn't classify 208987, 209343
Sorry, prediction pasa_asmbl_32050.p1 fails validation.
(CAG)	 CC	208987-209343	GT	AGG
(GAT)	 AG	209526-209675	GT	GAG
-recovered pasa_asmbl_32050.p1, terminal, 209526, 209675
-recovered pasa_asmbl_32050.p1, internal, 209526, 209675
Valid prediction for HiQ_model.g34615.t1
Valid prediction for snap_scaffold_24-snap.188-T1
Valid prediction for Augustus_model.g34619.t1
Couldn't classify 35736, 35802
Couldn't classify 35905, 36107
Sorry, prediction CodingQuarry_transcript_37221-T1 fails validation.
(ATG)	 CT	35736-35802	CT	GCC
(CTG)	 GC	35905-36107	GC	AAG
Valid prediction for GlimmerHMM_glimmerT_51928-T1
Valid prediction for GlimmerHMM_glimmerT_51913-T1
Valid prediction for GlimmerHMM_glimmerT_51908-T1
Valid prediction for pasa_asmbl_32038.p1
Valid prediction for pasa_asmbl_32028.p1
Valid prediction for pasa_asmbl_32650.p1
Valid prediction for Augustus_model.g34612.t1
Valid prediction for GlimmerHMM_glimmerT_51926-T1
Valid prediction for GlimmerHMM_glimmerT_51909-T1
Valid prediction for HiQ_model.g34609.t1
Valid prediction for snap_scaffold_24-snap.174-T1
Valid prediction for GlimmerHMM_glimmerT_51920-T1
Valid prediction for snap_scaffold_24-snap.176-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_51919-T1
Valid prediction for Augustus_model.g34618.t1
Valid prediction for snap_scaffold_24-snap.157-T1
Valid prediction for snap_scaffold_24-snap.165-T1
Valid prediction for snap_scaffold_24-snap.200-T1
Valid prediction for Augustus_model.g34608.t1
Valid prediction for snap_scaffold_24-snap.159-T1
Valid prediction for snap_scaffold_24-snap.172-T1
Valid prediction for GlimmerHMM_glimmerT_51922-T1
Valid prediction for snap_scaffold_24-snap.167-T1
Valid prediction for snap_scaffold_24-snap.156-T1
Valid prediction for snap_scaffold_24-snap.175-T1
Couldn't classify 108181, 108229
Sorry, prediction pasa_asmbl_32705.p1 fails validation.
(GGG)	 TG	108181-108229	GT	AGG
(AGC)	 AG	110363-110534	GT	AGG
(TGG)	 AG	110656-110877	GT	AGG
(TGA)	 AG	110988-111938	GT	AGG
(AGC)	 AG	112287-112468	GT	TGG
(AAA)	 AG	112597-112764	GT	AGG
(GAG)	 AG	113002-113132	GT	AGG
(GTA)	 AG	113307-113444	GT	ATG
(TGT)	 AG	113874-114017	GG	GAG
-recovered pasa_asmbl_32705.p1, terminal, 113874, 114017
-recovered pasa_asmbl_32705.p1, internal, 110363, 110534
-recovered pasa_asmbl_32705.p1, internal, 110656, 110877
-recovered pasa_asmbl_32705.p1, internal, 110988, 111938
-recovered pasa_asmbl_32705.p1, internal, 112287, 112468
-recovered pasa_asmbl_32705.p1, internal, 112597, 112764
-recovered pasa_asmbl_32705.p1, internal, 113002, 113132
-recovered pasa_asmbl_32705.p1, internal, 113307, 113444
Valid prediction for snap_scaffold_24-snap.189-T1
Valid prediction for snap_scaffold_24-snap.169-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.185-T1
Valid prediction for snap_scaffold_24-snap.183-T1
Valid prediction for snap_scaffold_24-snap.178-T1
Valid prediction for GlimmerHMM_glimmerT_51927-T1
Valid prediction for GlimmerHMM_glimmerT_51929-T1
Valid prediction for snap_scaffold_24-snap.195-T1
Valid prediction for snap_scaffold_24-snap.192-T1
Valid prediction for GlimmerHMM_glimmerT_51907-T1
Valid prediction for snap_scaffold_24-snap.162-T1
Valid prediction for GlimmerHMM_glimmerT_51912-T1
Valid prediction for GlimmerHMM_glimmerT_51924-T1
Valid prediction for GlimmerHMM_glimmerT_51914-T1
Valid prediction for snap_scaffold_24-snap.158-T1
Valid prediction for snap_scaffold_24-snap.168-T1
Valid prediction for snap_scaffold_24-snap.198-T1
Valid prediction for GlimmerHMM_glimmerT_51931-T1
Valid prediction for snap_scaffold_24-snap.196-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.160-T1
Valid prediction for HiQ_model.g34617.t1
Valid prediction for snap_scaffold_24-snap.154-T1
Valid prediction for GlimmerHMM_glimmerT_51925-T1
Valid prediction for snap_scaffold_24-snap.186-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6395, rend_intergenic: 4853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10732, rend_intergenic: 6931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23986, rend_intergenic: 10876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34310, rend_intergenic: 31656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51739, rend_intergenic: 49555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53313, rend_intergenic: 51789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83911, rend_intergenic: 55120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94173, rend_intergenic: 93035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110653, rend_intergenic: 107203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171339, rend_intergenic: 169470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190361, rend_intergenic: 187623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206238, rend_intergenic: 196412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208577, rend_intergenic: 206681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211515, rend_intergenic: 208648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220437, rend_intergenic: 216105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 221026
-exon list size: 475


building trellis

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20.8    
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23.9    
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24.5    
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25.8    
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27.7    
27.9    
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28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
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53.7    
53.9    
54.1    
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54.7    
54.9    
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55.6    
55.8    
56.0    
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56.4    
56.6    
56.8    
57.0    
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57.4    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
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70.6    
70.9    
71.1    
71.3    
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71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
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    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 6395, rend_intergenic: 4853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10732, rend_intergenic: 6931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23986, rend_intergenic: 10876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34310, rend_intergenic: 31656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51739, rend_intergenic: 49555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53313, rend_intergenic: 51789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83911, rend_intergenic: 55120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94173, rend_intergenic: 93035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110653, rend_intergenic: 107203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171339, rend_intergenic: 169470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190361, rend_intergenic: 187623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206238, rend_intergenic: 196412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208577, rend_intergenic: 206681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211515, rend_intergenic: 208648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220437, rend_intergenic: 216105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 209434 - 221026
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
22.2    
27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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

-building DP trellis

-building trellis in range 209676 - 221026
-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 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 210319 - 221026
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal

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