-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_882479-1105190

-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_25-snap.219-T1
Valid prediction for Augustus_model.g35609.t1
Couldn't classify 48265, 48372
Sorry, prediction pasa_asmbl_33354.p1 fails validation.
(ATT)	 AG	48265-48372	GT	TGG
(GAG)	 AG	48698-48858	GT	AAG
(ATT)	 AG	49016-49118	TC	GAT
add_exon() Sorry, pasa_asmbl_33354.p1 48698-48858-terminal-2 is invalid.
-recovered pasa_asmbl_33354.p1, terminal, 48698, 48858
-recovered pasa_asmbl_33354.p1, terminal, 49016, 49118
-recovered pasa_asmbl_33354.p1, internal, 48265, 48372
-recovered pasa_asmbl_33354.p1, internal, 48698, 48858
Valid prediction for Augustus_model.g35615.t1
Valid prediction for snap_scaffold_25-snap.210-T1
Valid prediction for snap_scaffold_25-snap.206-T1
Valid prediction for snap_scaffold_25-snap.212-T1
Valid prediction for snap_scaffold_25-snap.204-T1
Valid prediction for Augustus_model.g35614.t1
Valid prediction for Augustus_model.g35606.t1
Couldn't classify 96002, 96095
Couldn't classify 96237, 96481
Sorry, prediction pasa_asmbl_33359.p1 fails validation.
(CAG)	 CT	96002-96095	GT	AGG
(ACT)	 AG	96237-96481	GA	AGG
Couldn't classify 100131, 100301
Couldn't classify 102870, 102941
Sorry, prediction pasa_asmbl_33363.p1 fails validation.
(TCT)	 TC	100131-100301	GT	AGG
(GAG)	 AG	101091-101200	GT	TAG
(CGT)	 AG	101833-101974	GT	AGG
(CCG)	 AG	102870-102941	TA	GGT
-recovered pasa_asmbl_33363.p1, internal, 101091, 101200
-recovered pasa_asmbl_33363.p1, internal, 101833, 101974
Valid prediction for GlimmerHMM_glimmerT_53557-T1
Valid prediction for GlimmerHMM_glimmerT_53568-T1
Valid prediction for Augustus_model.g35610.t1
Valid prediction for snap_scaffold_25-snap.190-T1
Valid prediction for snap_scaffold_25-snap.184-T1
Valid prediction for GlimmerHMM_glimmerT_53554-T1
Valid prediction for GlimmerHMM_glimmerT_53559-T1
Valid prediction for snap_scaffold_25-snap.200-T1
Valid prediction for snap_scaffold_25-snap.209-T1
Valid prediction for snap_scaffold_25-snap.214-T1
Valid prediction for snap_scaffold_25-snap.215-T1
Valid prediction for snap_scaffold_25-snap.195-T1
Valid prediction for snap_scaffold_25-snap.178-T1
Valid prediction for GlimmerHMM_glimmerT_53551-T1
Valid prediction for snap_scaffold_25-snap.203-T1
Valid prediction for snap_scaffold_25-snap.208-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53563-T1
Valid prediction for snap_scaffold_25-snap.180-T1
Valid prediction for snap_scaffold_25-snap.193-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.185-T1
Valid prediction for snap_scaffold_25-snap.189-T1
Valid prediction for GlimmerHMM_glimmerT_53565-T1
Valid prediction for snap_scaffold_25-snap.183-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53558-T1
Valid prediction for GlimmerHMM_glimmerT_53556-T1
Valid prediction for GlimmerHMM_glimmerT_53552-T1
Couldn't classify 96596, 96789
Couldn't classify 96925, 97081
Sorry, prediction pasa_asmbl_33361.p1 fails validation.
(GGA)	 AG	96596-96789	GT	AGG
(CTC)	 AG	96925-97081	GT	GGG
-recovered pasa_asmbl_33361.p1, internal, 96596, 96789
-recovered pasa_asmbl_33361.p1, internal, 96925, 97081
Valid prediction for GlimmerHMM_glimmerT_53560-T1
Valid prediction for snap_scaffold_25-snap.199-T1
Valid prediction for snap_scaffold_25-snap.216-T1
Valid prediction for snap_scaffold_25-snap.197-T1
Valid prediction for snap_scaffold_25-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_53571-T1
Valid prediction for GlimmerHMM_glimmerT_53572-T1
Valid prediction for CodingQuarry_transcript_38638-T1
Valid prediction for snap_scaffold_25-snap.181-T1
Valid prediction for Augustus_model.g35611.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_53569-T1
Valid prediction for Augustus_model.g35617.t1
Valid prediction for Augustus_model.g35604.t1
Valid prediction for snap_scaffold_25-snap.217-T1
Valid prediction for GlimmerHMM_glimmerT_53564-T1
Valid prediction for snap_scaffold_25-snap.207-T1
Valid prediction for HiQ_model.g35613.t1
Valid prediction for snap_scaffold_25-snap.188-T1
Valid prediction for snap_scaffold_25-snap.218-T1
Valid prediction for Augustus_model.g35616.t1
Valid prediction for GlimmerHMM_glimmerT_53570-T1
Valid prediction for CodingQuarry_transcript_38639-T1
Valid prediction for snap_scaffold_25-snap.194-T1
Valid prediction for Augustus_model.g35618.t1
Valid prediction for snap_scaffold_25-snap.202-T1
Valid prediction for GlimmerHMM_glimmerT_53550-T1
Valid prediction for HiQ_model.g35612.t1
Valid prediction for GlimmerHMM_glimmerT_53567-T1
Valid prediction for snap_scaffold_25-snap.186-T1
Valid prediction for snap_scaffold_25-snap.187-T1
Valid prediction for pasa_asmbl_34016.p1
Valid prediction for GlimmerHMM_glimmerT_53561-T1
Valid prediction for snap_scaffold_25-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_53562-T1
Couldn't classify 105328, 105648
Sorry, prediction pasa_asmbl_34020.p1 fails validation.
(GCT)	 AA	105328-105648	GT	AGG
(GTC)	 AG	105744-106625	TT	GAT
-recovered pasa_asmbl_34020.p1, terminal, 105744, 106625
Valid prediction for GlimmerHMM_glimmerT_53548-T1
Valid prediction for snap_scaffold_25-snap.201-T1
Valid prediction for snap_scaffold_25-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_53566-T1
Valid prediction for snap_scaffold_25-snap.211-T1
Couldn't classify 166405, 166492
Sorry, prediction pasa_asmbl_34014.p1 fails validation.
(GGG)	 CT	166405-166492	GT	AGG
(GTT)	 AG	166945-167124	GT	ACG
(GAA)	 AG	167788-167896	GT	GGG
(GTA)	 AG	168693-168769	GT	GGG
(CGC)	 AG	169274-169456	GT	AAG
(TTT)	 AG	169993-170178	GT	ACG
(AAA)	 AG	170602-170799	GT	AGG
(AGA)	 AG	170882-171049	GT	AGG
(GGA)	 AG	171142-171309	GT	AGG
(GAA)	 AG	171469-171627	GT	CCG
(AAA)	 AG	172055-172231	GT	ACG
(CTA)	 AG	172470-172664	GT	AAG
(CAG)	 AG	172817-172881	AC	AAA
add_exon() Sorry, pasa_asmbl_34014.p1 169274-169456-terminal-1 is invalid.
-recovered pasa_asmbl_34014.p1, terminal, 169274, 169456
-recovered pasa_asmbl_34014.p1, terminal, 172817, 172881
-recovered pasa_asmbl_34014.p1, internal, 166945, 167124
-recovered pasa_asmbl_34014.p1, internal, 167788, 167896
-recovered pasa_asmbl_34014.p1, internal, 168693, 168769
-recovered pasa_asmbl_34014.p1, internal, 169274, 169456
-recovered pasa_asmbl_34014.p1, internal, 169993, 170178
-recovered pasa_asmbl_34014.p1, internal, 170602, 170799
-recovered pasa_asmbl_34014.p1, internal, 170882, 171049
-recovered pasa_asmbl_34014.p1, internal, 171142, 171309
-recovered pasa_asmbl_34014.p1, internal, 171469, 171627
-recovered pasa_asmbl_34014.p1, internal, 172055, 172231
-recovered pasa_asmbl_34014.p1, internal, 172470, 172664
Valid prediction for Augustus_model.g35607.t1
Valid prediction for Augustus_model.g35608.t1
Couldn't classify 213115, 213157
Couldn't classify 216725, 216825
Sorry, prediction pasa_asmbl_34013.p1 fails validation.
(GCT)	 GG	213115-213157	GT	TGG
(CAA)	 AG	214704-215003	GT	GGG
(GTC)	 AG	216725-216825	GG	TGG
-recovered pasa_asmbl_34013.p1, internal, 214704, 215003
Valid prediction for GlimmerHMM_glimmerT_53555-T1
Valid prediction for Augustus_model.g35605.t1
Valid prediction for GlimmerHMM_glimmerT_53549-T1
Valid prediction for snap_scaffold_25-snap.196-T1
Couldn't classify 79811, 79836
Sorry, prediction pasa_asmbl_34022.p1 fails validation.
(TTA)	 TG	79811-79836	GT	TGG
(TGA)	 AG	81563-81704	GT	AGG
(GTG)	 AG	82159-82361	GT	TGG
(GAA)	 AG	82650-82714	GT	AGG
(GCG)	 AG	83037-83201	GT	AGG
(GAA)	 AG	83316-83338	AC	AAA
-recovered pasa_asmbl_34022.p1, terminal, 83316, 83338
-recovered pasa_asmbl_34022.p1, internal, 81563, 81704
-recovered pasa_asmbl_34022.p1, internal, 82159, 82361
-recovered pasa_asmbl_34022.p1, internal, 82650, 82714
-recovered pasa_asmbl_34022.p1, internal, 83037, 83201
Valid prediction for snap_scaffold_25-snap.192-T1
Valid prediction for snap_scaffold_25-snap.213-T1
Valid prediction for GlimmerHMM_glimmerT_53553-T1
Valid prediction for pasa_asmbl_34015.p1
Valid prediction for snap_scaffold_25-snap.205-T1
Valid prediction for snap_scaffold_25-snap.198-T1
Valid prediction for snap_scaffold_25-snap.179-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7404, rend_intergenic: 5780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8937, rend_intergenic: 7786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17161, rend_intergenic: 12198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28209, rend_intergenic: 17401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49118, rend_intergenic: 36589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65750, rend_intergenic: 60241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77490, rend_intergenic: 72329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84060, rend_intergenic: 77576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90527, rend_intergenic: 84074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91942, rend_intergenic: 91053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109778, rend_intergenic: 93988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135079, rend_intergenic: 132190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155486, rend_intergenic: 140104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171523, rend_intergenic: 155729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175485, rend_intergenic: 173256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195698, rend_intergenic: 183316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208289, rend_intergenic: 195748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217858, rend_intergenic: 215971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222712
-exon list size: 401


building trellis

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14.4    
14.6    
14.9    
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16.6    
16.9    
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17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
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22.3    
22.6    
22.8    
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23.3    
23.6    
23.8    
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24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.8    
27.0    
27.3    
27.5    
27.8    
28.0    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.1    
52.4    
52.6    
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53.1    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.1    
57.3    
57.6    
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58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
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63.0    
63.3    
63.5    
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64.0    
64.3    
64.5    
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65.0    
65.3    
65.5    
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66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
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68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
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70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
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72.0    
72.2    
72.5    
72.7    
73.0    
73.2    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
75.9    
76.2    
76.4    
76.7    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
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78.7    
78.9    
79.2    
79.4    
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80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
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81.9    
82.1    
82.4    
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82.9    
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83.4    
83.6    
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91.6    
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92.3    
92.6    
92.8    
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93.8    
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94.3    
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95.3    
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96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 7404, rend_intergenic: 5780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8937, rend_intergenic: 7786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17161, rend_intergenic: 12198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28209, rend_intergenic: 17401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49118, rend_intergenic: 36589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65750, rend_intergenic: 60241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77490, rend_intergenic: 72329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84060, rend_intergenic: 77576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90527, rend_intergenic: 84074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91942, rend_intergenic: 91053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109778, rend_intergenic: 93988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135079, rend_intergenic: 132190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155486, rend_intergenic: 140104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171523, rend_intergenic: 155729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175485, rend_intergenic: 173256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195698, rend_intergenic: 183316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208289, rend_intergenic: 195748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217858, rend_intergenic: 215971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support