-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_17806573-18057979

-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_5481-T1
Valid prediction for snap_scaffold_2-snap.3469-T1
Valid prediction for GlimmerHMM_glimmerT_5446-T1
Valid prediction for snap_scaffold_2-snap.3455-T1
Valid prediction for Augustus_model.g3681.t1
Valid prediction for snap_scaffold_2-snap.3462-T1
Couldn't classify 177549, 177576
Sorry, prediction pasa_asmbl_25214.p1 fails validation.
(GTT)	 CA	177549-177576	GT	GGG
(ATG)	 AG	177697-177785	GT	AGG
(GAC)	 AG	178321-178372	GT	AGG
(TTT)	 AG	178480-178577	GT	GGG
(TTA)	 AG	178707-178821	GT	TGG
(GTA)	 AG	178937-179098	GT	GCG
(TGG)	 AG	179209-179282	GT	AGG
(CAA)	 AG	179372-179503	CA	AAC
add_exon() Sorry, pasa_asmbl_25214.p1 177697-177785-initial-1 is invalid.
-recovered pasa_asmbl_25214.p1, initial, 177697, 177785
-recovered pasa_asmbl_25214.p1, terminal, 179372, 179503
-recovered pasa_asmbl_25214.p1, internal, 177697, 177785
-recovered pasa_asmbl_25214.p1, internal, 178321, 178372
-recovered pasa_asmbl_25214.p1, internal, 178480, 178577
-recovered pasa_asmbl_25214.p1, internal, 178707, 178821
-recovered pasa_asmbl_25214.p1, internal, 178937, 179098
-recovered pasa_asmbl_25214.p1, internal, 179209, 179282
Valid prediction for GlimmerHMM_glimmerT_5444-T1
Valid prediction for snap_scaffold_2-snap.3484-T1
Valid prediction for Augustus_model.g3682.t1
Valid prediction for snap_scaffold_2-snap.3453-T1
Valid prediction for GlimmerHMM_glimmerT_5456-T1
Valid prediction for snap_scaffold_2-snap.3466-T1
Valid prediction for pasa_asmbl_25213.p1
Valid prediction for Augustus_model.g3675.t1
Valid prediction for GlimmerHMM_glimmerT_5457-T1
Couldn't classify 147049, 147204
Sorry, prediction pasa_asmbl_25207.p1 fails validation.
(CAG)	 CC	147049-147204	GT	AGG
(ATG)	 AG	147432-147642	GT	TGG
(TGA)	 AG	148152-148353	GT	CTG
(GCA)	 AG	148655-148862	AA	GAA
-recovered pasa_asmbl_25207.p1, initial, 147432, 147642
-recovered pasa_asmbl_25207.p1, terminal, 148655, 148862
-recovered pasa_asmbl_25207.p1, internal, 147432, 147642
-recovered pasa_asmbl_25207.p1, internal, 148152, 148353
Valid prediction for CodingQuarry_transcript_28833-T1
Valid prediction for CodingQuarry_transcript_28835-T1
Valid prediction for Augustus_model.g3687.t1
Valid prediction for snap_scaffold_2-snap.3497-T1
Valid prediction for snap_scaffold_2-snap.3488-T1
Valid prediction for snap_scaffold_2-snap.3505-T1
Valid prediction for GlimmerHMM_glimmerT_5475-T1
Valid prediction for snap_scaffold_2-snap.3493-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5447-T1
Valid prediction for snap_scaffold_2-snap.3489-T1
Valid prediction for GlimmerHMM_glimmerT_5462-T1
Valid prediction for GlimmerHMM_glimmerT_5466-T1
Valid prediction for HiQ_model.g3688.t1
Valid prediction for Augustus_model.g3683.t1
Valid prediction for snap_scaffold_2-snap.3502-T1
Valid prediction for GlimmerHMM_glimmerT_5459-T1
Valid prediction for snap_scaffold_2-snap.3454-T1
Valid prediction for GlimmerHMM_glimmerT_5470-T1
Valid prediction for snap_scaffold_2-snap.3467-T1
Valid prediction for snap_scaffold_2-snap.3498-T1
Valid prediction for Augustus_model.g3699.t1
Valid prediction for snap_scaffold_2-snap.3461-T1
Valid prediction for GlimmerHMM_glimmerT_5477-T1
Couldn't classify 99673, 99729
Couldn't classify 100867, 100878
Sorry, prediction pasa_asmbl_25199.p1 fails validation.
(AGC)	 AG	99673-99729	GT	GGG
(GCA)	 AG	100360-100484	GT	CAG
(GGA)	 AG	100613-100715	GT	TCG
(ACC)	 AG	100867-100878	AA	GGA
-recovered pasa_asmbl_25199.p1, internal, 99673, 99729
-recovered pasa_asmbl_25199.p1, internal, 100360, 100484
-recovered pasa_asmbl_25199.p1, internal, 100613, 100715
Valid prediction for snap_scaffold_2-snap.3474-T1
Valid prediction for snap_scaffold_2-snap.3471-T1
Valid prediction for GlimmerHMM_glimmerT_5480-T1
Valid prediction for GlimmerHMM_glimmerT_5445-T1
Valid prediction for GlimmerHMM_glimmerT_5461-T1
Valid prediction for CodingQuarry_transcript_28832-T1
Valid prediction for Augustus_model.g3679.t1
Valid prediction for GlimmerHMM_glimmerT_5469-T1
Valid prediction for snap_scaffold_2-snap.3458-T1
Valid prediction for GlimmerHMM_glimmerT_5460-T1
Valid prediction for GlimmerHMM_glimmerT_5453-T1
Valid prediction for Augustus_model.g3695.t1
Valid prediction for GlimmerHMM_glimmerT_5482-T1
Valid prediction for snap_scaffold_2-snap.3499-T1
Valid prediction for snap_scaffold_2-snap.3490-T1
Valid prediction for GlimmerHMM_glimmerT_5452-T1
Valid prediction for snap_scaffold_2-snap.3463-T1
Valid prediction for snap_scaffold_2-snap.3491-T1
Valid prediction for GlimmerHMM_glimmerT_5443-T1
Valid prediction for pasa_asmbl_25212.p1
Valid prediction for Augustus_model.g3674.t1
Valid prediction for HiQ_model.g3694.t1
Valid prediction for snap_scaffold_2-snap.3481-T1
Valid prediction for Augustus_model.g3676.t1
Valid prediction for snap_scaffold_2-snap.3452-T1
Couldn't classify 107443, 107499
Couldn't classify 110863, 110879
Sorry, prediction pasa_asmbl_25200.p1 fails validation.
(CTG)	 TG	107443-107499	GT	GGG
(GTA)	 AG	108483-108591	GT	TGG
(TGT)	 AG	108952-109171	GT	AGG
(AGC)	 AG	109681-109865	GT	GGG
(CCG)	 AG	109996-110091	GT	CAG
(AGA)	 AG	110178-110260	GT	GAG
(GAC)	 AG	110422-110632	GT	CAG
(CCA)	 AG	110863-110879	AA	ACA
-recovered pasa_asmbl_25200.p1, internal, 108483, 108591
-recovered pasa_asmbl_25200.p1, internal, 108952, 109171
-recovered pasa_asmbl_25200.p1, internal, 109681, 109865
-recovered pasa_asmbl_25200.p1, internal, 109996, 110091
-recovered pasa_asmbl_25200.p1, internal, 110178, 110260
-recovered pasa_asmbl_25200.p1, internal, 110422, 110632
Valid prediction for snap_scaffold_2-snap.3460-T1
Valid prediction for CodingQuarry_transcript_28834-T1
Valid prediction for GlimmerHMM_glimmerT_5478-T1
Valid prediction for snap_scaffold_2-snap.3468-T1
Valid prediction for snap_scaffold_2-snap.3504-T1
Couldn't classify 239666, 240596
Sorry, prediction pasa_asmbl_25219.p1 fails validation.
(AGC)	 AA	239666-240596	GT	AGG
(GGA)	 AG	240898-240953	CA	AAC
-recovered pasa_asmbl_25219.p1, terminal, 240898, 240953
Valid prediction for GlimmerHMM_glimmerT_5455-T1
Valid prediction for Augustus_model.g3692.t1
Valid prediction for snap_scaffold_2-snap.3450-T1
Valid prediction for GlimmerHMM_glimmerT_5473-T1
Valid prediction for snap_scaffold_2-snap.3475-T1
Couldn't classify 115324, 115631
Couldn't classify 117040, 117056
Sorry, prediction pasa_asmbl_25204.p1 fails validation.
(CCC)	 CC	115324-115631	GT	AGG
(CCC)	 AG	115940-116157	GT	AGG
(GAG)	 AG	116491-116634	GT	GGG
(GTG)	 AG	117040-117056	CA	GGC
-recovered pasa_asmbl_25204.p1, internal, 115940, 116157
-recovered pasa_asmbl_25204.p1, internal, 116491, 116634
Valid prediction for snap_scaffold_2-snap.3477-T1
Valid prediction for Augustus_model.g3684.t1
Valid prediction for snap_scaffold_2-snap.3473-T1
Valid prediction for snap_scaffold_2-snap.3495-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_2-snap.3457-T1
Valid prediction for HiQ_model.g3677.t1
Valid prediction for GlimmerHMM_glimmerT_5451-T1
Valid prediction for GlimmerHMM_glimmerT_5476-T1
Valid prediction for Augustus_model.g3680.t1
Valid prediction for HiQ_model.g3700.t1
Valid prediction for snap_scaffold_2-snap.3483-T1
Valid prediction for GlimmerHMM_glimmerT_5484-T1
Valid prediction for snap_scaffold_2-snap.3479-T1
Couldn't classify 65735, 65755
Couldn't classify 67036, 67091
Sorry, prediction pasa_asmbl_24007.p1 fails validation.
(TAC)	 CC	65735-65755	GT	AGG
(GTG)	 AG	66091-66196	GT	AGG
(CGG)	 AG	66318-66478	GT	TGG
(TAT)	 AG	66701-66761	GT	AGG
(TGA)	 AG	67036-67091	GC	TGG
-recovered pasa_asmbl_24007.p1, internal, 66091, 66196
-recovered pasa_asmbl_24007.p1, internal, 66318, 66478
-recovered pasa_asmbl_24007.p1, internal, 66701, 66761
-recovered pasa_asmbl_24007.p1, internal, 67036, 67091
Valid prediction for GlimmerHMM_glimmerT_5479-T1
Valid prediction for Augustus_model.g3689.t1
Valid prediction for Augustus_model.g3698.t1
Valid prediction for pasa_asmbl_23753.p1
Valid prediction for Augustus_model.g3696.t1
Couldn't classify 217470, 217567
Sorry, prediction pasa_asmbl_23758.p1 fails validation.
(ATG)	 AT	216599-217340	GT	AGG
(TGC)	 AG	217470-217567	CC	GCC
-recovered pasa_asmbl_23758.p1, initial, 216599, 217340
Valid prediction for snap_scaffold_2-snap.3482-T1
Valid prediction for Augustus_model.g3686.t1
Valid prediction for pasa_asmbl_23763.p1
Valid prediction for pasa_asmbl_23966.p2
Valid prediction for snap_scaffold_2-snap.3480-T1
Valid prediction for snap_scaffold_2-snap.3478-T1
Valid prediction for GlimmerHMM_glimmerT_5450-T1
Valid prediction for snap_scaffold_2-snap.3470-T1
Valid prediction for GlimmerHMM_glimmerT_5474-T1
Valid prediction for snap_scaffold_2-snap.3476-T1
Valid prediction for snap_scaffold_2-snap.3496-T1
Valid prediction for GlimmerHMM_glimmerT_5465-T1
Valid prediction for GlimmerHMM_glimmerT_5448-T1
Valid prediction for GlimmerHMM_glimmerT_5472-T1
Valid prediction for GlimmerHMM_glimmerT_5468-T1
Valid prediction for CodingQuarry_transcript_28836-T1
Valid prediction for CodingQuarry_transcript_28831-T1
Valid prediction for snap_scaffold_2-snap.3506-T1
Valid prediction for pasa_asmbl_23760.p1
Valid prediction for snap_scaffold_2-snap.3503-T1
Valid prediction for snap_scaffold_2-snap.3459-T1
Valid prediction for GlimmerHMM_glimmerT_5483-T1
Valid prediction for GlimmerHMM_glimmerT_5464-T1
Valid prediction for GlimmerHMM_glimmerT_5463-T1
Valid prediction for snap_scaffold_2-snap.3492-T1
Valid prediction for GlimmerHMM_glimmerT_5471-T1
Valid prediction for pasa_asmbl_23759.p1
Valid prediction for pasa_asmbl_23754.p1
Valid prediction for snap_scaffold_2-snap.3501-T1
Valid prediction for GlimmerHMM_glimmerT_5449-T1
Valid prediction for snap_scaffold_2-snap.3456-T1
Valid prediction for Augustus_model.g3685.t1
Valid prediction for CodingQuarry_transcript_28828-T1
Valid prediction for snap_scaffold_2-snap.3486-T1
Valid prediction for snap_scaffold_2-snap.3451-T1
Valid prediction for GlimmerHMM_glimmerT_5458-T1
Valid prediction for snap_scaffold_2-snap.3494-T1
Valid prediction for GlimmerHMM_glimmerT_5467-T1
Valid prediction for Augustus_model.g3690.t1
Valid prediction for snap_scaffold_2-snap.3500-T1
Valid prediction for Augustus_model.g3697.t1
Valid prediction for snap_scaffold_2-snap.3472-T1
Valid prediction for snap_scaffold_2-snap.3487-T1
Valid prediction for HiQ_model.g3691.t1
Valid prediction for snap_scaffold_2-snap.3485-T1
Valid prediction for snap_scaffold_2-snap.3465-T1
Valid prediction for snap_scaffold_2-snap.3464-T1
Valid prediction for Augustus_model.g3678.t1
Valid prediction for CodingQuarry_transcript_28830-T1
Valid prediction for CodingQuarry_transcript_28829-T1
Valid prediction for GlimmerHMM_glimmerT_5454-T1
Valid prediction for Augustus_model.g3693.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10466, rend_intergenic: 6603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60451, rend_intergenic: 58183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69207, rend_intergenic: 66889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94150, rend_intergenic: 92906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112262, rend_intergenic: 106466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138173, rend_intergenic: 131966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187315, rend_intergenic: 184493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191416, rend_intergenic: 187649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203989, rend_intergenic: 191561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216533, rend_intergenic: 204931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222682, rend_intergenic: 217833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225006, rend_intergenic: 222815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240024, rend_intergenic: 227019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 251407
-exon list size: 680


building trellis

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67.0    
67.2    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 10466, rend_intergenic: 6603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60451, rend_intergenic: 58183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69207, rend_intergenic: 66889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94150, rend_intergenic: 92906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112262, rend_intergenic: 106466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138173, rend_intergenic: 131966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187315, rend_intergenic: 184493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191416, rend_intergenic: 187649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203989, rend_intergenic: 191561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216533, rend_intergenic: 204931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222682, rend_intergenic: 217833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225006, rend_intergenic: 222815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240024, rend_intergenic: 227019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 39 predictions persist after filtering for low support