-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_12627615-12820036

-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 95692, 95823
Couldn't classify 97781, 97882
Sorry, prediction pasa_asmbl_51174.p1 fails validation.
(GAC)	 CA	95692-95823	GT	TGG
(GTT)	 AG	95955-96020	GT	TGG
(AGT)	 AG	96099-96179	GT	AGG
(ATA)	 AG	96350-96453	GT	AGG
(TCC)	 AG	96549-96657	GT	CTG
(CGT)	 AG	96765-96944	GT	AGG
(GTG)	 AG	97255-97379	GT	AGG
(TGA)	 AG	97556-97682	GT	AGG
(CGG)	 AG	97781-97882	CA	TCC
-recovered pasa_asmbl_51174.p1, internal, 95955, 96020
-recovered pasa_asmbl_51174.p1, internal, 96099, 96179
-recovered pasa_asmbl_51174.p1, internal, 96350, 96453
-recovered pasa_asmbl_51174.p1, internal, 96549, 96657
-recovered pasa_asmbl_51174.p1, internal, 96765, 96944
-recovered pasa_asmbl_51174.p1, internal, 97255, 97379
-recovered pasa_asmbl_51174.p1, internal, 97556, 97682
Valid prediction for snap_scaffold_7-snap.2380-T1
Valid prediction for snap_scaffold_7-snap.2383-T1
Valid prediction for snap_scaffold_7-snap.2404-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.31322_t
Valid prediction for CodingQuarry_transcript_57526-T1
Valid prediction for GeneMark_model.31327_t
Valid prediction for GlimmerHMM_glimmerT_18701-T1
Valid prediction for Augustus_model.g12652.t1
Couldn't classify 76355, 76687
Sorry, prediction pasa_asmbl_51173.p2 fails validation.
(ACA)	 AC	76355-76687	AA	GAA
Valid prediction for GeneMark_model.31334_t
Couldn't classify 34265, 34588
Sorry, prediction pasa_asmbl_51167.p1 fails validation.
(AGG)	 CC	34265-34588	AG	TCA
Valid prediction for snap_scaffold_7-snap.2385-T1
Valid prediction for GeneMark_model.31300_t
Valid prediction for snap_scaffold_7-snap.2401-T1
Valid prediction for GlimmerHMM_glimmerT_18697-T1
Couldn't classify 6053, 6502
Sorry, prediction pasa_asmbl_50072.p1 fails validation.
(CAT)	 AA	6053-6502	AT	GAA
Valid prediction for GeneMark_model.31313_t
Valid prediction for GeneMark_model.31328_t
Valid prediction for GeneMark_model.31304_t
Valid prediction for Augustus_model.g12644.t1
Valid prediction for Augustus_model.g12645.t1
Valid prediction for snap_scaffold_7-snap.2371-T1
Valid prediction for GlimmerHMM_glimmerT_18696-T1
Valid prediction for GeneMark_model.31317_t
Valid prediction for snap_scaffold_7-snap.2396-T1
Valid prediction for snap_scaffold_7-snap.2388-T1
Valid prediction for snap_scaffold_7-snap.2391-T1
Valid prediction for Augustus_model.g12653.t1
Couldn't classify 120556, 120742
Sorry, prediction pasa_asmbl_51178.p1 fails validation.
(ACC)	 TG	120556-120742	GT	AGG
(TGC)	 AG	121616-121690	GT	AGG
(ACG)	 AG	122045-122194	GT	AGG
(TCA)	 AG	124349-124916	GT	AGG
(ACC)	 AG	125049-125227	GT	TAG
(GCT)	 AG	125549-125705	GT	AGG
(GAG)	 AG	126066-126121	GT	ACG
(AGA)	 AG	127065-127126	GT	AGG
(TTA)	 AG	127430-127567	GT	AGG
(GCT)	 AG	127777-127853	GT	AGG
(GTT)	 AG	128045-128060	GG	GAG
-recovered pasa_asmbl_51178.p1, terminal, 128045, 128060
-recovered pasa_asmbl_51178.p1, internal, 121616, 121690
-recovered pasa_asmbl_51178.p1, internal, 122045, 122194
-recovered pasa_asmbl_51178.p1, internal, 124349, 124916
-recovered pasa_asmbl_51178.p1, internal, 125049, 125227
-recovered pasa_asmbl_51178.p1, internal, 125549, 125705
-recovered pasa_asmbl_51178.p1, internal, 126066, 126121
-recovered pasa_asmbl_51178.p1, internal, 127065, 127126
-recovered pasa_asmbl_51178.p1, internal, 127430, 127567
-recovered pasa_asmbl_51178.p1, internal, 127777, 127853
Valid prediction for GlimmerHMM_glimmerT_18704-T1
Valid prediction for CodingQuarry_transcript_57530-T1
Couldn't classify 98795, 98852
Sorry, prediction pasa_asmbl_51175.p1 fails validation.
(AGG)	 AC	98795-98852	GT	AGG
(TGG)	 AG	98964-99115	GT	AGG
(GTG)	 AG	99246-99431	GT	AGG
(ATC)	 AG	99684-99756	GT	AGG
(AGG)	 AG	99863-100005	GT	AGG
(GAA)	 AG	100202-100341	GT	AAG
(GTA)	 AG	100430-100610	GT	AGG
(ATC)	 AG	100720-100827	AC	AAA
-recovered pasa_asmbl_51175.p1, terminal, 100720, 100827
-recovered pasa_asmbl_51175.p1, internal, 98964, 99115
-recovered pasa_asmbl_51175.p1, internal, 99246, 99431
-recovered pasa_asmbl_51175.p1, internal, 99684, 99756
-recovered pasa_asmbl_51175.p1, internal, 99863, 100005
-recovered pasa_asmbl_51175.p1, internal, 100202, 100341
-recovered pasa_asmbl_51175.p1, internal, 100430, 100610
Valid prediction for GlimmerHMM_glimmerT_18690-T1
Valid prediction for GeneMark_model.31309_t
Valid prediction for GlimmerHMM_glimmerT_18709-T1
Valid prediction for GeneMark_model.31319_t
Valid prediction for snap_scaffold_7-snap.2382-T1
Couldn't classify 70964, 71024
Couldn't classify 75263, 75461
Sorry, prediction pasa_asmbl_51171.p1 fails validation.
(GAC)	 AG	70964-71024	GT	AGG
(GGC)	 AG	71838-71959	GT	AGG
(GAC)	 AG	72887-72974	GT	AGG
(GGT)	 AG	73452-73539	GT	AAG
(GAC)	 AG	74373-74476	GT	TGG
(AGA)	 AG	74604-74730	GT	CGG
(GAA)	 AG	74811-74903	GT	AAG
(CAT)	 AG	75077-75160	GT	AGG
(GGT)	 AG	75263-75461	GG	AGG
-recovered pasa_asmbl_51171.p1, internal, 70964, 71024
-recovered pasa_asmbl_51171.p1, internal, 71838, 71959
-recovered pasa_asmbl_51171.p1, internal, 72887, 72974
-recovered pasa_asmbl_51171.p1, internal, 73452, 73539
-recovered pasa_asmbl_51171.p1, internal, 74373, 74476
-recovered pasa_asmbl_51171.p1, internal, 74604, 74730
-recovered pasa_asmbl_51171.p1, internal, 74811, 74903
-recovered pasa_asmbl_51171.p1, internal, 75077, 75160
Valid prediction for GlimmerHMM_glimmerT_18703-T1
Valid prediction for snap_scaffold_7-snap.2395-T1
Valid prediction for GeneMark_model.31329_t
Valid prediction for snap_scaffold_7-snap.2374-T1
Valid prediction for snap_scaffold_7-snap.2393-T1
Valid prediction for GeneMark_model.31311_t
Couldn't classify 35339, 35525
Couldn't classify 36751, 36921
Sorry, prediction pasa_asmbl_51168.p1 fails validation.
(CCC)	 TG	35339-35525	GT	TGG
(CCT)	 AG	35638-35798	GT	GGG
(GAG)	 AG	35991-36101	GT	TGG
(TTC)	 AG	36751-36921	CT	CCC
-recovered pasa_asmbl_51168.p1, internal, 35638, 35798
-recovered pasa_asmbl_51168.p1, internal, 35991, 36101
Valid prediction for GeneMark_model.31324_t
Valid prediction for GlimmerHMM_glimmerT_18698-T1
Valid prediction for snap_scaffold_7-snap.2407-T1
Couldn't classify 13059, 13161
Sorry, prediction pasa_asmbl_51164.p1 fails validation.
(TTT)	 GT	13059-13161	GT	ATG
(TCA)	 AG	13285-13399	GT	AGG
(ATC)	 AG	14174-14236	GT	AGG
(CCG)	 AG	14469-14623	GT	CGG
(AGC)	 AG	14864-14959	GT	AGG
(GAG)	 AG	15130-15245	TG	AGT
-recovered pasa_asmbl_51164.p1, terminal, 15130, 15245
-recovered pasa_asmbl_51164.p1, internal, 13285, 13399
-recovered pasa_asmbl_51164.p1, internal, 14174, 14236
-recovered pasa_asmbl_51164.p1, internal, 14469, 14623
-recovered pasa_asmbl_51164.p1, internal, 14864, 14959
Valid prediction for snap_scaffold_7-snap.2378-T1
Valid prediction for snap_scaffold_7-snap.2406-T1
Valid prediction for Augustus_model.g12637.t1
Valid prediction for GeneMark_model.31305_t
Valid prediction for GeneMark_model.31315_t
Valid prediction for GlimmerHMM_glimmerT_18699-T1
Valid prediction for GeneMark_model.31331_t
Valid prediction for Augustus_model.g12642.t1
Valid prediction for Augustus_model.g12647.t1
Valid prediction for Augustus_model.g12649.t1
Valid prediction for GlimmerHMM_glimmerT_18712-T1
Valid prediction for GeneMark_model.31308_t

-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_18710-T1
Valid prediction for GeneMark_model.31326_t
Valid prediction for pasa_asmbl_50074.p1
Valid prediction for snap_scaffold_7-snap.2386-T1
Valid prediction for GeneMark_model.31318_t
Valid prediction for snap_scaffold_7-snap.2402-T1
Valid prediction for GlimmerHMM_glimmerT_18713-T1
Valid prediction for HiQ_model.g12639.t1
Valid prediction for GeneMark_model.31306_t
Valid prediction for Augustus_model.g12646.t1
Couldn't classify 164137, 164247
Couldn't classify 164808, 164924
Sorry, prediction pasa_asmbl_50079.p1 fails validation.
(GCG)	 CA	164137-164247	GT	AGG
(CTG)	 AG	164369-164515	GT	TGG
(ACG)	 AG	164808-164924	GT	GGG
-recovered pasa_asmbl_50079.p1, internal, 164369, 164515
-recovered pasa_asmbl_50079.p1, internal, 164808, 164924
Valid prediction for snap_scaffold_7-snap.2377-T1
Valid prediction for Augustus_model.g12648.t1
Valid prediction for snap_scaffold_7-snap.2375-T1
Valid prediction for GlimmerHMM_glimmerT_18694-T1
Valid prediction for GeneMark_model.31314_t
Valid prediction for GeneMark_model.31302_t
Valid prediction for GeneMark_model.31307_t
Valid prediction for snap_scaffold_7-snap.2389-T1
Valid prediction for snap_scaffold_7-snap.2405-T1
Valid prediction for GeneMark_model.31316_t
Valid prediction for GeneMark_model.31321_t
Valid prediction for GeneMark_model.31333_t
Valid prediction for snap_scaffold_7-snap.2384-T1
Valid prediction for GeneMark_model.31298_t
Valid prediction for GeneMark_model.31303_t
Valid prediction for Augustus_model.g12640.t1
Valid prediction for Augustus_model.g12651.t1
Valid prediction for GeneMark_model.31312_t
Valid prediction for snap_scaffold_7-snap.2392-T1
Valid prediction for CodingQuarry_transcript_57527-T1
Valid prediction for GeneMark_model.31320_t
Valid prediction for GlimmerHMM_glimmerT_18691-T1
Valid prediction for GlimmerHMM_glimmerT_18706-T1
Valid prediction for GlimmerHMM_glimmerT_18705-T1
Valid prediction for GeneMark_model.31310_t
Valid prediction for GeneMark_model.31299_t
Valid prediction for snap_scaffold_7-snap.2397-T1
Valid prediction for GeneMark_model.31330_t
Valid prediction for Augustus_model.g12641.t1
Valid prediction for snap_scaffold_7-snap.2400-T1
Valid prediction for GlimmerHMM_glimmerT_18692-T1
Valid prediction for GlimmerHMM_glimmerT_18700-T1
Valid prediction for snap_scaffold_7-snap.2399-T1
Valid prediction for GlimmerHMM_glimmerT_18689-T1
Valid prediction for CodingQuarry_transcript_57525-T1
Couldn't classify 87979, 88186
Sorry, prediction pasa_asmbl_50080.p1 fails validation.
(GTC)	 AC	87979-88186	GT	AGG
(GGA)	 AG	88725-88998	GT	GGG
(ACT)	 AG	89256-89412	GT	AGG
(GTG)	 AG	89702-89878	AA	AAA
-recovered pasa_asmbl_50080.p1, terminal, 89702, 89878
-recovered pasa_asmbl_50080.p1, internal, 88725, 88998
-recovered pasa_asmbl_50080.p1, internal, 89256, 89412
Valid prediction for GlimmerHMM_glimmerT_18707-T1
Valid prediction for snap_scaffold_7-snap.2398-T1
Valid prediction for snap_scaffold_7-snap.2379-T1
Valid prediction for CodingQuarry_transcript_57528-T1
Valid prediction for Augustus_model.g12650.t1
Valid prediction for GeneMark_model.31332_t
Valid prediction for snap_scaffold_7-snap.2381-T1
Valid prediction for GeneMark_model.31323_t
Valid prediction for snap_scaffold_7-snap.2387-T1
Valid prediction for snap_scaffold_7-snap.2390-T1
Valid prediction for GlimmerHMM_glimmerT_18702-T1
Valid prediction for GlimmerHMM_glimmerT_18693-T1
Valid prediction for snap_scaffold_7-snap.2372-T1
Valid prediction for Augustus_model.g12643.t1
Couldn't classify 166013, 166067
Sorry, prediction pasa_asmbl_50078.p1 fails validation.
(TCT)	 AA	166013-166067	GT	AGG
(GTG)	 AG	166262-166305	GT	AGG
(AAC)	 AG	166400-166434	GT	AGG
(TGC)	 AG	166554-166806	GA	GAG
-recovered pasa_asmbl_50078.p1, terminal, 166554, 166806
-recovered pasa_asmbl_50078.p1, internal, 166262, 166305
-recovered pasa_asmbl_50078.p1, internal, 166400, 166434
Valid prediction for pasa_asmbl_50075.p1
Valid prediction for Augustus_model.g12654.t1
Valid prediction for snap_scaffold_7-snap.2394-T1
Valid prediction for snap_scaffold_7-snap.2376-T1
Valid prediction for GeneMark_model.31301_t
Valid prediction for snap_scaffold_7-snap.2403-T1
Valid prediction for GlimmerHMM_glimmerT_18695-T1
Valid prediction for snap_scaffold_7-snap.2408-T1
Valid prediction for GlimmerHMM_glimmerT_18708-T1
Valid prediction for Augustus_model.g12638.t1
Valid prediction for snap_scaffold_7-snap.2373-T1
Valid prediction for GlimmerHMM_glimmerT_18711-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10591, rend_intergenic: 3074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50687, rend_intergenic: 45846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67573, rend_intergenic: 58666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76327, rend_intergenic: 70440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88218, rend_intergenic: 82889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99446, rend_intergenic: 97279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100825, rend_intergenic: 99669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128287, rend_intergenic: 118804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166486, rend_intergenic: 160353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186509, rend_intergenic: 177074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188055, rend_intergenic: 186781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192422
-exon list size: 572


building trellis

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70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.4    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.2    
73.3    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.1    
80.3    
80.5    
80.7    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 10591, rend_intergenic: 3074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50687, rend_intergenic: 45846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67573, rend_intergenic: 58666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76327, rend_intergenic: 70440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88218, rend_intergenic: 82889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99446, rend_intergenic: 97279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100825, rend_intergenic: 99669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128287, rend_intergenic: 118804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166486, rend_intergenic: 160353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186509, rend_intergenic: 177074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188055, rend_intergenic: 186781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support