-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_10873837-11092662

-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 GeneMark_model.26606_t
Valid prediction for GlimmerHMM_glimmerT_15819-T1
Valid prediction for HiQ_model.g10584.t1
Valid prediction for snap_scaffold_6-snap.2335-T1
Valid prediction for snap_scaffold_6-snap.2337-T1
Valid prediction for GeneMark_model.26620_t
Couldn't classify 164715, 164983
Couldn't classify 165497, 165527
Sorry, prediction pasa_asmbl_47254.p1 fails validation.
(GAC)	 CA	164715-164983	GT	AGG
(TGG)	 AG	165497-165527	GC	TGG
-recovered pasa_asmbl_47254.p1, internal, 165497, 165527
Couldn't classify 20330, 20356
Sorry, prediction pasa_asmbl_47240.p1 fails validation.
(CTC)	 CC	20330-20356	GT	TGG
(TCT)	 AG	21582-21774	GT	AAG
(AAC)	 AG	22119-22287	GT	TGG
(GTT)	 AG	22398-22533	GT	AGG
(ATG)	 AG	23504-23690	GT	AGG
(GAG)	 AG	23968-24128	GC	AGG
(ATC)	 AG	24339-24440	GT	TGG
(GGA)	 AG	24600-24695	GT	AGG
(TCA)	 AG	24908-25027	GT	TGG
(GGT)	 AG	25240-25296	AT	AGA
-recovered pasa_asmbl_47240.p1, initial, 23504, 23690
add_exon() Sorry, pasa_asmbl_47240.p1 21582-21774-terminal-3 is invalid.
-recovered pasa_asmbl_47240.p1, terminal, 21582, 21774
-recovered pasa_asmbl_47240.p1, terminal, 25240, 25296
-recovered pasa_asmbl_47240.p1, internal, 21582, 21774
-recovered pasa_asmbl_47240.p1, internal, 22119, 22287
-recovered pasa_asmbl_47240.p1, internal, 22398, 22533
-recovered pasa_asmbl_47240.p1, internal, 23504, 23690
-recovered pasa_asmbl_47240.p1, internal, 23968, 24128
-recovered pasa_asmbl_47240.p1, internal, 24339, 24440
-recovered pasa_asmbl_47240.p1, internal, 24600, 24695
-recovered pasa_asmbl_47240.p1, internal, 24908, 25027
Valid prediction for snap_scaffold_6-snap.2349-T1
Valid prediction for GeneMark_model.26614_t
Valid prediction for Augustus_model.g10591.t1
Valid prediction for snap_scaffold_6-snap.2353-T1
Valid prediction for GlimmerHMM_glimmerT_15824-T1
Valid prediction for GeneMark_model.26609_t
Valid prediction for HiQ_model.g10578.t1
Valid prediction for Augustus_model.g10585.t1
Valid prediction for GeneMark_model.26628_t
Valid prediction for GlimmerHMM_glimmerT_15802-T1
Valid prediction for GlimmerHMM_glimmerT_15818-T1
Valid prediction for snap_scaffold_6-snap.2364-T1
Valid prediction for snap_scaffold_6-snap.2351-T1
Valid prediction for Augustus_model.g10599.t1
Valid prediction for GeneMark_model.26633_t
Valid prediction for GlimmerHMM_glimmerT_15817-T1
Valid prediction for GlimmerHMM_glimmerT_15801-T1
Valid prediction for snap_scaffold_6-snap.2338-T1
Couldn't classify 96294, 96417
Sorry, prediction pasa_asmbl_47251.p1 fails validation.
(GTT)	 TC	96294-96417	GT	AGG
(ATG)	 AG	96863-97005	GT	AGG
(GTG)	 AG	97152-97233	GT	TGG
(TTG)	 AG	97338-97522	GT	CAG
(ACC)	 AG	97658-97778	GT	AGG
(ACG)	 AG	98056-98208	GT	AGG
(GTG)	 AG	98376-98536	GT	AGG
(GTG)	 AG	98706-98972	GT	TGG
(GAA)	 AG	99195-99309	GT	GGG
(GCT)	 AG	99666-99883	GT	AGG
(AAT)	 AG	100287-100485	GT	AGG
(GAG)	 AG	100816-100985	GT	GGG
(ACC)	 AG	101215-101277	GT	AGG
(ATG)	 AG	101617-101973	GG	GAG
-recovered pasa_asmbl_47251.p1, initial, 96863, 97005
-recovered pasa_asmbl_47251.p1, terminal, 101617, 101973
-recovered pasa_asmbl_47251.p1, internal, 96863, 97005
-recovered pasa_asmbl_47251.p1, internal, 97152, 97233
-recovered pasa_asmbl_47251.p1, internal, 97338, 97522
-recovered pasa_asmbl_47251.p1, internal, 97658, 97778
-recovered pasa_asmbl_47251.p1, internal, 98056, 98208
-recovered pasa_asmbl_47251.p1, internal, 98376, 98536
-recovered pasa_asmbl_47251.p1, internal, 98706, 98972
-recovered pasa_asmbl_47251.p1, internal, 99195, 99309
-recovered pasa_asmbl_47251.p1, internal, 99666, 99883
-recovered pasa_asmbl_47251.p1, internal, 100287, 100485
-recovered pasa_asmbl_47251.p1, internal, 100816, 100985
-recovered pasa_asmbl_47251.p1, internal, 101215, 101277
Valid prediction for CodingQuarry_transcript_55072-T1
Valid prediction for GlimmerHMM_glimmerT_15830-T1
Valid prediction for GeneMark_model.26597_t
Couldn't classify 15521, 15526
Sorry, prediction pasa_asmbl_47238.p1 fails validation.
(GAT)	 CA	15521-15526	GT	ACG
(CAA)	 AG	15814-15951	GT	AGG
(TGG)	 AG	16094-16183	GT	AGG
(GAG)	 AG	16260-16367	GT	AGG
(GCC)	 AG	16455-16788	GT	CGG
(CCA)	 AG	17128-17219	GT	AGG
(GAA)	 AG	17311-17391	GG	AAG
-recovered pasa_asmbl_47238.p1, terminal, 17311, 17391
-recovered pasa_asmbl_47238.p1, internal, 15814, 15951
-recovered pasa_asmbl_47238.p1, internal, 16094, 16183
-recovered pasa_asmbl_47238.p1, internal, 16260, 16367
-recovered pasa_asmbl_47238.p1, internal, 16455, 16788
-recovered pasa_asmbl_47238.p1, internal, 17128, 17219
Valid prediction for GeneMark_model.26621_t
Valid prediction for GlimmerHMM_glimmerT_15814-T1
Valid prediction for snap_scaffold_6-snap.2367-T1
Valid prediction for snap_scaffold_6-snap.2340-T1
Valid prediction for GlimmerHMM_glimmerT_15809-T1
Valid prediction for GlimmerHMM_glimmerT_15798-T1
Valid prediction for GeneMark_model.26611_t
Valid prediction for snap_scaffold_6-snap.2332-T1
Valid prediction for snap_scaffold_6-snap.2348-T1
Valid prediction for snap_scaffold_6-snap.2350-T1
Valid prediction for HiQ_model.g10580.t1
Valid prediction for GeneMark_model.26600_t
Valid prediction for snap_scaffold_6-snap.2342-T1
Valid prediction for GeneMark_model.26618_t
Valid prediction for GlimmerHMM_glimmerT_15810-T1
Valid prediction for snap_scaffold_6-snap.2331-T1
Valid prediction for Augustus_model.g10575.t1
Valid prediction for snap_scaffold_6-snap.2361-T1
Valid prediction for HiQ_model.g10589.t1
Valid prediction for Augustus_model.g10582.t1
Valid prediction for GeneMark_model.26630_t
Valid prediction for pasa_asmbl_47250.p1
Valid prediction for GeneMark_model.26612_t
Valid prediction for snap_scaffold_6-snap.2363-T1
Valid prediction for snap_scaffold_6-snap.2334-T1
Valid prediction for GlimmerHMM_glimmerT_15820-T1
Valid prediction for snap_scaffold_6-snap.2369-T1
Valid prediction for GeneMark_model.26623_t
Valid prediction for snap_scaffold_6-snap.2357-T1
Valid prediction for GeneMark_model.26631_t
Valid prediction for Augustus_model.g10590.t1
Valid prediction for GeneMark_model.26615_t
Valid prediction for GlimmerHMM_glimmerT_15825-T1
Valid prediction for GeneMark_model.26598_t
Valid prediction for Augustus_model.g10581.t1
Valid prediction for GlimmerHMM_glimmerT_15799-T1
Valid prediction for Augustus_model.g10592.t1
Valid prediction for snap_scaffold_6-snap.2343-T1
Valid prediction for HiQ_model.g10576.t1
Valid prediction for GlimmerHMM_glimmerT_15803-T1
Valid prediction for GlimmerHMM_glimmerT_15829-T1
Valid prediction for GlimmerHMM_glimmerT_15806-T1
Valid prediction for GeneMark_model.26613_t
Valid prediction for snap_scaffold_6-snap.2356-T1
Valid prediction for snap_scaffold_6-snap.2362-T1
Valid prediction for Augustus_model.g10595.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 GeneMark_model.26599_t
Valid prediction for snap_scaffold_6-snap.2346-T1
Valid prediction for GlimmerHMM_glimmerT_15816-T1
Valid prediction for Augustus_model.g10583.t1
Valid prediction for pasa_asmbl_48658.p1
Valid prediction for GlimmerHMM_glimmerT_15811-T1
Valid prediction for snap_scaffold_6-snap.2358-T1
Valid prediction for GlimmerHMM_glimmerT_15812-T1
Couldn't classify 213802, 213904
Sorry, prediction pasa_asmbl_48657.p1 fails validation.
(AAG)	 GG	213802-213904	GT	AGG
(CCA)	 AG	214598-214669	GT	AGG
(AGT)	 AG	214935-215093	GT	AGG
(AGA)	 AG	215219-215312	GT	AGG
(TAT)	 AG	216072-216483	CA	GAC
-recovered pasa_asmbl_48657.p1, terminal, 216072, 216483
-recovered pasa_asmbl_48657.p1, internal, 214598, 214669
-recovered pasa_asmbl_48657.p1, internal, 214935, 215093
-recovered pasa_asmbl_48657.p1, internal, 215219, 215312
Valid prediction for snap_scaffold_6-snap.2347-T1
Valid prediction for pasa_asmbl_48672.p1
Valid prediction for GeneMark_model.26596_t
Valid prediction for GeneMark_model.26617_t
Valid prediction for GeneMark_model.26616_t
Valid prediction for GlimmerHMM_glimmerT_15822-T1
Valid prediction for GeneMark_model.26619_t
Valid prediction for Augustus_model.g10598.t1
Valid prediction for snap_scaffold_6-snap.2344-T1
Valid prediction for GeneMark_model.26603_t
Valid prediction for GlimmerHMM_glimmerT_15813-T1
Valid prediction for GeneMark_model.26607_t
Valid prediction for GeneMark_model.26608_t
Valid prediction for snap_scaffold_6-snap.2352-T1
Valid prediction for GlimmerHMM_glimmerT_15800-T1
Valid prediction for GeneMark_model.26601_t
Valid prediction for snap_scaffold_6-snap.2354-T1
Valid prediction for GlimmerHMM_glimmerT_15797-T1
Valid prediction for GlimmerHMM_glimmerT_15821-T1
Valid prediction for GlimmerHMM_glimmerT_15826-T1
Valid prediction for pasa_asmbl_48661.p1
Valid prediction for Augustus_model.g10587.t1
Valid prediction for HiQ_model.g10594.t1
Valid prediction for snap_scaffold_6-snap.2365-T1
Valid prediction for snap_scaffold_6-snap.2355-T1
Valid prediction for snap_scaffold_6-snap.2359-T1
Valid prediction for Augustus_model.g10579.t1
Valid prediction for GlimmerHMM_glimmerT_15808-T1
Valid prediction for snap_scaffold_6-snap.2333-T1
Valid prediction for snap_scaffold_6-snap.2330-T1
Valid prediction for GlimmerHMM_glimmerT_15827-T1
Valid prediction for GlimmerHMM_glimmerT_15823-T1
Valid prediction for HiQ_model.g10586.t1
Couldn't classify 71406, 71513
Sorry, prediction pasa_asmbl_48669.p1 fails validation.
(CAG)	 TG	71406-71513	GT	ACG
(AAG)	 AG	72282-72358	GT	GGG
(GAA)	 AG	72536-72647	GT	AGG
(GTG)	 AG	72890-72966	GT	AGG
(GTG)	 AG	73253-73370	GT	AGG
(GAT)	 AG	74431-74499	GT	TGG
(CTG)	 AG	74608-74689	GT	AGG
(ACT)	 AG	74789-74916	GT	AGG
(GGC)	 AG	75596-75707	GT	TGG
(GAG)	 AG	75969-76050	GT	AAG
(TGT)	 AG	76255-76335	GT	AGG
(GTA)	 AG	76429-76542	GT	GGG
(CAC)	 AG	76751-76842	GT	TGG
(ACA)	 AG	77066-77412	GC	AAG
-recovered pasa_asmbl_48669.p1, terminal, 77066, 77412
-recovered pasa_asmbl_48669.p1, internal, 72282, 72358
-recovered pasa_asmbl_48669.p1, internal, 72536, 72647
-recovered pasa_asmbl_48669.p1, internal, 72890, 72966
-recovered pasa_asmbl_48669.p1, internal, 73253, 73370
-recovered pasa_asmbl_48669.p1, internal, 74431, 74499
-recovered pasa_asmbl_48669.p1, internal, 74608, 74689
-recovered pasa_asmbl_48669.p1, internal, 74789, 74916
-recovered pasa_asmbl_48669.p1, internal, 75596, 75707
-recovered pasa_asmbl_48669.p1, internal, 75969, 76050
-recovered pasa_asmbl_48669.p1, internal, 76255, 76335
-recovered pasa_asmbl_48669.p1, internal, 76429, 76542
-recovered pasa_asmbl_48669.p1, internal, 76751, 76842
-recovered pasa_asmbl_48669.p1, internal, 77066, 77412
Valid prediction for CodingQuarry_transcript_55070-T1
Valid prediction for snap_scaffold_6-snap.2366-T1
Valid prediction for Augustus_model.g10597.t1
Valid prediction for GeneMark_model.26626_t
Valid prediction for GeneMark_model.26625_t
Couldn't classify 188816, 188851
Sorry, prediction pasa_asmbl_48659.p1 fails validation.
(CAC)	 GC	188816-188851	GT	GAG
(ATC)	 AG	189630-189788	GT	GGG
(TTG)	 AG	190751-190850	GT	AGG
(GCT)	 AG	191323-191455	GT	GGG
(TTC)	 AG	191545-191682	GT	GGG
(ACA)	 AG	191923-192129	GT	TGG
(GTA)	 AG	192292-192412	GT	AGG
(AAA)	 AG	192569-192712	CA	AGC
-recovered pasa_asmbl_48659.p1, terminal, 192569, 192712
-recovered pasa_asmbl_48659.p1, internal, 189630, 189788
-recovered pasa_asmbl_48659.p1, internal, 190751, 190850
-recovered pasa_asmbl_48659.p1, internal, 191323, 191455
-recovered pasa_asmbl_48659.p1, internal, 191545, 191682
-recovered pasa_asmbl_48659.p1, internal, 191923, 192129
-recovered pasa_asmbl_48659.p1, internal, 192292, 192412
Valid prediction for GlimmerHMM_glimmerT_15804-T1
Valid prediction for Augustus_model.g10574.t1
Valid prediction for GlimmerHMM_glimmerT_15805-T1
Valid prediction for snap_scaffold_6-snap.2345-T1
Valid prediction for snap_scaffold_6-snap.2328-T1
Valid prediction for GeneMark_model.26627_t
Valid prediction for GeneMark_model.26632_t
Valid prediction for Augustus_model.g10596.t1
Valid prediction for snap_scaffold_6-snap.2339-T1
Valid prediction for snap_scaffold_6-snap.2360-T1
Valid prediction for Augustus_model.g10588.t1
Valid prediction for Augustus_model.g10593.t1
Valid prediction for GeneMark_model.26629_t
Valid prediction for snap_scaffold_6-snap.2336-T1
Valid prediction for GlimmerHMM_glimmerT_15828-T1
Valid prediction for GeneMark_model.26624_t
Valid prediction for snap_scaffold_6-snap.2329-T1
Valid prediction for snap_scaffold_6-snap.2368-T1
Valid prediction for GlimmerHMM_glimmerT_15807-T1
Valid prediction for HiQ_model.g10577.t1
Valid prediction for snap_scaffold_6-snap.2341-T1
Valid prediction for GlimmerHMM_glimmerT_15815-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34210, rend_intergenic: 27155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52358, rend_intergenic: 50648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114815, rend_intergenic: 112449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115090, rend_intergenic: 114840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124946, rend_intergenic: 116611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211833, rend_intergenic: 207928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218826
-exon list size: 564


building trellis

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67.1    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.4    
68.6    
68.7    
68.9    
69.1    
69.3    
69.4    
69.6    
69.8    
70.0    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
73.0    
73.1    
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    
76.9    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
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    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 34210, rend_intergenic: 27155  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52358, rend_intergenic: 50648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114815, rend_intergenic: 112449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115090, rend_intergenic: 114840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124946, rend_intergenic: 116611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211833, rend_intergenic: 207928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support