-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_5851754-5985661

-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 Augustus_model.g38061.t1
Valid prediction for GeneMark_model.99653_t
Valid prediction for GeneMark_model.99648_t
Valid prediction for GlimmerHMM_glimmerT_57112-T1
Valid prediction for GeneMark_model.99657_t
Valid prediction for GlimmerHMM_glimmerT_57102-T1
Valid prediction for GlimmerHMM_glimmerT_57101-T1
Valid prediction for GeneMark_model.99640_t
Valid prediction for GlimmerHMM_glimmerT_57129-T1
Valid prediction for GeneMark_model.99651_t
Valid prediction for snap_scaffold_26-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_57104-T1
Valid prediction for snap_scaffold_26-snap.1346-T1
Valid prediction for snap_scaffold_26-snap.1343-T1
Valid prediction for pasa_asmbl_35578.p1
Valid prediction for CodingQuarry_transcript_40276-T1
Valid prediction for snap_scaffold_26-snap.1332-T1
Valid prediction for GlimmerHMM_glimmerT_57100-T1
Valid prediction for Augustus_model.g38066.t1
Valid prediction for GlimmerHMM_glimmerT_57114-T1
Valid prediction for GlimmerHMM_glimmerT_57121-T1
Valid prediction for snap_scaffold_26-snap.1338-T1
Couldn't classify 116759, 116902
Couldn't classify 118825, 118888
Sorry, prediction pasa_asmbl_35585.p1 fails validation.
(CGC)	 AT	116759-116902	GT	AGG
(GAA)	 AG	117116-117145	GT	AGG
(CTG)	 AG	117689-117805	GT	AGG
(GTG)	 AG	117907-117953	GT	GCG
(GCC)	 AG	118036-118187	GT	AGG
(GTC)	 AG	118279-118383	GT	TGG
(GTT)	 AG	118520-118715	GT	AGG
(GAG)	 AG	118825-118888	GA	ACG
-recovered pasa_asmbl_35585.p1, internal, 117116, 117145
-recovered pasa_asmbl_35585.p1, internal, 117689, 117805
-recovered pasa_asmbl_35585.p1, internal, 117907, 117953
-recovered pasa_asmbl_35585.p1, internal, 118036, 118187
-recovered pasa_asmbl_35585.p1, internal, 118279, 118383
-recovered pasa_asmbl_35585.p1, internal, 118520, 118715
Valid prediction for GeneMark_model.99659_t
Valid prediction for GlimmerHMM_glimmerT_57120-T1
Valid prediction for snap_scaffold_26-snap.1329-T1
Valid prediction for snap_scaffold_26-snap.1340-T1
Couldn't classify 75726, 76031
Sorry, prediction pasa_asmbl_35582.p1 fails validation.
(TTA)	 GT	75726-76031	GT	AGG
(GCT)	 AG	76131-76325	GT	TGG
(CAA)	 AG	76645-76700	GT	AAG
(GGG)	 AG	76791-76943	GT	AAG
(AGA)	 AG	77095-77295	GT	AGG
(GCA)	 AG	77433-77550	GT	TGG
(GCT)	 AG	77647-77775	GC	GAG
-recovered pasa_asmbl_35582.p1, terminal, 77647, 77775
-recovered pasa_asmbl_35582.p1, internal, 76131, 76325
-recovered pasa_asmbl_35582.p1, internal, 76645, 76700
-recovered pasa_asmbl_35582.p1, internal, 76791, 76943
-recovered pasa_asmbl_35582.p1, internal, 77095, 77295
-recovered pasa_asmbl_35582.p1, internal, 77433, 77550
-recovered pasa_asmbl_35582.p1, internal, 77647, 77775
Valid prediction for snap_scaffold_26-snap.1362-T1
Valid prediction for GeneMark_model.99661_t
Valid prediction for snap_scaffold_26-snap.1354-T1
Valid prediction for Augustus_model.g38048.t1
Valid prediction for HiQ_model.g38057.t1
Valid prediction for GeneMark_model.99649_t
Valid prediction for GeneMark_model.99670_t
Valid prediction for Augustus_model.g38064.t1
Couldn't classify 131573, 131649
Sorry, prediction pasa_asmbl_35592.p1 fails validation.
(CTC)	 CT	131573-131649	GT	GTG
(GTT)	 AG	131760-131973	GT	AGG
(CTC)	 AG	132229-132336	AA	AGA
-recovered pasa_asmbl_35592.p1, terminal, 132229, 132336
-recovered pasa_asmbl_35592.p1, internal, 131760, 131973
Valid prediction for snap_scaffold_26-snap.1335-T1
Valid prediction for GeneMark_model.99645_t
Valid prediction for GeneMark_model.99664_t
Valid prediction for GlimmerHMM_glimmerT_57107-T1
Valid prediction for pasa_asmbl_35575.p1
Valid prediction for Augustus_model.g38056.t1
Valid prediction for GlimmerHMM_glimmerT_57128-T1
Valid prediction for GlimmerHMM_glimmerT_57113-T1
Valid prediction for CodingQuarry_transcript_40284-T1
Valid prediction for GeneMark_model.99655_t
Valid prediction for Augustus_model.g38051.t1
Valid prediction for snap_scaffold_26-snap.1334-T1
Valid prediction for GeneMark_model.99668_t
Valid prediction for snap_scaffold_26-snap.1348-T1
Valid prediction for GlimmerHMM_glimmerT_57117-T1
Valid prediction for GlimmerHMM_glimmerT_57122-T1
Valid prediction for pasa_asmbl_35574.p1
Valid prediction for snap_scaffold_26-snap.1326-T1
Valid prediction for HiQ_model.g38067.t1
Valid prediction for CodingQuarry_transcript_40281-T1
Valid prediction for HiQ_model.g38045.t1
Valid prediction for GlimmerHMM_glimmerT_57127-T1
Valid prediction for pasa_asmbl_35576.p1
Valid prediction for CodingQuarry_transcript_40278-T1
Valid prediction for GlimmerHMM_glimmerT_57115-T1
Valid prediction for Augustus_model.g38050.t1
Valid prediction for pasa_asmbl_35587.p1
Valid prediction for Augustus_model.g38043.t1
Valid prediction for GlimmerHMM_glimmerT_57110-T1
Valid prediction for GeneMark_model.99642_t
Valid prediction for snap_scaffold_26-snap.1342-T1
Valid prediction for snap_scaffold_26-snap.1336-T1
Valid prediction for snap_scaffold_26-snap.1327-T1
Valid prediction for snap_scaffold_26-snap.1337-T1
Valid prediction for Augustus_model.g38053.t1
Valid prediction for GlimmerHMM_glimmerT_57109-T1
Valid prediction for GlimmerHMM_glimmerT_57125-T1
Valid prediction for snap_scaffold_26-snap.1341-T1
Valid prediction for snap_scaffold_26-snap.1359-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 HiQ_model.g38044.t1
Valid prediction for GlimmerHMM_glimmerT_57124-T1
Valid prediction for GeneMark_model.99656_t
Couldn't classify 24618, 24866
Sorry, prediction pasa_asmbl_34929.p1 fails validation.
(CGT)	 AT	24618-24866	GT	AGG
(AAA)	 AG	25800-25926	GT	AGG
(GTC)	 AG	26038-26125	GT	AGG
(TAT)	 AG	26255-26366	GT	CGG
(ATC)	 AG	27425-27583	GT	AGG
(GTT)	 AG	28147-28299	GT	AGG
(ATT)	 AG	28428-28535	GT	AGG
(GTA)	 AG	28677-28844	GT	AGG
(ACA)	 AG	28947-29097	GT	AGG
(CAA)	 AG	29221-29405	GG	GAG
-recovered pasa_asmbl_34929.p1, terminal, 29221, 29405
-recovered pasa_asmbl_34929.p1, internal, 25800, 25926
-recovered pasa_asmbl_34929.p1, internal, 26038, 26125
-recovered pasa_asmbl_34929.p1, internal, 26255, 26366
-recovered pasa_asmbl_34929.p1, internal, 27425, 27583
-recovered pasa_asmbl_34929.p1, internal, 28147, 28299
-recovered pasa_asmbl_34929.p1, internal, 28428, 28535
-recovered pasa_asmbl_34929.p1, internal, 28677, 28844
-recovered pasa_asmbl_34929.p1, internal, 28947, 29097
Valid prediction for snap_scaffold_26-snap.1351-T1
Couldn't classify 74782, 74838
Sorry, prediction pasa_asmbl_34920.p2 fails validation.
(TGC)	 GC	74782-74838	GT	TGG
(GTG)	 AG	75044-75158	GT	AGG
(AGC)	 AG	75271-75446	GG	GAG
-recovered pasa_asmbl_34920.p2, terminal, 75271, 75446
-recovered pasa_asmbl_34920.p2, internal, 75044, 75158
Valid prediction for Augustus_model.g38058.t1
Valid prediction for GlimmerHMM_glimmerT_57116-T1
Valid prediction for GeneMark_model.99652_t
Valid prediction for snap_scaffold_26-snap.1360-T1
Valid prediction for GeneMark_model.99666_t
Valid prediction for pasa_asmbl_34924.p1
Valid prediction for Augustus_model.g38054.t1
Valid prediction for pasa_asmbl_34908.p1
Valid prediction for CodingQuarry_transcript_40280-T1
Valid prediction for GlimmerHMM_glimmerT_57126-T1
Valid prediction for HiQ_model.g38062.t1
Valid prediction for snap_scaffold_26-snap.1339-T1
Valid prediction for GeneMark_model.99667_t
Valid prediction for Augustus_model.g38055.t1
Valid prediction for snap_scaffold_26-snap.1333-T1
Valid prediction for GlimmerHMM_glimmerT_57106-T1
Valid prediction for snap_scaffold_26-snap.1352-T1
Valid prediction for GlimmerHMM_glimmerT_57118-T1
Valid prediction for GlimmerHMM_glimmerT_57105-T1
Valid prediction for snap_scaffold_26-snap.1344-T1
Valid prediction for snap_scaffold_26-snap.1350-T1
Valid prediction for CodingQuarry_transcript_40279-T1
Valid prediction for GeneMark_model.99662_t
Valid prediction for HiQ_model.g38047.t1
Valid prediction for GeneMark_model.99663_t
Valid prediction for snap_scaffold_26-snap.1353-T1
Valid prediction for CodingQuarry_transcript_40282-T1
Valid prediction for GeneMark_model.99643_t
Valid prediction for CodingQuarry_transcript_40277-T1
Valid prediction for Augustus_model.g38046.t1
Valid prediction for snap_scaffold_26-snap.1347-T1
Couldn't classify 51640, 51694
Sorry, prediction pasa_asmbl_35135.p2 fails validation.
(ATG)	 AA	50362-50448	GT	AGG
(GAT)	 AG	50691-50942	GT	CGG
(CAG)	 AG	51048-51203	GT	AGG
(ATG)	 AG	51337-51485	GT	GAG
(TAC)	 AG	51640-51694	AC	GAA
-recovered pasa_asmbl_35135.p2, initial, 50362, 50448
-recovered pasa_asmbl_35135.p2, initial, 51337, 51485
-recovered pasa_asmbl_35135.p2, internal, 50691, 50942
-recovered pasa_asmbl_35135.p2, internal, 51048, 51203
-recovered pasa_asmbl_35135.p2, internal, 51337, 51485
Valid prediction for GlimmerHMM_glimmerT_57123-T1
Valid prediction for GeneMark_model.99669_t
Valid prediction for GlimmerHMM_glimmerT_57108-T1
Valid prediction for HiQ_model.g38049.t1
Valid prediction for pasa_asmbl_34917.p1
Valid prediction for snap_scaffold_26-snap.1355-T1
Valid prediction for snap_scaffold_26-snap.1361-T1
Valid prediction for Augustus_model.g38059.t1
Valid prediction for snap_scaffold_26-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_57119-T1
Valid prediction for snap_scaffold_26-snap.1349-T1
Couldn't classify 51851, 52054
Couldn't classify 54278, 54310
Sorry, prediction pasa_asmbl_35128.p1 fails validation.
(GAG)	 CG	51851-52054	GT	AGG
(GGG)	 AG	52172-52397	GT	GGG
(GCC)	 AG	52508-52620	GT	AGG
(ACT)	 AG	52720-52789	GC	AGG
(GAT)	 AG	52882-53024	GT	TGG
(AAA)	 AG	53161-53351	GT	AGG
(GAT)	 AG	53467-53596	GT	GGG
(CCT)	 AG	53714-53818	GC	AGG
(GTC)	 AG	53932-54014	GT	AGG
(GAT)	 AG	54121-54184	GT	AGG
(ACG)	 AG	54278-54310	AA	CCA
-recovered pasa_asmbl_35128.p1, internal, 52172, 52397
-recovered pasa_asmbl_35128.p1, internal, 52508, 52620
-recovered pasa_asmbl_35128.p1, internal, 52720, 52789
-recovered pasa_asmbl_35128.p1, internal, 52882, 53024
-recovered pasa_asmbl_35128.p1, internal, 53161, 53351
-recovered pasa_asmbl_35128.p1, internal, 53467, 53596
-recovered pasa_asmbl_35128.p1, internal, 53714, 53818
-recovered pasa_asmbl_35128.p1, internal, 53932, 54014
-recovered pasa_asmbl_35128.p1, internal, 54121, 54184
Valid prediction for CodingQuarry_transcript_40283-T1
Valid prediction for HiQ_model.g38052.t1
Valid prediction for snap_scaffold_26-snap.1330-T1
Couldn't classify 49271, 49429
Couldn't classify 49804, 49842
Sorry, prediction pasa_asmbl_34923.p1 fails validation.
(CTG)	 AA	49271-49429	GT	AGG
(GTG)	 AG	49541-49666	GT	ATG
(ATG)	 AG	49804-49842	GA	AGG
-recovered pasa_asmbl_34923.p1, internal, 49541, 49666
Valid prediction for GeneMark_model.99658_t
Valid prediction for GlimmerHMM_glimmerT_57103-T1
Couldn't classify 70385, 70532
Couldn't classify 72927, 72941
Sorry, prediction pasa_asmbl_34921.p1 fails validation.
(GAC)	 AG	70385-70532	GT	CGG
(TGG)	 AG	70643-70767	GT	CGG
(GAC)	 AG	70888-71103	GT	GGG
(GAA)	 AG	71214-71317	GT	AGG
(GGA)	 AG	71739-71823	GT	AGG
(GAG)	 AG	72625-72702	GT	TGG
(GGG)	 AG	72927-72941	AC	GGA
-recovered pasa_asmbl_34921.p1, internal, 70385, 70532
-recovered pasa_asmbl_34921.p1, internal, 70643, 70767
-recovered pasa_asmbl_34921.p1, internal, 70888, 71103
-recovered pasa_asmbl_34921.p1, internal, 71214, 71317
-recovered pasa_asmbl_34921.p1, internal, 71739, 71823
-recovered pasa_asmbl_34921.p1, internal, 72625, 72702
Valid prediction for snap_scaffold_26-snap.1328-T1
Valid prediction for GeneMark_model.99646_t
Valid prediction for pasa_asmbl_34906.p1
Valid prediction for GeneMark_model.99650_t
Valid prediction for snap_scaffold_26-snap.1357-T1
Valid prediction for snap_scaffold_26-snap.1358-T1
Valid prediction for GeneMark_model.99654_t
Valid prediction for GeneMark_model.99641_t
Valid prediction for HiQ_model.g38063.t1
Valid prediction for GlimmerHMM_glimmerT_57111-T1
Valid prediction for GeneMark_model.99644_t
Valid prediction for Augustus_model.g38065.t1
Valid prediction for snap_scaffold_26-snap.1331-T1
Valid prediction for GeneMark_model.99660_t
Valid prediction for Augustus_model.g38060.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 100510, rend_intergenic: 97811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 133908
-exon list size: 532


building trellis

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89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 100510, rend_intergenic: 97811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support