-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_800432-1075028

-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_22-snap.177-T1
Valid prediction for GeneMark_model.86727_t
Valid prediction for snap_scaffold_22-snap.181-T1
Valid prediction for Augustus_model.g33630.t1
Valid prediction for pasa_asmbl_29196.p1
Valid prediction for GeneMark_model.86746_t
Valid prediction for GlimmerHMM_glimmerT_50118-T1
Couldn't classify 149129, 149140
Sorry, prediction pasa_asmbl_29199.p1 fails validation.
(TAT)	 AG	149129-149140	GT	AGG
(GAC)	 AG	149387-150046	GG	GAG
-recovered pasa_asmbl_29199.p1, terminal, 149387, 150046
-recovered pasa_asmbl_29199.p1, internal, 149129, 149140
Valid prediction for snap_scaffold_22-snap.170-T1
Valid prediction for snap_scaffold_22-snap.189-T1
Valid prediction for HiQ_model.g33638.t1
Valid prediction for snap_scaffold_22-snap.185-T1
Valid prediction for Augustus_model.g33620.t1
Valid prediction for GeneMark_model.86729_t
Valid prediction for Augustus_model.g33640.t1
Couldn't classify 107065, 107097
Couldn't classify 114974, 115112
Sorry, prediction pasa_asmbl_29194.p1 fails validation.
(GGA)	 TG	107065-107097	GT	AGG
(GGC)	 AG	109733-109879	GT	AGG
(GTC)	 AG	111139-111349	GT	AAG
(CTG)	 AG	112091-112281	GT	AGG
(GTG)	 AG	114641-114741	GT	AGG
(GCA)	 AG	114974-115112	GT	AGG
add_exon() Sorry, pasa_asmbl_29194.p1 114641-114741-terminal-2 is invalid.
-recovered pasa_asmbl_29194.p1, terminal, 114641, 114741
-recovered pasa_asmbl_29194.p1, internal, 109733, 109879
-recovered pasa_asmbl_29194.p1, internal, 111139, 111349
-recovered pasa_asmbl_29194.p1, internal, 112091, 112281
-recovered pasa_asmbl_29194.p1, internal, 114641, 114741
-recovered pasa_asmbl_29194.p1, internal, 114974, 115112
Valid prediction for GlimmerHMM_glimmerT_50094-T1
Valid prediction for snap_scaffold_22-snap.198-T1
Valid prediction for Augustus_model.g33633.t1
Valid prediction for snap_scaffold_22-snap.202-T1
Valid prediction for GlimmerHMM_glimmerT_50097-T1
Valid prediction for GlimmerHMM_glimmerT_50109-T1
Valid prediction for snap_scaffold_22-snap.180-T1
Valid prediction for GeneMark_model.86734_t
Valid prediction for Augustus_model.g33627.t1
Valid prediction for CodingQuarry_transcript_34042-T1
Valid prediction for snap_scaffold_22-snap.194-T1
Valid prediction for pasa_asmbl_29212.p1
Valid prediction for GeneMark_model.86725_t
Valid prediction for snap_scaffold_22-snap.205-T1
Valid prediction for snap_scaffold_22-snap.196-T1
Couldn't classify 181732, 181770
Sorry, prediction pasa_asmbl_29724.p2 fails validation.
(CTG)	 CG	181732-181770	GT	TGG
(GAA)	 AG	182122-182191	GT	AGG
(AGA)	 AG	182683-182870	GT	AGG
(ATC)	 AG	183028-183130	GT	GGG
(AAC)	 AG	183279-183364	GT	GGG
(CCC)	 AG	183743-183942	GT	CAG
(GCT)	 AG	184251-184362	CC	AGC
-recovered pasa_asmbl_29724.p2, terminal, 184251, 184362
-recovered pasa_asmbl_29724.p2, internal, 182122, 182191
-recovered pasa_asmbl_29724.p2, internal, 182683, 182870
-recovered pasa_asmbl_29724.p2, internal, 183028, 183130
-recovered pasa_asmbl_29724.p2, internal, 183279, 183364
-recovered pasa_asmbl_29724.p2, internal, 183743, 183942
Valid prediction for snap_scaffold_22-snap.203-T1
Valid prediction for snap_scaffold_22-snap.195-T1
Valid prediction for GlimmerHMM_glimmerT_50114-T1
Valid prediction for CodingQuarry_transcript_34043-T1
Valid prediction for GlimmerHMM_glimmerT_50098-T1
Couldn't classify 98189, 98293
Sorry, prediction pasa_asmbl_29190.p1 fails validation.
(ATG)	 AG	94868-95014	GT	AGG
(AGG)	 AG	95167-95250	GT	AGG
(GTT)	 AG	95597-95708	GT	AGG
(ACC)	 AG	97047-97228	GT	AGG
(AAC)	 AG	98189-98293	GC	TAG
-recovered pasa_asmbl_29190.p1, initial, 94868, 95014
-recovered pasa_asmbl_29190.p1, internal, 94868, 95014
-recovered pasa_asmbl_29190.p1, internal, 95167, 95250
-recovered pasa_asmbl_29190.p1, internal, 95597, 95708
-recovered pasa_asmbl_29190.p1, internal, 97047, 97228
-recovered pasa_asmbl_29190.p1, internal, 98189, 98293
Valid prediction for GeneMark_model.86716_t
Valid prediction for snap_scaffold_22-snap.173-T1
Valid prediction for GeneMark_model.86749_t
Valid prediction for GlimmerHMM_glimmerT_50095-T1
Valid prediction for pasa_asmbl_29214.p1
Valid prediction for GeneMark_model.86741_t
Valid prediction for GeneMark_model.86751_t
Valid prediction for GlimmerHMM_glimmerT_50102-T1
Valid prediction for snap_scaffold_22-snap.175-T1
Valid prediction for GeneMark_model.86736_t
Valid prediction for GlimmerHMM_glimmerT_50092-T1
Valid prediction for GeneMark_model.86719_t
Valid prediction for snap_scaffold_22-snap.206-T1
Valid prediction for Augustus_model.g33623.t1
Valid prediction for GeneMark_model.86718_t
Valid prediction for GeneMark_model.86740_t
Couldn't classify 98632, 98650
Couldn't classify 100312, 100348
Sorry, prediction pasa_asmbl_29193.p1 fails validation.
(GCC)	 CT	98632-98650	GT	CGG
(GTC)	 AG	99065-99150	GT	AGG
(CTG)	 AG	99886-100003	GT	AGG
(AGA)	 AG	100150-100216	GT	GAG
(GAC)	 AG	100312-100348	AG	GGA
-recovered pasa_asmbl_29193.p1, internal, 99065, 99150
-recovered pasa_asmbl_29193.p1, internal, 99886, 100003
-recovered pasa_asmbl_29193.p1, internal, 100150, 100216
Valid prediction for Augustus_model.g33626.t1
Valid prediction for Augustus_model.g33625.t1
Valid prediction for GlimmerHMM_glimmerT_50105-T1
Valid prediction for GlimmerHMM_glimmerT_50121-T1
Valid prediction for GlimmerHMM_glimmerT_50106-T1
Valid prediction for GeneMark_model.86733_t
Valid prediction for snap_scaffold_22-snap.169-T1
Valid prediction for snap_scaffold_22-snap.171-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 145221, 145227
Couldn't classify 148544, 148620
Sorry, prediction pasa_asmbl_29198.p1 fails validation.
(GTC)	 AC	145221-145227	GT	CTG
(TCG)	 AG	145406-145533	GT	TGG
(GTG)	 AG	145699-145825	GT	CGG
(GCC)	 AG	146053-146153	GT	TAG
(GTG)	 AG	147192-147408	GT	AGG
(AAG)	 AG	147767-147874	GT	CAG
(GTC)	 AG	148544-148620	GA	AAG
-recovered pasa_asmbl_29198.p1, internal, 145406, 145533
-recovered pasa_asmbl_29198.p1, internal, 145699, 145825
-recovered pasa_asmbl_29198.p1, internal, 146053, 146153
-recovered pasa_asmbl_29198.p1, internal, 147192, 147408
-recovered pasa_asmbl_29198.p1, internal, 147767, 147874
Valid prediction for HiQ_model.g33629.t1
Valid prediction for snap_scaffold_22-snap.191-T1
Valid prediction for Augustus_model.g33622.t1
Valid prediction for GlimmerHMM_glimmerT_50117-T1
Valid prediction for snap_scaffold_22-snap.199-T1
Valid prediction for pasa_asmbl_29208.p1
Valid prediction for CodingQuarry_transcript_34040-T1
Valid prediction for GeneMark_model.86742_t
Valid prediction for snap_scaffold_22-snap.200-T1
Valid prediction for snap_scaffold_22-snap.201-T1
Valid prediction for pasa_asmbl_29200.p1
Valid prediction for snap_scaffold_22-snap.174-T1
Valid prediction for GlimmerHMM_glimmerT_50108-T1
Valid prediction for HiQ_model.g33632.t1
Valid prediction for snap_scaffold_22-snap.167-T1
Valid prediction for CodingQuarry_transcript_34044-T1
Valid prediction for snap_scaffold_22-snap.178-T1
Couldn't classify 141937, 142087
Couldn't classify 144213, 144362
Sorry, prediction pasa_asmbl_29197.p1 fails validation.
(GTG)	 TA	141937-142087	GT	GGG
(CTT)	 AG	143268-143417	GT	CAG
(TCC)	 AG	143722-143879	GT	CTG
(GAG)	 AG	144213-144362	CG	ACC
-recovered pasa_asmbl_29197.p1, internal, 143268, 143417
-recovered pasa_asmbl_29197.p1, internal, 143722, 143879
Valid prediction for snap_scaffold_22-snap.190-T1
Valid prediction for snap_scaffold_22-snap.183-T1
Couldn't classify 158738, 158924
Sorry, prediction pasa_asmbl_29202.p1 fails validation.
(TGT)	 CG	158738-158924	GT	TGG
(CCG)	 AG	161152-161243	GT	GGG
(GTG)	 AG	161595-161627	GT	CGG
(AAA)	 AG	161733-161753	GT	TGG
(GAA)	 AG	162164-162229	TA	AGT
-recovered pasa_asmbl_29202.p1, terminal, 162164, 162229
-recovered pasa_asmbl_29202.p1, internal, 161152, 161243
-recovered pasa_asmbl_29202.p1, internal, 161595, 161627
-recovered pasa_asmbl_29202.p1, internal, 161733, 161753
Valid prediction for GlimmerHMM_glimmerT_50099-T1
Valid prediction for GeneMark_model.86737_t
Valid prediction for GeneMark_model.86720_t
Valid prediction for GlimmerHMM_glimmerT_50104-T1
Valid prediction for snap_scaffold_22-snap.186-T1
Valid prediction for CodingQuarry_transcript_34046-T1
Valid prediction for Augustus_model.g33639.t1
Valid prediction for GeneMark_model.86728_t
Valid prediction for GlimmerHMM_glimmerT_50116-T1
Valid prediction for HiQ_model.g33631.t1
Valid prediction for snap_scaffold_22-snap.179-T1
Valid prediction for HiQ_model.g33636.t1
Valid prediction for GlimmerHMM_glimmerT_50111-T1
Valid prediction for GlimmerHMM_glimmerT_50112-T1
Valid prediction for GeneMark_model.86731_t
Valid prediction for GeneMark_model.86726_t
Valid prediction for Augustus_model.g33619.t1
Couldn't classify 216296, 216342
Couldn't classify 216379, 216473
Sorry, prediction CodingQuarry_transcript_34047-T1 fails validation.
(ATG)	 CA	214832-214848	GT	CTG
(AAA)	 AG	215045-215167	GT	AGG
(AGG)	 AG	215290-215380	GT	AGG
(GAT)	 AG	215853-215938	GT	AGG
(CTC)	 AG	216296-216342	CT	TGC
(CTC)	 CC	216379-216473	CT	AGC
-recovered CodingQuarry_transcript_34047-T1, initial, 214832, 214848
-recovered CodingQuarry_transcript_34047-T1, internal, 215045, 215167
-recovered CodingQuarry_transcript_34047-T1, internal, 215290, 215380
-recovered CodingQuarry_transcript_34047-T1, internal, 215853, 215938
Valid prediction for GeneMark_model.86745_t
Valid prediction for Augustus_model.g33634.t1
Valid prediction for GeneMark_model.86723_t
Valid prediction for GlimmerHMM_glimmerT_50120-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_22-snap.176-T1
Valid prediction for Augustus_model.g33641.t1
Valid prediction for GeneMark_model.86730_t
Valid prediction for GlimmerHMM_glimmerT_50107-T1
Valid prediction for GlimmerHMM_glimmerT_50119-T1
Valid prediction for snap_scaffold_22-snap.187-T1
Valid prediction for GeneMark_model.86724_t
Valid prediction for Augustus_model.g33621.t1
Valid prediction for snap_scaffold_22-snap.168-T1
Valid prediction for snap_scaffold_22-snap.184-T1
Valid prediction for Augustus_model.g33635.t1
Valid prediction for GeneMark_model.86748_t
Valid prediction for Augustus_model.g33618.t1
Valid prediction for snap_scaffold_22-snap.204-T1
Valid prediction for GlimmerHMM_glimmerT_50093-T1
Valid prediction for snap_scaffold_22-snap.197-T1
Valid prediction for snap_scaffold_22-snap.192-T1
Valid prediction for Augustus_model.g33637.t1
Valid prediction for GlimmerHMM_glimmerT_50103-T1
Valid prediction for GeneMark_model.86722_t
Valid prediction for GeneMark_model.86735_t
Valid prediction for GlimmerHMM_glimmerT_50113-T1
Valid prediction for GeneMark_model.86744_t
Valid prediction for Augustus_model.g33642.t1
Valid prediction for GlimmerHMM_glimmerT_50101-T1
Valid prediction for GeneMark_model.86750_t
Valid prediction for GlimmerHMM_glimmerT_50100-T1
Valid prediction for snap_scaffold_22-snap.193-T1
Valid prediction for snap_scaffold_22-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_50115-T1
Valid prediction for GeneMark_model.86739_t
Valid prediction for Augustus_model.g33628.t1
Valid prediction for GeneMark_model.86747_t
Valid prediction for GlimmerHMM_glimmerT_50096-T1
Valid prediction for snap_scaffold_22-snap.172-T1
Valid prediction for GeneMark_model.86732_t
Valid prediction for GeneMark_model.86717_t
Valid prediction for GlimmerHMM_glimmerT_50110-T1
Valid prediction for GeneMark_model.86738_t
Valid prediction for Augustus_model.g33624.t1
Valid prediction for GeneMark_model.86721_t
Valid prediction for snap_scaffold_22-snap.188-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 150046, rend_intergenic: 142325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166532, rend_intergenic: 164471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 274597
-exon list size: 583


building trellis

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87.7    
87.9    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
90.9    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 150046, rend_intergenic: 142325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166532, rend_intergenic: 164471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support