-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_3997278-4248275

-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.29767_t
Valid prediction for GlimmerHMM_glimmerT_17665-T1
Valid prediction for CodingQuarry_transcript_57332-T1
Valid prediction for GlimmerHMM_glimmerT_17678-T1
Valid prediction for GlimmerHMM_glimmerT_17688-T1
Couldn't classify 223877, 224285
Sorry, prediction pasa_asmbl_50607.p1 fails validation.
(GTC)	 CA	223877-224285	GT	ACG
(GAA)	 AG	224484-224534	GT	TGG
(CTT)	 AG	224784-224894	GT	ACG
(GTG)	 AG	225079-225106	GT	AGG
(CGA)	 AG	225412-225587	GT	AAG
(ATC)	 AG	227719-227756	GG	GAG
-recovered pasa_asmbl_50607.p1, terminal, 227719, 227756
-recovered pasa_asmbl_50607.p1, internal, 224484, 224534
-recovered pasa_asmbl_50607.p1, internal, 224784, 224894
-recovered pasa_asmbl_50607.p1, internal, 225079, 225106
-recovered pasa_asmbl_50607.p1, internal, 225412, 225587
Valid prediction for HiQ_model.g11833.t1
Valid prediction for snap_scaffold_7-snap.954-T1
Valid prediction for Augustus_model.g11852.t1
Couldn't classify 98266, 98350
Sorry, prediction pasa_asmbl_50599.p1 fails validation.
(ATG)	 CG	90549-90623	GT	CGG
(GTC)	 AG	91677-91733	GT	CAG
(GAA)	 AG	91845-91954	GT	CTG
(CCA)	 AG	92057-93095	GT	AGG
(GGT)	 AG	93227-93326	GT	AGG
(AAG)	 AG	93401-93571	GT	CTG
(TGC)	 AG	93662-93759	GT	CAG
(GTC)	 AG	94050-94230	GT	AGG
(GGC)	 AG	96720-96843	GT	AGG
(TGT)	 AG	98266-98350	CC	CAC
-recovered pasa_asmbl_50599.p1, initial, 90549, 90623
-recovered pasa_asmbl_50599.p1, internal, 91677, 91733
-recovered pasa_asmbl_50599.p1, internal, 91845, 91954
-recovered pasa_asmbl_50599.p1, internal, 92057, 93095
-recovered pasa_asmbl_50599.p1, internal, 93227, 93326
-recovered pasa_asmbl_50599.p1, internal, 93401, 93571
-recovered pasa_asmbl_50599.p1, internal, 93662, 93759
-recovered pasa_asmbl_50599.p1, internal, 94050, 94230
-recovered pasa_asmbl_50599.p1, internal, 96720, 96843
Valid prediction for snap_scaffold_7-snap.963-T1
Valid prediction for snap_scaffold_7-snap.948-T1
Valid prediction for Augustus_model.g11832.t1
Valid prediction for GlimmerHMM_glimmerT_17681-T1
Valid prediction for Augustus_model.g11844.t1
Valid prediction for snap_scaffold_7-snap.967-T1
Valid prediction for GlimmerHMM_glimmerT_17667-T1
Valid prediction for snap_scaffold_7-snap.962-T1
Valid prediction for Augustus_model.g11839.t1
Valid prediction for Augustus_model.g11840.t1
Valid prediction for GeneMark_model.29774_t
Valid prediction for GeneMark_model.29780_t
Valid prediction for GeneMark_model.29784_t
Valid prediction for GeneMark_model.29797_t
Valid prediction for GlimmerHMM_glimmerT_17676-T1
Valid prediction for GlimmerHMM_glimmerT_17671-T1
Valid prediction for GlimmerHMM_glimmerT_17677-T1
Valid prediction for snap_scaffold_7-snap.972-T1
Valid prediction for HiQ_model.g11835.t1
Valid prediction for snap_scaffold_7-snap.953-T1
Valid prediction for GeneMark_model.29795_t
Valid prediction for Augustus_model.g11841.t1
Valid prediction for Augustus_model.g11831.t1
Valid prediction for GlimmerHMM_glimmerT_17664-T1
Valid prediction for snap_scaffold_7-snap.958-T1
Valid prediction for snap_scaffold_7-snap.982-T1
Valid prediction for GeneMark_model.29792_t
Valid prediction for snap_scaffold_7-snap.949-T1
Valid prediction for GeneMark_model.29788_t
Valid prediction for snap_scaffold_7-snap.960-T1
Valid prediction for pasa_asmbl_50586.p1
Valid prediction for GeneMark_model.29781_t
Valid prediction for GeneMark_model.29782_t
Valid prediction for snap_scaffold_7-snap.966-T1
Couldn't classify 56103, 56160
Sorry, prediction pasa_asmbl_50595.p1 fails validation.
(GCC)	 AG	56103-56160	GT	AGG
(CGA)	 AG	56311-56398	GT	TTG
(CTT)	 AG	57354-57484	GT	AGG
(TGC)	 AG	57682-57796	GT	AGG
(AGA)	 AG	58074-58192	GT	TGG
(GTG)	 AG	58299-58389	GT	AGG
(GTA)	 AG	60524-60619	GT	AGG
(AGG)	 AG	60749-60842	GT	AGG
(AGG)	 AG	61187-61344	GT	AAG
(ACC)	 AG	61475-61583	GA	AGG
-recovered pasa_asmbl_50595.p1, terminal, 61475, 61583
-recovered pasa_asmbl_50595.p1, internal, 56103, 56160
-recovered pasa_asmbl_50595.p1, internal, 56311, 56398
-recovered pasa_asmbl_50595.p1, internal, 57354, 57484
-recovered pasa_asmbl_50595.p1, internal, 57682, 57796
-recovered pasa_asmbl_50595.p1, internal, 58074, 58192
-recovered pasa_asmbl_50595.p1, internal, 58299, 58389
-recovered pasa_asmbl_50595.p1, internal, 60524, 60619
-recovered pasa_asmbl_50595.p1, internal, 60749, 60842
-recovered pasa_asmbl_50595.p1, internal, 61187, 61344
Valid prediction for CodingQuarry_transcript_57334-T1
Valid prediction for snap_scaffold_7-snap.965-T1
Valid prediction for pasa_asmbl_50603.p1
Valid prediction for GeneMark_model.29790_t
Valid prediction for GlimmerHMM_glimmerT_17686-T1
Valid prediction for GeneMark_model.29775_t
Valid prediction for GlimmerHMM_glimmerT_17683-T1
Valid prediction for GeneMark_model.29769_t
Valid prediction for snap_scaffold_7-snap.983-T1
Valid prediction for HiQ_model.g11846.t1
Valid prediction for CodingQuarry_transcript_57328-T1
Valid prediction for Augustus_model.g11848.t1
Valid prediction for snap_scaffold_7-snap.985-T1
Valid prediction for snap_scaffold_7-snap.973-T1
Valid prediction for HiQ_model.g11850.t1
Valid prediction for GeneMark_model.29786_t
Valid prediction for snap_scaffold_7-snap.964-T1
Valid prediction for CodingQuarry_transcript_57333-T1
Valid prediction for GeneMark_model.29772_t
Valid prediction for CodingQuarry_transcript_57323-T1
Valid prediction for GlimmerHMM_glimmerT_17673-T1
Valid prediction for snap_scaffold_7-snap.959-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_7-snap.952-T1
Valid prediction for snap_scaffold_7-snap.974-T1
Valid prediction for HiQ_model.g11837.t1
Valid prediction for Augustus_model.g11838.t1
Valid prediction for Augustus_model.g11853.t1
Valid prediction for CodingQuarry_transcript_57330-T1
Valid prediction for snap_scaffold_7-snap.986-T1
Valid prediction for GlimmerHMM_glimmerT_17674-T1
Valid prediction for snap_scaffold_7-snap.950-T1
Valid prediction for GeneMark_model.29798_t
Valid prediction for pasa_asmbl_49664.p1
Valid prediction for GeneMark_model.29783_t
Valid prediction for GeneMark_model.29768_t
Couldn't classify 203098, 203231
Sorry, prediction pasa_asmbl_49663.p1 fails validation.
(ATG)	 CC	201371-201471	GT	AAG
(GAT)	 AG	201886-201940	GT	AAG
(TCT)	 AG	202726-202847	GT	AGG
(GAC)	 AG	202944-203023	GT	TGG
(GAT)	 AG	203098-203231	TG	GGT
-recovered pasa_asmbl_49663.p1, initial, 201371, 201471
-recovered pasa_asmbl_49663.p1, internal, 201886, 201940
-recovered pasa_asmbl_49663.p1, internal, 202726, 202847
-recovered pasa_asmbl_49663.p1, internal, 202944, 203023
Valid prediction for snap_scaffold_7-snap.956-T1
Valid prediction for GlimmerHMM_glimmerT_17666-T1
Valid prediction for snap_scaffold_7-snap.957-T1
Valid prediction for Augustus_model.g11842.t1
Couldn't classify 95099, 95193
Sorry, prediction pasa_asmbl_49670.p1 fails validation.
(CCT)	 GT	95099-95193	GT	AGG
(AAT)	 AG	95282-95529	GT	AGG
(GGA)	 AG	95858-95895	GT	TGG
(AAT)	 AG	96095-96118	GT	GAG
-recovered pasa_asmbl_49670.p1, terminal, 96095, 96118
-recovered pasa_asmbl_49670.p1, internal, 95282, 95529
-recovered pasa_asmbl_49670.p1, internal, 95858, 95895
-recovered pasa_asmbl_49670.p1, internal, 96095, 96118
Valid prediction for Augustus_model.g11836.t1
Couldn't classify 84663, 84701
Couldn't classify 91918, 91999
Sorry, prediction pasa_asmbl_49671.p1 fails validation.
(TTT)	 TG	84663-84701	GT	AGG
(GTG)	 AG	85152-85251	GT	AGG
(GGA)	 AG	85832-85876	GT	AGG
(ATG)	 AG	88570-88620	GT	AGG
(ACA)	 AG	88729-88803	GT	ATG
(CCT)	 AG	90289-90475	GT	AGG
(ATA)	 AG	91918-91999	GG	AAG
-recovered pasa_asmbl_49671.p1, initial, 88570, 88620
-recovered pasa_asmbl_49671.p1, internal, 85152, 85251
-recovered pasa_asmbl_49671.p1, internal, 85832, 85876
-recovered pasa_asmbl_49671.p1, internal, 88570, 88620
-recovered pasa_asmbl_49671.p1, internal, 88729, 88803
-recovered pasa_asmbl_49671.p1, internal, 90289, 90475
Valid prediction for GlimmerHMM_glimmerT_17669-T1
Valid prediction for Augustus_model.g11849.t1
Valid prediction for snap_scaffold_7-snap.977-T1
Valid prediction for GeneMark_model.29770_t
Valid prediction for snap_scaffold_7-snap.975-T1
Valid prediction for GeneMark_model.29791_t
Valid prediction for snap_scaffold_7-snap.951-T1
Valid prediction for Augustus_model.g11847.t1
Valid prediction for GeneMark_model.29773_t
Valid prediction for snap_scaffold_7-snap.947-T1
Valid prediction for GlimmerHMM_glimmerT_17687-T1
Valid prediction for snap_scaffold_7-snap.970-T1
Valid prediction for snap_scaffold_7-snap.944-T1
Valid prediction for snap_scaffold_7-snap.968-T1
Valid prediction for Augustus_model.g11834.t1
Valid prediction for GeneMark_model.29777_t
Valid prediction for GlimmerHMM_glimmerT_17682-T1
Valid prediction for Augustus_model.g11851.t1
Valid prediction for Augustus_model.g11830.t1
Valid prediction for GeneMark_model.29785_t
Valid prediction for GeneMark_model.29771_t
Valid prediction for GlimmerHMM_glimmerT_17679-T1
Valid prediction for GeneMark_model.29796_t
Valid prediction for GeneMark_model.29776_t
Valid prediction for snap_scaffold_7-snap.981-T1
Valid prediction for GlimmerHMM_glimmerT_17685-T1
Valid prediction for Augustus_model.g11845.t1
Valid prediction for GeneMark_model.29778_t
Couldn't classify 242265, 242291
Sorry, prediction pasa_asmbl_49656.p1 fails validation.
(CGC)	 CA	242265-242291	GT	AGG
(GTT)	 AG	243329-243450	GT	TGG
(CTT)	 AG	243589-243827	GT	AGG
(TGA)	 AG	244263-244390	GT	AGG
(GCT)	 AG	244893-244994	GT	TGG
(GGT)	 AG	245127-245293	GT	AGG
(GAT)	 AG	246154-246284	GT	AGG
(GTT)	 AG	247105-247265	GA	GAG
-recovered pasa_asmbl_49656.p1, terminal, 247105, 247265
-recovered pasa_asmbl_49656.p1, internal, 243329, 243450
-recovered pasa_asmbl_49656.p1, internal, 243589, 243827
-recovered pasa_asmbl_49656.p1, internal, 244263, 244390
-recovered pasa_asmbl_49656.p1, internal, 244893, 244994
-recovered pasa_asmbl_49656.p1, internal, 245127, 245293
-recovered pasa_asmbl_49656.p1, internal, 246154, 246284
Valid prediction for pasa_asmbl_49669.p1
Valid prediction for CodingQuarry_transcript_57327-T1
Valid prediction for GeneMark_model.29794_t
Valid prediction for Augustus_model.g11843.t1
Valid prediction for GeneMark_model.29793_t
Valid prediction for CodingQuarry_transcript_57331-T1
Valid prediction for snap_scaffold_7-snap.976-T1
Couldn't classify 203637, 203720
Sorry, prediction pasa_asmbl_49658.p1 fails validation.
(TAC)	 TC	203637-203720	GC	AGG
(AAT)	 AG	203856-204023	GT	AGG
(GCG)	 AG	204109-204483	GT	AGG
(GAG)	 AG	204575-204765	GT	AGG
(GTA)	 AG	204948-205090	GT	AGG
(GGA)	 AG	207013-207123	GT	TGG
(GTT)	 AG	207347-207451	GT	AAG
(ATT)	 AG	207606-207757	TG	AGT
-recovered pasa_asmbl_49658.p1, terminal, 207606, 207757
-recovered pasa_asmbl_49658.p1, internal, 203856, 204023
-recovered pasa_asmbl_49658.p1, internal, 204109, 204483
-recovered pasa_asmbl_49658.p1, internal, 204575, 204765
-recovered pasa_asmbl_49658.p1, internal, 204948, 205090
-recovered pasa_asmbl_49658.p1, internal, 207013, 207123
-recovered pasa_asmbl_49658.p1, internal, 207347, 207451
Valid prediction for snap_scaffold_7-snap.979-T1
Valid prediction for CodingQuarry_transcript_57326-T1
Valid prediction for snap_scaffold_7-snap.984-T1
Valid prediction for snap_scaffold_7-snap.980-T1
Valid prediction for GlimmerHMM_glimmerT_17663-T1
Valid prediction for snap_scaffold_7-snap.955-T1
Valid prediction for GlimmerHMM_glimmerT_17680-T1
Valid prediction for GlimmerHMM_glimmerT_17675-T1
Valid prediction for GeneMark_model.29787_t
Valid prediction for GeneMark_model.29789_t
Valid prediction for snap_scaffold_7-snap.978-T1
Valid prediction for GlimmerHMM_glimmerT_17670-T1
Valid prediction for snap_scaffold_7-snap.945-T1
Valid prediction for GeneMark_model.29766_t
Valid prediction for snap_scaffold_7-snap.946-T1
Valid prediction for snap_scaffold_7-snap.961-T1
Valid prediction for CodingQuarry_transcript_57325-T1
Valid prediction for snap_scaffold_7-snap.971-T1
Valid prediction for GlimmerHMM_glimmerT_17684-T1
Valid prediction for CodingQuarry_transcript_57329-T1
Valid prediction for GlimmerHMM_glimmerT_17672-T1
Valid prediction for GlimmerHMM_glimmerT_17668-T1
Valid prediction for snap_scaffold_7-snap.969-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 224263, rend_intergenic: 221175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239776, rend_intergenic: 239209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 250998
-exon list size: 542


building trellis

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82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 224263, rend_intergenic: 221175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 239776, rend_intergenic: 239209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support