-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_4150229-4300705

-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 GlimmerHMM_glimmerT_48696-T1
Valid prediction for GeneMark_model.84521_t
Valid prediction for Augustus_model.g32579.t1
Valid prediction for Augustus_model.g32575.t1
Valid prediction for snap_scaffold_21-snap.802-T1
Couldn't classify 94797, 95037
Sorry, prediction pasa_asmbl_28541.p1 fails validation.
(CAG)	 TG	94797-95037	GT	CGG
(CGG)	 AG	95174-95341	GT	CGG
(GCA)	 AG	95818-96041	GT	AGG
(TCG)	 AG	96404-96593	GT	TGG
(CTC)	 AG	96756-97173	GT	AGG
(TAC)	 AG	97410-97635	GT	AGG
(ATC)	 AG	97807-97998	GT	AGG
(CGA)	 AG	98713-98936	GT	AGG
(GGC)	 AG	99259-99401	GT	AGG
(ACT)	 AG	99530-99688	GT	AGG
(ACT)	 AG	100638-100826	GT	GGG
(AAT)	 AG	101043-101194	GT	AGG
(GGT)	 AG	101400-101564	GT	AGG
(GCA)	 AG	102241-102341	GT	AGG
(ATT)	 AG	102526-102658	CA	AAC
-recovered pasa_asmbl_28541.p1, terminal, 102526, 102658
-recovered pasa_asmbl_28541.p1, internal, 95174, 95341
-recovered pasa_asmbl_28541.p1, internal, 95818, 96041
-recovered pasa_asmbl_28541.p1, internal, 96404, 96593
-recovered pasa_asmbl_28541.p1, internal, 96756, 97173
-recovered pasa_asmbl_28541.p1, internal, 97410, 97635
-recovered pasa_asmbl_28541.p1, internal, 97807, 97998
-recovered pasa_asmbl_28541.p1, internal, 98713, 98936
-recovered pasa_asmbl_28541.p1, internal, 99259, 99401
-recovered pasa_asmbl_28541.p1, internal, 99530, 99688
-recovered pasa_asmbl_28541.p1, internal, 100638, 100826
-recovered pasa_asmbl_28541.p1, internal, 101043, 101194
-recovered pasa_asmbl_28541.p1, internal, 101400, 101564
-recovered pasa_asmbl_28541.p1, internal, 102241, 102341
Valid prediction for GlimmerHMM_glimmerT_48691-T1
Valid prediction for snap_scaffold_21-snap.793-T1
Valid prediction for GlimmerHMM_glimmerT_48689-T1
Valid prediction for GeneMark_model.84510_t
Valid prediction for snap_scaffold_21-snap.800-T1
Valid prediction for GeneMark_model.84497_t
Valid prediction for GlimmerHMM_glimmerT_48675-T1
Valid prediction for snap_scaffold_21-snap.814-T1
Valid prediction for snap_scaffold_21-snap.818-T1
Valid prediction for GlimmerHMM_glimmerT_48698-T1
Valid prediction for GeneMark_model.84523_t
Valid prediction for GlimmerHMM_glimmerT_48682-T1
Couldn't classify 89715, 89810
Couldn't classify 91776, 91802
Sorry, prediction pasa_asmbl_28540.p1 fails validation.
(CGC)	 AC	89715-89810	GT	CGG
(CCT)	 AG	90608-90698	GT	TAG
(GTT)	 AG	91467-91681	GT	AGG
(GAC)	 AG	91776-91802	CT	AGC
-recovered pasa_asmbl_28540.p1, internal, 90608, 90698
-recovered pasa_asmbl_28540.p1, internal, 91467, 91681
Valid prediction for Augustus_model.g32587.t1
Valid prediction for Augustus_model.g32583.t1
Valid prediction for Augustus_model.g32580.t1
Valid prediction for Augustus_model.g32582.t1
Valid prediction for Augustus_model.g32584.t1
Valid prediction for GlimmerHMM_glimmerT_48676-T1
Valid prediction for GlimmerHMM_glimmerT_48690-T1
Valid prediction for snap_scaffold_21-snap.815-T1
Couldn't classify 12152, 12243
Couldn't classify 12868, 12930
Sorry, prediction pasa_asmbl_29039.p1 fails validation.
(GGT)	 CA	12152-12243	GT	ATG
(GGC)	 AG	12406-12496	GT	CGG
(CCG)	 AG	12634-12741	GT	AGG
(CTG)	 AG	12868-12930	GT	AGG
-recovered pasa_asmbl_29039.p1, internal, 12406, 12496
-recovered pasa_asmbl_29039.p1, internal, 12634, 12741
-recovered pasa_asmbl_29039.p1, internal, 12868, 12930
Valid prediction for GeneMark_model.84518_t
Valid prediction for GeneMark_model.84520_t
Valid prediction for Augustus_model.g32585.t1
Valid prediction for GeneMark_model.84495_t
Valid prediction for GeneMark_model.84492_t
Valid prediction for GeneMark_model.84500_t
Valid prediction for GlimmerHMM_glimmerT_48699-T1
Valid prediction for snap_scaffold_21-snap.797-T1
Valid prediction for GlimmerHMM_glimmerT_48693-T1
Valid prediction for GeneMark_model.84529_t
Valid prediction for GeneMark_model.84505_t
Valid prediction for snap_scaffold_21-snap.820-T1
Valid prediction for GeneMark_model.84507_t
Valid prediction for Augustus_model.g32578.t1
Valid prediction for GlimmerHMM_glimmerT_48679-T1
Couldn't classify 120253, 120276
Sorry, prediction pasa_asmbl_29021.p1 fails validation.
(GCC)	 TG	120253-120276	GT	AGG
(ATC)	 AG	120539-120644	GT	AGG
(TTC)	 AG	120809-120985	GT	CCG
(GCC)	 AG	121089-121264	AC	AGA
-recovered pasa_asmbl_29021.p1, terminal, 121089, 121264
-recovered pasa_asmbl_29021.p1, internal, 120539, 120644
-recovered pasa_asmbl_29021.p1, internal, 120809, 120985
Valid prediction for snap_scaffold_21-snap.807-T1
Valid prediction for snap_scaffold_21-snap.811-T1
Valid prediction for GeneMark_model.84516_t
Valid prediction for GeneMark_model.84525_t
Valid prediction for GeneMark_model.84512_t
Valid prediction for GlimmerHMM_glimmerT_48686-T1
Valid prediction for GeneMark_model.84502_t
Valid prediction for GeneMark_model.84532_t
Valid prediction for snap_scaffold_21-snap.819-T1
Valid prediction for GeneMark_model.84503_t
Couldn't classify 105830, 106092
Couldn't classify 108255, 108302
Sorry, prediction pasa_asmbl_28542.p1 fails validation.
(AGC)	 TC	105830-106092	GT	AGG
(ACA)	 AG	106250-106388	GT	AGG
(GTG)	 AG	106501-106603	GT	AGG
(AGC)	 AG	106742-106855	GT	AGG
(TGT)	 AG	108037-108167	GT	TGG
(GTG)	 AG	108255-108302	TA	ACT
-recovered pasa_asmbl_28542.p1, internal, 106250, 106388
-recovered pasa_asmbl_28542.p1, internal, 106501, 106603
-recovered pasa_asmbl_28542.p1, internal, 106742, 106855
-recovered pasa_asmbl_28542.p1, internal, 108037, 108167
Valid prediction for Augustus_model.g32586.t1
Valid prediction for snap_scaffold_21-snap.792-T1
Valid prediction for GeneMark_model.84508_t
Valid prediction for GeneMark_model.84513_t
Valid prediction for snap_scaffold_21-snap.809-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.84514_t
Valid prediction for GlimmerHMM_glimmerT_48680-T1
Valid prediction for GlimmerHMM_glimmerT_48692-T1
Valid prediction for GeneMark_model.84527_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_48697-T1
Valid prediction for GlimmerHMM_glimmerT_48684-T1
Valid prediction for GlimmerHMM_glimmerT_48677-T1
Valid prediction for GlimmerHMM_glimmerT_48678-T1
Valid prediction for GeneMark_model.84494_t
Valid prediction for GeneMark_model.84498_t
Valid prediction for snap_scaffold_21-snap.798-T1
Valid prediction for snap_scaffold_21-snap.812-T1
Valid prediction for GeneMark_model.84499_t
Valid prediction for snap_scaffold_21-snap.794-T1
Valid prediction for snap_scaffold_21-snap.817-T1
Valid prediction for snap_scaffold_21-snap.796-T1
Couldn't classify 128733, 128784
Sorry, prediction pasa_asmbl_27593.p1 fails validation.
(CTT)	 GT	128733-128784	GT	TGG
(GTC)	 AG	128933-129009	GT	AGG
(GAT)	 AG	129176-129276	GT	TGG
(CCT)	 AG	129370-129523	GT	AGG
(GGG)	 AG	129648-129806	GT	AGG
(CTA)	 AG	129935-130000	GT	AGG
(CAC)	 AG	130112-130213	GT	AGG
(CAT)	 AG	130352-130486	CG	GAC
-recovered pasa_asmbl_27593.p1, terminal, 130352, 130486
-recovered pasa_asmbl_27593.p1, internal, 128933, 129009
-recovered pasa_asmbl_27593.p1, internal, 129176, 129276
-recovered pasa_asmbl_27593.p1, internal, 129370, 129523
-recovered pasa_asmbl_27593.p1, internal, 129648, 129806
-recovered pasa_asmbl_27593.p1, internal, 129935, 130000
-recovered pasa_asmbl_27593.p1, internal, 130112, 130213
Valid prediction for snap_scaffold_21-snap.808-T1
Valid prediction for GeneMark_model.84519_t
Valid prediction for GeneMark_model.84509_t
Valid prediction for GlimmerHMM_glimmerT_48695-T1
Valid prediction for Augustus_model.g32577.t1
Valid prediction for snap_scaffold_21-snap.816-T1
Valid prediction for GlimmerHMM_glimmerT_48694-T1
Valid prediction for GeneMark_model.84517_t
Valid prediction for snap_scaffold_21-snap.804-T1
Valid prediction for snap_scaffold_21-snap.801-T1
Valid prediction for GlimmerHMM_glimmerT_48681-T1
Valid prediction for snap_scaffold_21-snap.803-T1
Valid prediction for GeneMark_model.84531_t
Valid prediction for snap_scaffold_21-snap.806-T1
Valid prediction for GeneMark_model.84491_t
Valid prediction for GeneMark_model.84526_t
Valid prediction for Augustus_model.g32581.t1
Valid prediction for GeneMark_model.84501_t
Valid prediction for snap_scaffold_21-snap.805-T1
Valid prediction for GeneMark_model.84493_t
Valid prediction for GeneMark_model.84524_t
Valid prediction for GlimmerHMM_glimmerT_48688-T1
Valid prediction for Augustus_model.g32576.t1
Valid prediction for Augustus_model.g32588.t1
Valid prediction for snap_scaffold_21-snap.810-T1
Valid prediction for snap_scaffold_21-snap.799-T1
Valid prediction for GeneMark_model.84530_t
Valid prediction for snap_scaffold_21-snap.795-T1
Valid prediction for GeneMark_model.84528_t
Valid prediction for GeneMark_model.84522_t
Valid prediction for GlimmerHMM_glimmerT_48687-T1
Valid prediction for GeneMark_model.84496_t
Valid prediction for GlimmerHMM_glimmerT_48685-T1
Valid prediction for GeneMark_model.84490_t
Valid prediction for GlimmerHMM_glimmerT_48674-T1
Valid prediction for GeneMark_model.84504_t
Valid prediction for CodingQuarry_transcript_32444-T1
Couldn't classify 128345, 128651
Sorry, prediction pasa_asmbl_27594.p1 fails validation.
(ATG)	 CC	127802-127827	GT	AGG
(GAG)	 AG	128345-128651	GC	CGG
-recovered pasa_asmbl_27594.p1, initial, 127802, 127827
-recovered pasa_asmbl_27594.p1, internal, 128345, 128651
Valid prediction for snap_scaffold_21-snap.813-T1
Valid prediction for GeneMark_model.84515_t
Valid prediction for GeneMark_model.84506_t
Valid prediction for GlimmerHMM_glimmerT_48683-T1
Valid prediction for GeneMark_model.84511_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34983, rend_intergenic: 31436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43293, rend_intergenic: 41868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57299, rend_intergenic: 53274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76734, rend_intergenic: 65278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83249, rend_intergenic: 76763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94417, rend_intergenic: 83297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102815, rend_intergenic: 100021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124158, rend_intergenic: 105835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131306, rend_intergenic: 128639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150477
-exon list size: 686


building trellis

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85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 34983, rend_intergenic: 31436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43293, rend_intergenic: 41868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57299, rend_intergenic: 53274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76734, rend_intergenic: 65278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83249, rend_intergenic: 76763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94417, rend_intergenic: 83297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102815, rend_intergenic: 100021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124158, rend_intergenic: 105835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131306, rend_intergenic: 128639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support