-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_7481914-7636756

-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.g26472.t1
Valid prediction for pasa_asmbl_17145.p1
Valid prediction for GlimmerHMM_glimmerT_39403-T1
Valid prediction for snap_scaffold_16-snap.1388-T1
Valid prediction for GlimmerHMM_glimmerT_39400-T1
Valid prediction for GeneMark_model.67460_t
Valid prediction for GlimmerHMM_glimmerT_39413-T1
Valid prediction for GeneMark_model.67480_t
Valid prediction for snap_scaffold_16-snap.1400-T1
Valid prediction for CodingQuarry_transcript_19971-T1
Valid prediction for Augustus_model.g26475.t1
Valid prediction for Augustus_model.g26483.t1
Valid prediction for GlimmerHMM_glimmerT_39393-T1
Valid prediction for HiQ_model.g26467.t1
Valid prediction for GeneMark_model.67464_t
Valid prediction for GlimmerHMM_glimmerT_39395-T1
Couldn't classify 36046, 36216
Sorry, prediction pasa_asmbl_17139.p1 fails validation.
(GTA)	 GT	36046-36216	GT	CAG
(AAT)	 AG	37253-37385	GT	AGG
(AGG)	 AG	37712-37838	GT	GGG
(ACA)	 AG	37989-38081	GT	AGG
(CAC)	 AG	38194-38306	GT	AGG
(CTG)	 AG	38440-38483	CC	AAC
add_exon() Sorry, pasa_asmbl_17139.p1 37253-37385-terminal-3 is invalid.
-recovered pasa_asmbl_17139.p1, terminal, 37253, 37385
-recovered pasa_asmbl_17139.p1, terminal, 38440, 38483
-recovered pasa_asmbl_17139.p1, internal, 37253, 37385
-recovered pasa_asmbl_17139.p1, internal, 37712, 37838
-recovered pasa_asmbl_17139.p1, internal, 37989, 38081
-recovered pasa_asmbl_17139.p1, internal, 38194, 38306
Valid prediction for CodingQuarry_transcript_19967-T1
Valid prediction for snap_scaffold_16-snap.1384-T1
Valid prediction for Augustus_model.g26481.t1
Valid prediction for GeneMark_model.67457_t
Valid prediction for pasa_asmbl_17138.p1
Valid prediction for snap_scaffold_16-snap.1402-T1
Valid prediction for GlimmerHMM_glimmerT_39406-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1385-T1
Valid prediction for GeneMark_model.67477_t
Valid prediction for pasa_asmbl_17136.p1
Valid prediction for CodingQuarry_transcript_19966-T1
Valid prediction for snap_scaffold_16-snap.1389-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_39401-T1
Couldn't classify 120334, 120405
Sorry, prediction pasa_asmbl_17152.p1 fails validation.
(TAC)	 AG	120334-120405	GT	AGG
(AAC)	 AG	120531-120619	GT	AGG
(CTG)	 AG	120779-120884	GT	AGG
(ATG)	 AG	120957-121016	GT	TGG
(GGT)	 AG	121154-121245	GT	AGG
(ATG)	 AG	121379-121413	GT	CGG
(TGC)	 AG	121575-121654	GT	AGG
(CAA)	 AG	121752-121851	GT	AGG
(GAG)	 AG	121994-122118	GT	AGG
(GAT)	 AG	123933-124037	GT	CGG
(GAT)	 AG	124127-124253	GT	CCG
(GTA)	 AG	124426-124607	GT	TGG
(GCC)	 AG	124773-124916	AA	AGA
-recovered pasa_asmbl_17152.p1, initial, 120957, 121016
add_exon() Sorry, pasa_asmbl_17152.p1 121379-121413-initial-1 is invalid.
-recovered pasa_asmbl_17152.p1, initial, 121379, 121413
-recovered pasa_asmbl_17152.p1, terminal, 121752, 121851
-recovered pasa_asmbl_17152.p1, terminal, 124773, 124916
-recovered pasa_asmbl_17152.p1, internal, 120334, 120405
-recovered pasa_asmbl_17152.p1, internal, 120531, 120619
-recovered pasa_asmbl_17152.p1, internal, 120779, 120884
-recovered pasa_asmbl_17152.p1, internal, 120957, 121016
-recovered pasa_asmbl_17152.p1, internal, 121154, 121245
-recovered pasa_asmbl_17152.p1, internal, 121379, 121413
-recovered pasa_asmbl_17152.p1, internal, 121575, 121654
-recovered pasa_asmbl_17152.p1, internal, 121752, 121851
-recovered pasa_asmbl_17152.p1, internal, 121994, 122118
-recovered pasa_asmbl_17152.p1, internal, 123933, 124037
-recovered pasa_asmbl_17152.p1, internal, 124127, 124253
-recovered pasa_asmbl_17152.p1, internal, 124426, 124607
Valid prediction for GlimmerHMM_glimmerT_39397-T1
Couldn't classify 33653, 33758
Couldn't classify 36096, 36264
Sorry, prediction pasa_asmbl_17141.p1 fails validation.
(CAT)	 CC	33653-33758	GT	TTG
(TCA)	 AG	34421-34447	GT	CAG
(TAA)	 AG	35250-35344	GT	AGG
(TTC)	 AG	35446-35566	GT	AGG
(CTG)	 AG	35695-35764	GT	ATG
(GTG)	 AG	35857-35889	GT	TGG
(GGT)	 AG	36096-36264	CT	CCC
-recovered pasa_asmbl_17141.p1, internal, 34421, 34447
-recovered pasa_asmbl_17141.p1, internal, 35250, 35344
-recovered pasa_asmbl_17141.p1, internal, 35446, 35566
-recovered pasa_asmbl_17141.p1, internal, 35695, 35764
-recovered pasa_asmbl_17141.p1, internal, 35857, 35889
Valid prediction for HiQ_model.g26469.t1
Valid prediction for GlimmerHMM_glimmerT_39411-T1
Valid prediction for snap_scaffold_16-snap.1380-T1
Valid prediction for GeneMark_model.67452_t
Valid prediction for GeneMark_model.67469_t
Valid prediction for snap_scaffold_16-snap.1382-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_19968-T1
Valid prediction for GeneMark_model.67478_t
Valid prediction for CodingQuarry_transcript_19963-T1
Valid prediction for GlimmerHMM_glimmerT_39407-T1
Valid prediction for GeneMark_model.67453_t
Valid prediction for GeneMark_model.67471_t
Couldn't classify 78009, 78080
Couldn't classify 79376, 79405
Sorry, prediction pasa_asmbl_17150.p1 fails validation.
(GGA)	 AC	78009-78080	GT	AGG
(GTG)	 AG	78558-78763	GT	AAG
(CTA)	 AG	79142-79274	GT	AGG
(GCC)	 AG	79376-79405	GA	CAG
-recovered pasa_asmbl_17150.p1, internal, 78558, 78763
-recovered pasa_asmbl_17150.p1, internal, 79142, 79274
Valid prediction for snap_scaffold_16-snap.1394-T1
Valid prediction for HiQ_model.g26479.t1
Valid prediction for GlimmerHMM_glimmerT_39418-T1
Valid prediction for GeneMark_model.67459_t
Valid prediction for GlimmerHMM_glimmerT_39398-T1
Valid prediction for Augustus_model.g26476.t1
Couldn't classify 65685, 65752
Sorry, prediction pasa_asmbl_17147.p1 fails validation.
(ATG)	 TC	64795-64843	GT	TGG
(CAG)	 AG	65085-65209	GT	AGG
(GTG)	 AG	65302-65398	GT	TGG
(ATG)	 AG	65493-65573	GT	AGG
(GTA)	 AG	65685-65752	AG	ACA
-recovered pasa_asmbl_17147.p1, initial, 64795, 64843
-recovered pasa_asmbl_17147.p1, initial, 65493, 65573
-recovered pasa_asmbl_17147.p1, internal, 65085, 65209
-recovered pasa_asmbl_17147.p1, internal, 65302, 65398
-recovered pasa_asmbl_17147.p1, internal, 65493, 65573
Valid prediction for GlimmerHMM_glimmerT_39405-T1
Valid prediction for GeneMark_model.67466_t
Valid prediction for snap_scaffold_16-snap.1386-T1
Valid prediction for CodingQuarry_transcript_19965-T1
Valid prediction for GeneMark_model.67449_t
Valid prediction for GeneMark_model.67447_t
Valid prediction for HiQ_model.g26473.t1
Valid prediction for GlimmerHMM_glimmerT_39402-T1
Valid prediction for GeneMark_model.67455_t
Valid prediction for GeneMark_model.67462_t
Couldn't classify 48259, 48303
Sorry, prediction pasa_asmbl_17143.p1 fails validation.
(ACC)	 CC	48259-48303	GT	AGG
(TTG)	 AG	48416-48521	GT	CTG
(TGA)	 AG	48884-49041	GC	GAG
-recovered pasa_asmbl_17143.p1, terminal, 48884, 49041
-recovered pasa_asmbl_17143.p1, internal, 48416, 48521
-recovered pasa_asmbl_17143.p1, internal, 48884, 49041
Valid prediction for Augustus_model.g26471.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.67484_t
Valid prediction for snap_scaffold_16-snap.1395-T1
Valid prediction for GeneMark_model.67472_t
Valid prediction for snap_scaffold_16-snap.1392-T1
Valid prediction for snap_scaffold_16-snap.1403-T1
Valid prediction for GeneMark_model.67482_t
Valid prediction for snap_scaffold_16-snap.1390-T1
Valid prediction for snap_scaffold_16-snap.1387-T1
Valid prediction for pasa_asmbl_16361.p1
Valid prediction for CodingQuarry_transcript_19964-T1
Valid prediction for Augustus_model.g26482.t1
Valid prediction for Augustus_model.g26465.t1
Valid prediction for pasa_asmbl_16365.p1
Valid prediction for GeneMark_model.67468_t
Valid prediction for GlimmerHMM_glimmerT_39394-T1
Valid prediction for GeneMark_model.67467_t
Valid prediction for snap_scaffold_16-snap.1399-T1
Valid prediction for snap_scaffold_16-snap.1405-T1
Valid prediction for CodingQuarry_transcript_19973-T1
Valid prediction for snap_scaffold_16-snap.1383-T1
Valid prediction for GeneMark_model.67481_t
Valid prediction for GeneMark_model.67473_t
Couldn't classify 122048, 122497
Sorry, prediction pasa_asmbl_16360.p1 fails validation.
(ATT)	 CC	122048-122497	AT	GAA
Valid prediction for CodingQuarry_transcript_19972-T1
Valid prediction for GeneMark_model.67450_t
Valid prediction for snap_scaffold_16-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_39392-T1
Valid prediction for snap_scaffold_16-snap.1393-T1
Valid prediction for GeneMark_model.67454_t
Valid prediction for Augustus_model.g26470.t1
Valid prediction for snap_scaffold_16-snap.1396-T1
Valid prediction for HiQ_model.g26474.t1
Valid prediction for GlimmerHMM_glimmerT_39415-T1
Valid prediction for snap_scaffold_16-snap.1397-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_39416-T1
Valid prediction for CodingQuarry_transcript_19970-T1
Valid prediction for snap_scaffold_16-snap.1381-T1
Valid prediction for GeneMark_model.67474_t
Valid prediction for CodingQuarry_transcript_19969-T1
Valid prediction for pasa_asmbl_16367.p1
Valid prediction for Augustus_model.g26466.t1
Valid prediction for Augustus_model.g26468.t1
Valid prediction for GeneMark_model.67479_t
Valid prediction for GeneMark_model.67461_t
Valid prediction for HiQ_model.g26480.t1
Valid prediction for snap_scaffold_16-snap.1398-T1
Valid prediction for Augustus_model.g26478.t1
Valid prediction for GlimmerHMM_glimmerT_39399-T1
Valid prediction for GlimmerHMM_glimmerT_39410-T1
Valid prediction for GlimmerHMM_glimmerT_39404-T1
Valid prediction for GlimmerHMM_glimmerT_39408-T1
Valid prediction for GlimmerHMM_glimmerT_39417-T1
Valid prediction for GlimmerHMM_glimmerT_39396-T1
Valid prediction for GeneMark_model.67458_t
Valid prediction for GeneMark_model.67446_t
Valid prediction for pasa_asmbl_16358.p1
Valid prediction for GeneMark_model.67448_t
Valid prediction for GeneMark_model.67476_t
Valid prediction for GeneMark_model.67451_t
Valid prediction for HiQ_model.g26477.t1
Valid prediction for GlimmerHMM_glimmerT_39412-T1
Valid prediction for GeneMark_model.67470_t
Valid prediction for GeneMark_model.67483_t
Valid prediction for GlimmerHMM_glimmerT_39414-T1
Valid prediction for snap_scaffold_16-snap.1379-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1401-T1
Valid prediction for GlimmerHMM_glimmerT_39409-T1
Valid prediction for GeneMark_model.67456_t
Valid prediction for snap_scaffold_16-snap.1404-T1
Valid prediction for pasa_asmbl_16363.p1
Valid prediction for snap_scaffold_16-snap.1378-T1
Valid prediction for GeneMark_model.67463_t
Valid prediction for GeneMark_model.67465_t
Valid prediction for GeneMark_model.67475_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 62590, rend_intergenic: 60717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90214, rend_intergenic: 64851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100003, rend_intergenic: 97759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134548, rend_intergenic: 130044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154843
-exon list size: 612


building trellis

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91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 62590, rend_intergenic: 60717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90214, rend_intergenic: 64851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100003, rend_intergenic: 97759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134548, rend_intergenic: 130044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support