-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_5185983-5379207

-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_17-snap.1083-T1
Valid prediction for snap_scaffold_17-snap.1105-T1
Couldn't classify 177228, 177260
Couldn't classify 177935, 177953
Sorry, prediction pasa_asmbl_18637.p1 fails validation.
(GTG)	 AG	177228-177260	GT	TGG
(ACA)	 AG	177417-177524	GT	AGG
(CGC)	 AG	177635-177807	GT	ACG
(AAA)	 AG	177935-177953	AC	ACA
-recovered pasa_asmbl_18637.p1, internal, 177228, 177260
-recovered pasa_asmbl_18637.p1, internal, 177417, 177524
-recovered pasa_asmbl_18637.p1, internal, 177635, 177807
Valid prediction for snap_scaffold_17-snap.1092-T1
Valid prediction for GlimmerHMM_glimmerT_41198-T1
Valid prediction for snap_scaffold_17-snap.1085-T1
Valid prediction for Augustus_model.g27584.t1
Valid prediction for GlimmerHMM_glimmerT_41199-T1
Valid prediction for GlimmerHMM_glimmerT_41193-T1
Valid prediction for GlimmerHMM_glimmerT_41204-T1
Valid prediction for Augustus_model.g27593.t1
Valid prediction for snap_scaffold_17-snap.1079-T1
Valid prediction for GlimmerHMM_glimmerT_41186-T1
Valid prediction for snap_scaffold_17-snap.1094-T1
Valid prediction for GlimmerHMM_glimmerT_41184-T1
Valid prediction for GlimmerHMM_glimmerT_41205-T1
Valid prediction for Augustus_model.g27591.t1
Valid prediction for GlimmerHMM_glimmerT_41188-T1
Valid prediction for GeneMark_model.70997_t
Valid prediction for Augustus_model.g27592.t1
Valid prediction for GeneMark_model.70959_t
Valid prediction for GlimmerHMM_glimmerT_41183-T1
Couldn't classify 102235, 102573
Sorry, prediction pasa_asmbl_17943.p1 fails validation.
(CCC)	 AC	102235-102573	CA	GAC
Valid prediction for snap_scaffold_17-snap.1074-T1
Valid prediction for GeneMark_model.70986_t
Valid prediction for pasa_asmbl_17947.p1
Valid prediction for snap_scaffold_17-snap.1099-T1
Valid prediction for snap_scaffold_17-snap.1108-T1
Valid prediction for snap_scaffold_17-snap.1093-T1
Valid prediction for GlimmerHMM_glimmerT_41189-T1
Couldn't classify 144281, 145126
Sorry, prediction pasa_asmbl_17946.p1 fails validation.
(ATG)	 CG	144281-145126	GA	ATG
Valid prediction for Augustus_model.g27601.t1
Valid prediction for Augustus_model.g27583.t1
Valid prediction for GeneMark_model.70991_t
Valid prediction for Augustus_model.g27602.t1
Valid prediction for GeneMark_model.70961_t
Valid prediction for snap_scaffold_17-snap.1087-T1
Valid prediction for GlimmerHMM_glimmerT_41203-T1
Valid prediction for GeneMark_model.70956_t
Valid prediction for GeneMark_model.70964_t
Valid prediction for GeneMark_model.70996_t
Valid prediction for snap_scaffold_17-snap.1073-T1
Valid prediction for Augustus_model.g27588.t1
Valid prediction for GlimmerHMM_glimmerT_41190-T1
Valid prediction for GeneMark_model.70985_t
Valid prediction for snap_scaffold_17-snap.1080-T1
Valid prediction for GeneMark_model.70981_t
Valid prediction for Augustus_model.g27603.t1
Valid prediction for Augustus_model.g27594.t1
Valid prediction for snap_scaffold_17-snap.1101-T1
Valid prediction for snap_scaffold_17-snap.1098-T1
Couldn't classify 130423, 130526
Sorry, prediction pasa_asmbl_17944.p1 fails validation.
(CAG)	 CC	130423-130526	GT	TGG
(CTG)	 AG	130640-130774	GT	GGG
(ATT)	 AG	132465-132582	GT	AGG
(ATT)	 AG	133141-133233	GT	AGG
(GAT)	 AG	133683-133779	GT	AGG
(TGG)	 AG	136536-136587	GT	AGG
(AAC)	 AG	137062-137190	GT	AAG
(GAG)	 AG	138260-138395	GT	AGG
(CTG)	 AG	138805-138950	GT	AGG
(AAC)	 AG	139204-139240	AA	AAA
-recovered pasa_asmbl_17944.p1, terminal, 139204, 139240
-recovered pasa_asmbl_17944.p1, internal, 130640, 130774
-recovered pasa_asmbl_17944.p1, internal, 132465, 132582
-recovered pasa_asmbl_17944.p1, internal, 133141, 133233
-recovered pasa_asmbl_17944.p1, internal, 133683, 133779
-recovered pasa_asmbl_17944.p1, internal, 136536, 136587
-recovered pasa_asmbl_17944.p1, internal, 137062, 137190
-recovered pasa_asmbl_17944.p1, internal, 138260, 138395
-recovered pasa_asmbl_17944.p1, internal, 138805, 138950
Valid prediction for CodingQuarry_transcript_21940-T1
Valid prediction for Augustus_model.g27587.t1
Valid prediction for snap_scaffold_17-snap.1107-T1
Valid prediction for Augustus_model.g27600.t1
Valid prediction for snap_scaffold_17-snap.1096-T1
Valid prediction for GlimmerHMM_glimmerT_41197-T1
Valid prediction for GlimmerHMM_glimmerT_41202-T1
Valid prediction for GeneMark_model.70962_t
Valid prediction for GeneMark_model.70976_t
Valid prediction for HiQ_model.g27595.t1
Valid prediction for GeneMark_model.70968_t
Valid prediction for GlimmerHMM_glimmerT_41201-T1
Valid prediction for snap_scaffold_17-snap.1084-T1
Valid prediction for GeneMark_model.70971_t
Valid prediction for snap_scaffold_17-snap.1106-T1
Valid prediction for GeneMark_model.70973_t
Valid prediction for GeneMark_model.70993_t
Valid prediction for GeneMark_model.70978_t
Valid prediction for GeneMark_model.70974_t
Valid prediction for GeneMark_model.70989_t
Valid prediction for snap_scaffold_17-snap.1104-T1
Valid prediction for GeneMark_model.70995_t
Valid prediction for Augustus_model.g27596.t1
Valid prediction for Augustus_model.g27598.t1
Valid prediction for Augustus_model.g27586.t1
Valid prediction for GlimmerHMM_glimmerT_41191-T1
Valid prediction for GlimmerHMM_glimmerT_41196-T1
Valid prediction for GeneMark_model.70957_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 Augustus_model.g27585.t1
Valid prediction for snap_scaffold_17-snap.1100-T1
Valid prediction for snap_scaffold_17-snap.1076-T1
Valid prediction for snap_scaffold_17-snap.1075-T1
Valid prediction for snap_scaffold_17-snap.1090-T1
Couldn't classify 115396, 115465
Couldn't classify 117318, 117383
Sorry, prediction pasa_asmbl_18967.p1 fails validation.
(ATT)	 GT	115396-115465	GT	AGG
(GTT)	 AG	115593-115702	GT	TGG
(GCC)	 AG	115826-115918	GT	AGG
(CAA)	 AG	116705-116819	GT	CGG
(GGC)	 AG	117080-117201	GT	AGG
(CAA)	 AG	117318-117383	CT	TCC
-recovered pasa_asmbl_18967.p1, internal, 115593, 115702
-recovered pasa_asmbl_18967.p1, internal, 115826, 115918
-recovered pasa_asmbl_18967.p1, internal, 116705, 116819
-recovered pasa_asmbl_18967.p1, internal, 117080, 117201
Valid prediction for snap_scaffold_17-snap.1088-T1
Valid prediction for GeneMark_model.70994_t
Valid prediction for HiQ_model.g27590.t1
Valid prediction for GeneMark_model.70992_t
Valid prediction for snap_scaffold_17-snap.1081-T1
Couldn't classify 118314, 118379
Sorry, prediction pasa_asmbl_18966.p1 fails validation.
(CAG)	 CC	118314-118379	GC	TGG
(GTG)	 AG	118753-118948	GT	TGG
(AGA)	 AG	119056-119147	GT	AGG
(GCG)	 AG	119366-119521	GT	AGG
(AAA)	 AG	119706-119789	GT	ATG
(CGA)	 AG	119915-120115	GT	AGG
(GGT)	 AG	120383-120533	GT	AGG
(GTG)	 AG	120877-121041	GT	AGG
(CCG)	 AG	121416-121617	GT	ACG
(GTC)	 AG	123047-123126	GT	TGG
(ACG)	 AG	123322-123420	GT	AGG
(CCA)	 AG	124099-124230	GT	AGG
(GAA)	 AG	124322-124419	GT	GCG
(AAG)	 AG	124521-124688	AC	AGA
-recovered pasa_asmbl_18966.p1, terminal, 124521, 124688
-recovered pasa_asmbl_18966.p1, internal, 118753, 118948
-recovered pasa_asmbl_18966.p1, internal, 119056, 119147
-recovered pasa_asmbl_18966.p1, internal, 119366, 119521
-recovered pasa_asmbl_18966.p1, internal, 119706, 119789
-recovered pasa_asmbl_18966.p1, internal, 119915, 120115
-recovered pasa_asmbl_18966.p1, internal, 120383, 120533
-recovered pasa_asmbl_18966.p1, internal, 120877, 121041
-recovered pasa_asmbl_18966.p1, internal, 121416, 121617
-recovered pasa_asmbl_18966.p1, internal, 123047, 123126
-recovered pasa_asmbl_18966.p1, internal, 123322, 123420
-recovered pasa_asmbl_18966.p1, internal, 124099, 124230
-recovered pasa_asmbl_18966.p1, internal, 124322, 124419
Valid prediction for GeneMark_model.70960_t
Valid prediction for GeneMark_model.70972_t
Valid prediction for snap_scaffold_17-snap.1078-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.70969_t
Valid prediction for GeneMark_model.70988_t
Valid prediction for snap_scaffold_17-snap.1089-T1
Valid prediction for GeneMark_model.70987_t
Valid prediction for snap_scaffold_17-snap.1091-T1
Valid prediction for GeneMark_model.70965_t
Valid prediction for GeneMark_model.70970_t
Couldn't classify 111615, 111679
Sorry, prediction pasa_asmbl_18968.p2 fails validation.
(ATG)	 CG	109365-109406	GT	TGG
(AAC)	 AG	110526-110705	GT	AGG
(CAA)	 AG	110828-110918	GT	GGG
(TAA)	 AG	111615-111679	TA	CGT
-recovered pasa_asmbl_18968.p2, initial, 109365, 109406
-recovered pasa_asmbl_18968.p2, internal, 110526, 110705
-recovered pasa_asmbl_18968.p2, internal, 110828, 110918
Valid prediction for GeneMark_model.70977_t
Valid prediction for CodingQuarry_transcript_21939-T1
Valid prediction for Augustus_model.g27582.t1
Valid prediction for GeneMark_model.70979_t
Valid prediction for snap_scaffold_17-snap.1082-T1
Valid prediction for GeneMark_model.70975_t
Valid prediction for GlimmerHMM_glimmerT_41185-T1
Valid prediction for pasa_asmbl_18969.p1
Valid prediction for Augustus_model.g27599.t1
Valid prediction for GlimmerHMM_glimmerT_41195-T1
Valid prediction for snap_scaffold_17-snap.1077-T1
Valid prediction for GlimmerHMM_glimmerT_41200-T1
Valid prediction for GeneMark_model.70984_t
Valid prediction for snap_scaffold_17-snap.1102-T1
Valid prediction for GlimmerHMM_glimmerT_41192-T1
Valid prediction for GlimmerHMM_glimmerT_41194-T1
Valid prediction for snap_scaffold_17-snap.1086-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GeneMark_model.70980_t
Valid prediction for GeneMark_model.70983_t
Valid prediction for snap_scaffold_17-snap.1095-T1
Valid prediction for Augustus_model.g27597.t1
Valid prediction for GeneMark_model.70966_t
Valid prediction for snap_scaffold_17-snap.1103-T1
Valid prediction for GeneMark_model.70967_t
Valid prediction for Augustus_model.g27589.t1
Valid prediction for GlimmerHMM_glimmerT_41187-T1
Valid prediction for GeneMark_model.70958_t
Valid prediction for snap_scaffold_17-snap.1097-T1
Valid prediction for GeneMark_model.70990_t
Valid prediction for GeneMark_model.70963_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19426, rend_intergenic: 13536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27350, rend_intergenic: 23265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46800, rend_intergenic: 40354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64805, rend_intergenic: 58550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128920, rend_intergenic: 122635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139857, rend_intergenic: 130617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149236, rend_intergenic: 144893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158520, rend_intergenic: 151756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167264, rend_intergenic: 160188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193225
-exon list size: 594


building trellis

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95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 19426, rend_intergenic: 13536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27350, rend_intergenic: 23265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46800, rend_intergenic: 40354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64805, rend_intergenic: 58550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128920, rend_intergenic: 122635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139857, rend_intergenic: 130617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149236, rend_intergenic: 144893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158520, rend_intergenic: 151756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167264, rend_intergenic: 160188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support