-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_2220685-2349052

-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 HiQ_model.g34835.t1
Valid prediction for GeneMark_model.90083_t
Valid prediction for GeneMark_model.90075_t
Valid prediction for snap_scaffold_23-snap.420-T1
Valid prediction for snap_scaffold_23-snap.433-T1
Valid prediction for snap_scaffold_23-snap.439-T1
Valid prediction for GeneMark_model.90057_t
Valid prediction for snap_scaffold_23-snap.427-T1
Valid prediction for snap_scaffold_23-snap.412-T1
Valid prediction for GlimmerHMM_glimmerT_51826-T1
Valid prediction for GlimmerHMM_glimmerT_51823-T1
Valid prediction for GlimmerHMM_glimmerT_51822-T1
Valid prediction for snap_scaffold_23-snap.421-T1
Valid prediction for GlimmerHMM_glimmerT_51827-T1
Valid prediction for GeneMark_model.90082_t
Valid prediction for HiQ_model.g34828.t1
Valid prediction for GeneMark_model.90059_t
Valid prediction for GlimmerHMM_glimmerT_51831-T1
Valid prediction for GlimmerHMM_glimmerT_51833-T1
Valid prediction for Augustus_model.g34831.t1
Valid prediction for GeneMark_model.90061_t
Valid prediction for snap_scaffold_23-snap.410-T1
Couldn't classify 94915, 95027
Sorry, prediction pasa_asmbl_30691.p1 fails validation.
(CTT)	 TG	94915-95027	GT	AGG
(AAC)	 AG	95244-95379	GT	AGG
(GTG)	 AG	95466-95580	GT	CGG
(TGA)	 AG	95730-95921	GT	AAG
(TCA)	 AG	96196-96239	TT	GAT
-recovered pasa_asmbl_30691.p1, terminal, 96196, 96239
-recovered pasa_asmbl_30691.p1, internal, 95244, 95379
-recovered pasa_asmbl_30691.p1, internal, 95466, 95580
-recovered pasa_asmbl_30691.p1, internal, 95730, 95921
Valid prediction for snap_scaffold_23-snap.434-T1
Valid prediction for GeneMark_model.90077_t
Valid prediction for GlimmerHMM_glimmerT_51828-T1
Valid prediction for GeneMark_model.90054_t
Couldn't classify 47148, 47246
Couldn't classify 47746, 47830
Sorry, prediction pasa_asmbl_31225.p3 fails validation.
(TCC)	 AG	47148-47246	GT	GAG
(ATC)	 AG	47379-47497	GT	CCG
(CTT)	 AG	47746-47830	AA	GCA
-recovered pasa_asmbl_31225.p3, internal, 47148, 47246
-recovered pasa_asmbl_31225.p3, internal, 47379, 47497
Valid prediction for GeneMark_model.90073_t
Valid prediction for Augustus_model.g34830.t1
Valid prediction for snap_scaffold_23-snap.417-T1
Valid prediction for Augustus_model.g34840.t1
Valid prediction for CodingQuarry_transcript_35516-T1
Valid prediction for GeneMark_model.90052_t
Valid prediction for GlimmerHMM_glimmerT_51840-T1
Valid prediction for pasa_asmbl_30683.p1
Valid prediction for GeneMark_model.90065_t
Valid prediction for HiQ_model.g34833.t1
Valid prediction for Augustus_model.g34834.t1
Valid prediction for snap_scaffold_23-snap.426-T1
Valid prediction for CodingQuarry_transcript_35515-T1
Valid prediction for GeneMark_model.90069_t
Valid prediction for snap_scaffold_23-snap.429-T1
Valid prediction for Augustus_model.g34824.t1
Valid prediction for GlimmerHMM_glimmerT_51832-T1
Valid prediction for Augustus_model.g34827.t1
Valid prediction for pasa_asmbl_30685.p1
Valid prediction for GlimmerHMM_glimmerT_51834-T1
Valid prediction for snap_scaffold_23-snap.413-T1
Valid prediction for Augustus_model.g34832.t1
Valid prediction for GeneMark_model.90064_t
Valid prediction for GlimmerHMM_glimmerT_51835-T1
Valid prediction for GlimmerHMM_glimmerT_51837-T1
Valid prediction for snap_scaffold_23-snap.438-T1
Valid prediction for GlimmerHMM_glimmerT_51817-T1
Valid prediction for GeneMark_model.90055_t
Valid prediction for snap_scaffold_23-snap.425-T1
Valid prediction for GeneMark_model.90079_t
Valid prediction for snap_scaffold_23-snap.431-T1
Valid prediction for snap_scaffold_23-snap.418-T1
Valid prediction for snap_scaffold_23-snap.415-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 Augustus_model.g34823.t1
Valid prediction for GeneMark_model.90084_t
Valid prediction for GeneMark_model.90080_t
Valid prediction for Augustus_model.g34837.t1
Valid prediction for snap_scaffold_23-snap.416-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.90074_t
Couldn't classify 108267, 108341
Couldn't classify 116674, 116725
Sorry, prediction pasa_asmbl_31440.p1 fails validation.
(GGC)	 CA	108267-108341	GT	AGG
(ATT)	 AG	108536-108637	GT	ATG
(CCC)	 AG	110406-110480	GT	AGG
(CCG)	 AG	110699-110760	GT	AGG
(TGA)	 AG	110911-110962	GT	ATG
(TTG)	 AG	111279-111370	GT	ATG
(GTA)	 AG	111527-111626	GT	GGG
(GAC)	 AG	112027-112105	GT	CGG
(GAG)	 AG	114161-114291	GT	AGG
(CCC)	 AG	115535-115629	GT	GTG
(CGG)	 AG	115807-115914	GT	GGG
(GCA)	 AG	116674-116725	AT	GGA
-recovered pasa_asmbl_31440.p1, internal, 108536, 108637
-recovered pasa_asmbl_31440.p1, internal, 110406, 110480
-recovered pasa_asmbl_31440.p1, internal, 110699, 110760
-recovered pasa_asmbl_31440.p1, internal, 110911, 110962
-recovered pasa_asmbl_31440.p1, internal, 111279, 111370
-recovered pasa_asmbl_31440.p1, internal, 111527, 111626
-recovered pasa_asmbl_31440.p1, internal, 112027, 112105
-recovered pasa_asmbl_31440.p1, internal, 114161, 114291
-recovered pasa_asmbl_31440.p1, internal, 115535, 115629
-recovered pasa_asmbl_31440.p1, internal, 115807, 115914
Valid prediction for snap_scaffold_23-snap.437-T1
Valid prediction for Augustus_model.g34825.t1
Valid prediction for GeneMark_model.90056_t
Valid prediction for snap_scaffold_23-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_51818-T1
Valid prediction for GeneMark_model.90062_t
Valid prediction for GlimmerHMM_glimmerT_51821-T1
Valid prediction for GeneMark_model.90060_t
Valid prediction for snap_scaffold_23-snap.419-T1
Valid prediction for GeneMark_model.90058_t
Valid prediction for snap_scaffold_23-snap.422-T1
Valid prediction for snap_scaffold_23-snap.414-T1
Valid prediction for GeneMark_model.90068_t
Valid prediction for snap_scaffold_23-snap.424-T1
Valid prediction for Augustus_model.g34839.t1
Valid prediction for GeneMark_model.90067_t
Valid prediction for GeneMark_model.90063_t
Valid prediction for Augustus_model.g34838.t1
Valid prediction for pasa_asmbl_31950.p1
Valid prediction for GeneMark_model.90071_t
Valid prediction for Augustus_model.g34826.t1
Valid prediction for GlimmerHMM_glimmerT_51838-T1
Valid prediction for GlimmerHMM_glimmerT_51820-T1
Valid prediction for snap_scaffold_23-snap.430-T1
Valid prediction for GlimmerHMM_glimmerT_51825-T1
Valid prediction for GeneMark_model.90081_t
Valid prediction for snap_scaffold_23-snap.423-T1
Valid prediction for GeneMark_model.90076_t
Valid prediction for snap_scaffold_23-snap.435-T1
Valid prediction for GlimmerHMM_glimmerT_51839-T1
Valid prediction for Augustus_model.g34836.t1
Valid prediction for snap_scaffold_23-snap.411-T1
Valid prediction for Augustus_model.g34829.t1
Valid prediction for snap_scaffold_23-snap.436-T1
Valid prediction for GlimmerHMM_glimmerT_51830-T1
Valid prediction for GlimmerHMM_glimmerT_51836-T1
Valid prediction for GeneMark_model.90078_t
Valid prediction for GlimmerHMM_glimmerT_51824-T1
Valid prediction for GlimmerHMM_glimmerT_51829-T1
Valid prediction for Augustus_model.g34822.t1
Valid prediction for GlimmerHMM_glimmerT_51841-T1
Valid prediction for GlimmerHMM_glimmerT_51842-T1
Valid prediction for GeneMark_model.90070_t
Valid prediction for Augustus_model.g34821.t1
Valid prediction for snap_scaffold_23-snap.428-T1
Valid prediction for GeneMark_model.90051_t
Valid prediction for snap_scaffold_23-snap.432-T1
Valid prediction for GeneMark_model.90053_t
Valid prediction for GeneMark_model.90072_t
Valid prediction for GlimmerHMM_glimmerT_51819-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15260, rend_intergenic: 5465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19433, rend_intergenic: 15790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34933, rend_intergenic: 19657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79655, rend_intergenic: 70559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81452, rend_intergenic: 80384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90788, rend_intergenic: 86344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105179, rend_intergenic: 98535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110290, rend_intergenic: 107034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 128368
-exon list size: 604


building trellis

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98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 15260, rend_intergenic: 5465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19433, rend_intergenic: 15790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34933, rend_intergenic: 19657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79655, rend_intergenic: 70559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81452, rend_intergenic: 80384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90788, rend_intergenic: 86344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105179, rend_intergenic: 98535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110290, rend_intergenic: 107034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support