-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_16301052-16469788

-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.g5440.t1
Valid prediction for Augustus_model.g5450.t1
Valid prediction for snap_scaffold_3-snap.3142-T1
Valid prediction for GeneMark_model.13337_t
Valid prediction for GeneMark_model.13315_t
Valid prediction for GeneMark_model.13313_t
Valid prediction for snap_scaffold_3-snap.3157-T1
Valid prediction for snap_scaffold_3-snap.3153-T1
Valid prediction for snap_scaffold_3-snap.3139-T1
Valid prediction for snap_scaffold_3-snap.3154-T1
Valid prediction for CodingQuarry_transcript_46313-T1
Valid prediction for Augustus_model.g5446.t1
Valid prediction for GeneMark_model.13307_t
Valid prediction for HiQ_model.g5447.t1
Valid prediction for GeneMark_model.13330_t
Valid prediction for GeneMark_model.13332_t
Valid prediction for Augustus_model.g5451.t1
Valid prediction for GeneMark_model.13323_t
Valid prediction for CodingQuarry_transcript_46312-T1
Valid prediction for CodingQuarry_transcript_46314-T1
Valid prediction for snap_scaffold_3-snap.3150-T1
Valid prediction for GlimmerHMM_glimmerT_8186-T1
Valid prediction for GlimmerHMM_glimmerT_8197-T1
Valid prediction for GeneMark_model.13321_t
Valid prediction for snap_scaffold_3-snap.3140-T1
Valid prediction for GeneMark_model.13305_t
Valid prediction for GlimmerHMM_glimmerT_8184-T1
Valid prediction for snap_scaffold_3-snap.3156-T1
Valid prediction for snap_scaffold_3-snap.3163-T1
Valid prediction for snap_scaffold_3-snap.3162-T1
Valid prediction for GlimmerHMM_glimmerT_8196-T1
Valid prediction for GeneMark_model.13310_t
Valid prediction for GlimmerHMM_glimmerT_8192-T1
Valid prediction for GlimmerHMM_glimmerT_8182-T1
Valid prediction for CodingQuarry_transcript_46310-T1
Valid prediction for GeneMark_model.13327_t
Valid prediction for GeneMark_model.13335_t
Valid prediction for GeneMark_model.13317_t
Valid prediction for GeneMark_model.13336_t
Valid prediction for pasa_asmbl_40581.p1
Valid prediction for GeneMark_model.13320_t
Valid prediction for GlimmerHMM_glimmerT_8187-T1
Valid prediction for GlimmerHMM_glimmerT_8195-T1
Valid prediction for GeneMark_model.13303_t
Valid prediction for snap_scaffold_3-snap.3159-T1
Valid prediction for GlimmerHMM_glimmerT_8189-T1
Valid prediction for GeneMark_model.13302_t
Valid prediction for GeneMark_model.13325_t
Valid prediction for GeneMark_model.13300_t
Valid prediction for pasa_asmbl_40582.p1
Valid prediction for HiQ_model.g5449.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.13314_t
Valid prediction for GeneMark_model.13312_t
Valid prediction for Augustus_model.g5445.t1
Valid prediction for GlimmerHMM_glimmerT_8181-T1
Valid prediction for GeneMark_model.13311_t
Valid prediction for GeneMark_model.13326_t
Valid prediction for CodingQuarry_transcript_46308-T1
Valid prediction for GeneMark_model.13318_t
Valid prediction for Augustus_model.g5444.t1
Valid prediction for GlimmerHMM_glimmerT_8188-T1
Valid prediction for CodingQuarry_transcript_46311-T1
Valid prediction for GeneMark_model.13299_t
Valid prediction for HiQ_model.g5439.t1
Valid prediction for GlimmerHMM_glimmerT_8179-T1
Valid prediction for GeneMark_model.13308_t
Valid prediction for snap_scaffold_3-snap.3137-T1
Valid prediction for GeneMark_model.13316_t
Valid prediction for snap_scaffold_3-snap.3158-T1
Valid prediction for GlimmerHMM_glimmerT_8183-T1
Couldn't classify 28592, 28621
Couldn't classify 30035, 30237
Sorry, prediction pasa_asmbl_39458.p1 fails validation.
(GGA)	 TA	28592-28621	GT	AGG
(GTT)	 AG	28918-28948	GT	AGG
(ATA)	 AG	29070-29240	GT	AGG
(ACA)	 AG	29682-29921	GT	CGG
(ATG)	 AG	30035-30237	AG	AGA
-recovered pasa_asmbl_39458.p1, internal, 28918, 28948
-recovered pasa_asmbl_39458.p1, internal, 29070, 29240
-recovered pasa_asmbl_39458.p1, internal, 29682, 29921
Valid prediction for snap_scaffold_3-snap.3144-T1
Valid prediction for Augustus_model.g5437.t1
Couldn't classify 82222, 82299
Couldn't classify 86302, 86331
Sorry, prediction pasa_asmbl_39454.p1 fails validation.
(TTC)	 CC	82222-82299	GT	GAG
(AGT)	 AG	82409-82463	GT	TCG
(CGC)	 AG	82604-82682	GT	TGG
(GTC)	 AG	82910-83085	GT	AGG
(ATG)	 AG	83256-83328	GT	AGG
(CTC)	 AG	83879-84089	GT	AGG
(CAA)	 AG	85789-85950	GT	AGG
(GAG)	 AG	86302-86331	CA	AGC
-recovered pasa_asmbl_39454.p1, initial, 83256, 83328
-recovered pasa_asmbl_39454.p1, internal, 82409, 82463
-recovered pasa_asmbl_39454.p1, internal, 82604, 82682
-recovered pasa_asmbl_39454.p1, internal, 82910, 83085
-recovered pasa_asmbl_39454.p1, internal, 83256, 83328
-recovered pasa_asmbl_39454.p1, internal, 83879, 84089
-recovered pasa_asmbl_39454.p1, internal, 85789, 85950
Valid prediction for GeneMark_model.13333_t
Valid prediction for GlimmerHMM_glimmerT_8190-T1
Valid prediction for Augustus_model.g5443.t1
Valid prediction for GlimmerHMM_glimmerT_8180-T1
Valid prediction for GlimmerHMM_glimmerT_8194-T1
Valid prediction for snap_scaffold_3-snap.3151-T1
Couldn't classify 118787, 118886
Sorry, prediction pasa_asmbl_39448.p1 fails validation.
(AGA)	 GA	118787-118886	GT	CGG
(ACA)	 AG	119993-120064	GT	GGG
(ATG)	 AG	120339-120588	GT	AGG
(AAC)	 AG	121015-121207	GT	AGG
(GGC)	 AG	121549-121720	GT	AGG
(AGG)	 AG	121962-122024	GT	AGG
(GCT)	 AG	122252-122390	GT	CCG
(GGA)	 AG	123536-123690	GT	AGG
(ATC)	 AG	123854-123997	GT	AGG
(ACA)	 AG	124528-124695	GT	GGG
(CTG)	 AG	125870-126324	AT	AAA
add_exon() Sorry, pasa_asmbl_39448.p1 120339-120588-initial-1 is invalid.
-recovered pasa_asmbl_39448.p1, initial, 120339, 120588
add_exon() Sorry, pasa_asmbl_39448.p1 121962-122024-terminal-1 is invalid.
-recovered pasa_asmbl_39448.p1, terminal, 121962, 122024
-recovered pasa_asmbl_39448.p1, terminal, 125870, 126324
-recovered pasa_asmbl_39448.p1, internal, 119993, 120064
-recovered pasa_asmbl_39448.p1, internal, 120339, 120588
-recovered pasa_asmbl_39448.p1, internal, 121015, 121207
-recovered pasa_asmbl_39448.p1, internal, 121549, 121720
-recovered pasa_asmbl_39448.p1, internal, 121962, 122024
-recovered pasa_asmbl_39448.p1, internal, 122252, 122390
-recovered pasa_asmbl_39448.p1, internal, 123536, 123690
-recovered pasa_asmbl_39448.p1, internal, 123854, 123997
-recovered pasa_asmbl_39448.p1, internal, 124528, 124695
Valid prediction for Augustus_model.g5438.t1
Valid prediction for GeneMark_model.13329_t
Valid prediction for GeneMark_model.13322_t
Couldn't classify 30789, 31235
Sorry, prediction pasa_asmbl_39457.p1 fails validation.
(AGA)	 GC	30789-31235	CC	GCC
Valid prediction for GeneMark_model.13298_t
Valid prediction for HiQ_model.g5441.t1
Valid prediction for snap_scaffold_3-snap.3152-T1
Valid prediction for snap_scaffold_3-snap.3160-T1
Couldn't classify 128931, 129003
Sorry, prediction pasa_asmbl_39443.p1 fails validation.
(GAT)	 CA	128931-129003	GT	GGG
(ATG)	 AG	129295-129544	GT	AGG
(AAC)	 AG	129772-129952	GT	AGG
(GAC)	 AG	130247-130418	GT	AGG
(AGG)	 AG	130656-130718	GT	AGG
(GGT)	 AG	131163-131301	GT	CCG
(TGA)	 AG	131778-131932	GT	AGG
(ATC)	 AG	132122-132265	GT	AGG
(ACA)	 AG	133059-133226	GT	GGG
(CTG)	 AG	133412-133905	AA	GAA
add_exon() Sorry, pasa_asmbl_39443.p1 129295-129544-initial-1 is invalid.
-recovered pasa_asmbl_39443.p1, initial, 129295, 129544
add_exon() Sorry, pasa_asmbl_39443.p1 130656-130718-terminal-1 is invalid.
-recovered pasa_asmbl_39443.p1, terminal, 130656, 130718
-recovered pasa_asmbl_39443.p1, terminal, 133412, 133905
-recovered pasa_asmbl_39443.p1, internal, 129295, 129544
-recovered pasa_asmbl_39443.p1, internal, 129772, 129952
-recovered pasa_asmbl_39443.p1, internal, 130247, 130418
-recovered pasa_asmbl_39443.p1, internal, 130656, 130718
-recovered pasa_asmbl_39443.p1, internal, 131163, 131301
-recovered pasa_asmbl_39443.p1, internal, 131778, 131932
-recovered pasa_asmbl_39443.p1, internal, 132122, 132265
-recovered pasa_asmbl_39443.p1, internal, 133059, 133226
Valid prediction for Augustus_model.g5448.t1
Valid prediction for snap_scaffold_3-snap.3145-T1
Valid prediction for GlimmerHMM_glimmerT_8178-T1
Valid prediction for snap_scaffold_3-snap.3146-T1
Valid prediction for GeneMark_model.13328_t
Valid prediction for GeneMark_model.13319_t
Couldn't classify 31392, 32039
Sorry, prediction pasa_asmbl_39456.p1 fails validation.
(AAA)	 AC	31392-32039	TT	CTT
Valid prediction for GlimmerHMM_glimmerT_8185-T1
Valid prediction for GeneMark_model.13324_t
Valid prediction for GlimmerHMM_glimmerT_8177-T1
Valid prediction for snap_scaffold_3-snap.3141-T1
Valid prediction for GeneMark_model.13306_t
Couldn't classify 113498, 113543
Sorry, prediction pasa_asmbl_39451.p1 fails validation.
(AGG)	 CA	113498-113543	GT	TGG
(GTG)	 AG	113718-113853	GT	AGG
(GAC)	 AG	114096-114241	GT	CGG
(ACT)	 AG	114377-114516	CT	AGC
-recovered pasa_asmbl_39451.p1, terminal, 114377, 114516
-recovered pasa_asmbl_39451.p1, internal, 113718, 113853
-recovered pasa_asmbl_39451.p1, internal, 114096, 114241
Valid prediction for Augustus_model.g5435.t1
Valid prediction for snap_scaffold_3-snap.3161-T1
Valid prediction for snap_scaffold_3-snap.3143-T1
Valid prediction for GlimmerHMM_glimmerT_8191-T1
Valid prediction for GlimmerHMM_glimmerT_8193-T1
Valid prediction for snap_scaffold_3-snap.3148-T1
Valid prediction for snap_scaffold_3-snap.3155-T1
Valid prediction for snap_scaffold_3-snap.3138-T1
Valid prediction for GeneMark_model.13334_t
Valid prediction for snap_scaffold_3-snap.3164-T1
Valid prediction for pasa_asmbl_39455.p1
Valid prediction for Augustus_model.g5442.t1
Valid prediction for Augustus_model.g5436.t1
Valid prediction for snap_scaffold_3-snap.3147-T1
Valid prediction for snap_scaffold_3-snap.3149-T1
Couldn't classify 98532, 98607
Sorry, prediction pasa_asmbl_39452.p1 fails validation.
(CCT)	 GC	98532-98607	GT	GGG
(GAG)	 AG	99066-99209	GT	AGG
(GCA)	 AG	101020-101154	GT	TGG
(TTA)	 AG	101829-101929	GT	AGG
(TCG)	 AG	102349-102498	GT	ACG
(ATC)	 AG	102697-102856	GT	GGG
(CCT)	 AG	103285-103424	GT	AGG
(GTG)	 AG	103861-103944	AG	AGA
-recovered pasa_asmbl_39452.p1, terminal, 103861, 103944
-recovered pasa_asmbl_39452.p1, internal, 99066, 99209
-recovered pasa_asmbl_39452.p1, internal, 101020, 101154
-recovered pasa_asmbl_39452.p1, internal, 101829, 101929
-recovered pasa_asmbl_39452.p1, internal, 102349, 102498
-recovered pasa_asmbl_39452.p1, internal, 102697, 102856
-recovered pasa_asmbl_39452.p1, internal, 103285, 103424
Valid prediction for GeneMark_model.13309_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24263, rend_intergenic: 14164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28318, rend_intergenic: 25685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99243, rend_intergenic: 88615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111870, rend_intergenic: 107125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130325, rend_intergenic: 124960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168737
-exon list size: 525


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 24263, rend_intergenic: 14164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28318, rend_intergenic: 25685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99243, rend_intergenic: 88615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111870, rend_intergenic: 107125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130325, rend_intergenic: 124960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support