-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_12524200-12706141

-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_15-snap.2554-T1
Valid prediction for snap_scaffold_15-snap.2538-T1
Valid prediction for GeneMark_model.65251_t
Valid prediction for snap_scaffold_15-snap.2560-T1
Valid prediction for GlimmerHMM_glimmerT_37953-T1
Valid prediction for GeneMark_model.65263_t
Valid prediction for snap_scaffold_15-snap.2553-T1
Valid prediction for GlimmerHMM_glimmerT_37942-T1
Valid prediction for snap_scaffold_15-snap.2543-T1
Valid prediction for GeneMark_model.65273_t
Valid prediction for GlimmerHMM_glimmerT_37943-T1
Valid prediction for GeneMark_model.65278_t
Valid prediction for snap_scaffold_15-snap.2559-T1
Valid prediction for GeneMark_model.65283_t
Valid prediction for GlimmerHMM_glimmerT_37949-T1
Valid prediction for HiQ_model.g25447.t1
Valid prediction for pasa_asmbl_14526.p1
Valid prediction for snap_scaffold_15-snap.2558-T1
Valid prediction for GeneMark_model.65248_t
Valid prediction for Augustus_model.g25433.t1
Valid prediction for GlimmerHMM_glimmerT_37945-T1
Valid prediction for snap_scaffold_15-snap.2561-T1
Valid prediction for GeneMark_model.65271_t
Valid prediction for Augustus_model.g25435.t1
Valid prediction for Augustus_model.g25443.t1
Valid prediction for snap_scaffold_15-snap.2571-T1
Valid prediction for GeneMark_model.65270_t
Valid prediction for GlimmerHMM_glimmerT_37935-T1
Couldn't classify 106501, 107157
Sorry, prediction pasa_asmbl_14534.p1 fails validation.
(AGG)	 TC	106501-107157	CT	GAC
Valid prediction for snap_scaffold_15-snap.2570-T1
Valid prediction for GeneMark_model.65246_t
Valid prediction for snap_scaffold_15-snap.2541-T1
Valid prediction for GeneMark_model.65282_t
Valid prediction for snap_scaffold_15-snap.2555-T1
Valid prediction for HiQ_model.g25441.t1
Valid prediction for snap_scaffold_15-snap.2542-T1
Valid prediction for GlimmerHMM_glimmerT_37959-T1
Valid prediction for snap_scaffold_15-snap.2574-T1
Valid prediction for Augustus_model.g25431.t1
Valid prediction for GeneMark_model.65256_t
Valid prediction for GeneMark_model.65257_t
Valid prediction for Augustus_model.g25442.t1
Valid prediction for GlimmerHMM_glimmerT_37938-T1
Valid prediction for snap_scaffold_15-snap.2557-T1
Valid prediction for GeneMark_model.65254_t
Valid prediction for Augustus_model.g25444.t1
Valid prediction for snap_scaffold_15-snap.2566-T1
Valid prediction for CodingQuarry_transcript_18142-T1
Valid prediction for snap_scaffold_15-snap.2545-T1
Couldn't classify 13380, 13590
Sorry, prediction pasa_asmbl_14523.p1 fails validation.
(AGA)	 GC	13380-13590	GT	TGG
(ATG)	 AG	13918-14018	TG	AAT
-recovered pasa_asmbl_14523.p1, terminal, 13918, 14018
Valid prediction for CodingQuarry_transcript_18143-T1
Valid prediction for GeneMark_model.65268_t
Valid prediction for GlimmerHMM_glimmerT_37946-T1
Valid prediction for GeneMark_model.65261_t
Valid prediction for snap_scaffold_15-snap.2576-T1
Valid prediction for snap_scaffold_15-snap.2575-T1
Valid prediction for GlimmerHMM_glimmerT_37958-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.65255_t
Valid prediction for GeneMark_model.65272_t
Valid prediction for GeneMark_model.65249_t
Valid prediction for GeneMark_model.65260_t
Valid prediction for snap_scaffold_15-snap.2573-T1
Valid prediction for Augustus_model.g25445.t1
Couldn't classify 54609, 54700
Couldn't classify 58536, 58565
Sorry, prediction pasa_asmbl_15616.p1 fails validation.
(CTG)	 AG	54609-54700	GT	AGG
(CAA)	 AG	55054-55151	GT	AGG
(GTC)	 AG	55421-55500	GT	GAG
(ACC)	 AG	58023-58106	GT	ATG
(GAG)	 AG	58536-58565	AC	CCA
-recovered pasa_asmbl_15616.p1, internal, 54609, 54700
-recovered pasa_asmbl_15616.p1, internal, 55054, 55151
-recovered pasa_asmbl_15616.p1, internal, 55421, 55500
-recovered pasa_asmbl_15616.p1, internal, 58023, 58106
Valid prediction for snap_scaffold_15-snap.2572-T1
Valid prediction for snap_scaffold_15-snap.2563-T1
Valid prediction for Augustus_model.g25446.t1
Valid prediction for HiQ_model.g25432.t1
Valid prediction for snap_scaffold_15-snap.2549-T1
Valid prediction for GeneMark_model.65279_t
Valid prediction for snap_scaffold_15-snap.2567-T1
Valid prediction for snap_scaffold_15-snap.2562-T1
Valid prediction for GlimmerHMM_glimmerT_37941-T1
Valid prediction for GeneMark_model.65280_t
Valid prediction for CodingQuarry_transcript_18139-T1
Valid prediction for snap_scaffold_15-snap.2556-T1
Valid prediction for pasa_asmbl_15603.p1
Couldn't classify 60019, 60027
Couldn't classify 61829, 61843
Sorry, prediction pasa_asmbl_15615.p1 fails validation.
(ATT)	 GC	60019-60027	GT	GGG
(GTG)	 AG	60434-60650	GT	GGG
(ATC)	 AG	60886-60948	GT	CGG
(TGA)	 AG	61368-61609	GT	AGG
(GTG)	 AG	61829-61843	AT	AGA
-recovered pasa_asmbl_15615.p1, internal, 60434, 60650
-recovered pasa_asmbl_15615.p1, internal, 60886, 60948
-recovered pasa_asmbl_15615.p1, internal, 61368, 61609
Valid prediction for GlimmerHMM_glimmerT_37951-T1
Valid prediction for snap_scaffold_15-snap.2544-T1
Valid prediction for snap_scaffold_15-snap.2547-T1
Valid prediction for HiQ_model.g25440.t1
Valid prediction for HiQ_model.g25439.t1
Valid prediction for GlimmerHMM_glimmerT_37957-T1
Valid prediction for GlimmerHMM_glimmerT_37936-T1
Valid prediction for GlimmerHMM_glimmerT_37940-T1
Valid prediction for pasa_asmbl_15886.p1
Valid prediction for snap_scaffold_15-snap.2564-T1
Valid prediction for pasa_asmbl_15598.p1
Valid prediction for GeneMark_model.65276_t
Valid prediction for GeneMark_model.65250_t
Valid prediction for Augustus_model.g25437.t1
Valid prediction for GeneMark_model.65265_t
Valid prediction for GeneMark_model.65253_t
Valid prediction for GlimmerHMM_glimmerT_37955-T1
Valid prediction for snap_scaffold_15-snap.2546-T1
Valid prediction for GeneMark_model.65247_t
Valid prediction for snap_scaffold_15-snap.2551-T1
Couldn't classify 111178, 111316
Couldn't classify 111995, 112008
Sorry, prediction CodingQuarry_transcript_18140-T1 fails validation.
(ATG)	 AA	110511-110598	GT	TGG
(ATG)	 AG	110803-110840	GT	AGG
(TCC)	 AG	111178-111316	TG	TCT
(CTC)	 TC	111995-112008	CG	AAC
-recovered CodingQuarry_transcript_18140-T1, initial, 110511, 110598
add_exon() Sorry, CodingQuarry_transcript_18140-T1 110803-110840-initial-1 is invalid.
-recovered CodingQuarry_transcript_18140-T1, initial, 110803, 110840
-recovered CodingQuarry_transcript_18140-T1, internal, 110803, 110840
Valid prediction for GlimmerHMM_glimmerT_37937-T1
Valid prediction for GlimmerHMM_glimmerT_37939-T1
Valid prediction for GeneMark_model.65275_t
Valid prediction for pasa_asmbl_15617.p1
Valid prediction for snap_scaffold_15-snap.2548-T1
Valid prediction for CodingQuarry_transcript_18135-T1
Valid prediction for GlimmerHMM_glimmerT_37947-T1
Valid prediction for GeneMark_model.65267_t
Valid prediction for GlimmerHMM_glimmerT_37954-T1
Valid prediction for snap_scaffold_15-snap.2540-T1
Valid prediction for GlimmerHMM_glimmerT_37956-T1
Valid prediction for GlimmerHMM_glimmerT_37948-T1
Valid prediction for CodingQuarry_transcript_18136-T1
Valid prediction for Augustus_model.g25436.t1
Valid prediction for Augustus_model.g25430.t1
Valid prediction for GeneMark_model.65258_t
Valid prediction for snap_scaffold_15-snap.2552-T1
Valid prediction for GeneMark_model.65274_t
Valid prediction for GeneMark_model.65277_t
Valid prediction for GeneMark_model.65259_t
Valid prediction for GlimmerHMM_glimmerT_37952-T1
Valid prediction for snap_scaffold_15-snap.2539-T1
Couldn't classify 62075, 62183
Couldn't classify 65448, 65549
Sorry, prediction pasa_asmbl_15612.p1 fails validation.
(TCG)	 GC	62075-62183	GT	CAG
(GTT)	 AG	62552-62649	GT	AGG
(ATA)	 AG	62777-62861	GT	AGG
(AAG)	 AG	63051-63168	GT	AGG
(GGA)	 AG	63465-63582	GT	TGG
(GGC)	 AG	65448-65549	TC	CCT
-recovered pasa_asmbl_15612.p1, internal, 62552, 62649
-recovered pasa_asmbl_15612.p1, internal, 62777, 62861
-recovered pasa_asmbl_15612.p1, internal, 63051, 63168
-recovered pasa_asmbl_15612.p1, internal, 63465, 63582
Valid prediction for Augustus_model.g25438.t1
Valid prediction for snap_scaffold_15-snap.2569-T1
Valid prediction for Augustus_model.g25434.t1
Valid prediction for snap_scaffold_15-snap.2565-T1
Valid prediction for CodingQuarry_transcript_18141-T1
Valid prediction for CodingQuarry_transcript_18138-T1
Valid prediction for GlimmerHMM_glimmerT_37944-T1
Valid prediction for GeneMark_model.65281_t
Valid prediction for snap_scaffold_15-snap.2568-T1
Valid prediction for snap_scaffold_15-snap.2550-T1
Valid prediction for GeneMark_model.65262_t
Valid prediction for GlimmerHMM_glimmerT_37950-T1
Valid prediction for GeneMark_model.65284_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 132289, rend_intergenic: 129357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132723, rend_intergenic: 132303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145855, rend_intergenic: 142996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148280, rend_intergenic: 146972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181942
-exon list size: 518


building trellis

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98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 132289, rend_intergenic: 129357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132723, rend_intergenic: 132303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145855, rend_intergenic: 142996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148280, rend_intergenic: 146972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support