-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_16164433-16346776

-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 GlimmerHMM_glimmerT_10832-T1
Valid prediction for snap_scaffold_4-snap.3288-T1
Valid prediction for snap_scaffold_4-snap.3262-T1
Valid prediction for GlimmerHMM_glimmerT_10830-T1
Valid prediction for snap_scaffold_4-snap.3275-T1
Valid prediction for snap_scaffold_4-snap.3269-T1
Valid prediction for snap_scaffold_4-snap.3254-T1
Valid prediction for snap_scaffold_4-snap.3266-T1
Valid prediction for snap_scaffold_4-snap.3290-T1
Valid prediction for snap_scaffold_4-snap.3300-T1
Couldn't classify 117480, 117593
Sorry, prediction pasa_asmbl_42177.p1 fails validation.
(CTT)	 CC	117480-117593	GT	GGG
(GGA)	 AG	118113-118169	GT	GGG
(GCC)	 AG	118267-118333	GT	AGG
(GGT)	 AG	118667-118753	GT	AGG
(GAT)	 AG	119238-119323	GT	AGG
(AAG)	 AG	119554-119627	GT	CCG
(GAA)	 AG	119873-119980	GT	AGG
(TTT)	 AG	120342-120456	GT	AGG
(TTC)	 AG	120766-120867	GT	TGG
(GTA)	 AG	121128-121191	GT	AGG
(GTG)	 AG	121967-122016	GT	CGG
(GGA)	 AG	122818-122941	GT	AGG
(CCA)	 AG	123115-123219	GT	GAG
(GAC)	 AG	123369-123432	GT	AAG
(GTA)	 AG	123547-123603	GT	ACG
(GGG)	 AG	123721-123783	GT	AGG
(GTA)	 AG	123930-124006	GT	AGG
(CTT)	 AG	124285-124383	GT	TGG
(GTG)	 AG	124734-124780	GT	TGG
(GCA)	 AG	125998-126081	GA	AGG
-recovered pasa_asmbl_42177.p1, terminal, 125998, 126081
-recovered pasa_asmbl_42177.p1, internal, 118113, 118169
-recovered pasa_asmbl_42177.p1, internal, 118267, 118333
-recovered pasa_asmbl_42177.p1, internal, 118667, 118753
-recovered pasa_asmbl_42177.p1, internal, 119238, 119323
-recovered pasa_asmbl_42177.p1, internal, 119554, 119627
-recovered pasa_asmbl_42177.p1, internal, 119873, 119980
-recovered pasa_asmbl_42177.p1, internal, 120342, 120456
-recovered pasa_asmbl_42177.p1, internal, 120766, 120867
-recovered pasa_asmbl_42177.p1, internal, 121128, 121191
-recovered pasa_asmbl_42177.p1, internal, 121967, 122016
-recovered pasa_asmbl_42177.p1, internal, 122818, 122941
-recovered pasa_asmbl_42177.p1, internal, 123115, 123219
-recovered pasa_asmbl_42177.p1, internal, 123369, 123432
-recovered pasa_asmbl_42177.p1, internal, 123547, 123603
-recovered pasa_asmbl_42177.p1, internal, 123721, 123783
-recovered pasa_asmbl_42177.p1, internal, 123930, 124006
-recovered pasa_asmbl_42177.p1, internal, 124285, 124383
-recovered pasa_asmbl_42177.p1, internal, 124734, 124780
Valid prediction for snap_scaffold_4-snap.3265-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g7104.t1
Valid prediction for GlimmerHMM_glimmerT_10824-T1
Valid prediction for GlimmerHMM_glimmerT_10845-T1
Valid prediction for snap_scaffold_4-snap.3297-T1
Valid prediction for snap_scaffold_4-snap.3284-T1
Valid prediction for pasa_asmbl_41963.p1
Valid prediction for Augustus_model.g7100.t1
Valid prediction for snap_scaffold_4-snap.3281-T1
Valid prediction for GlimmerHMM_glimmerT_10831-T1
Valid prediction for GlimmerHMM_glimmerT_10836-T1
Valid prediction for GlimmerHMM_glimmerT_10834-T1
Valid prediction for snap_scaffold_4-snap.3289-T1
Valid prediction for Augustus_model.g7096.t1
Valid prediction for GlimmerHMM_glimmerT_10827-T1
Valid prediction for snap_scaffold_4-snap.3273-T1
Valid prediction for snap_scaffold_4-snap.3294-T1
Valid prediction for snap_scaffold_4-snap.3276-T1
Valid prediction for snap_scaffold_4-snap.3256-T1
Valid prediction for HiQ_model.g7101.t1
Valid prediction for GlimmerHMM_glimmerT_10825-T1
Valid prediction for GlimmerHMM_glimmerT_10838-T1
Valid prediction for snap_scaffold_4-snap.3263-T1
Valid prediction for GlimmerHMM_glimmerT_10837-T1
Valid prediction for GlimmerHMM_glimmerT_10835-T1
Valid prediction for GlimmerHMM_glimmerT_10822-T1
Valid prediction for snap_scaffold_4-snap.3295-T1
Valid prediction for snap_scaffold_4-snap.3277-T1
Valid prediction for snap_scaffold_4-snap.3278-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10826-T1
Valid prediction for GlimmerHMM_glimmerT_10818-T1
Valid prediction for GlimmerHMM_glimmerT_10839-T1
Valid prediction for snap_scaffold_4-snap.3271-T1
Valid prediction for snap_scaffold_4-snap.3259-T1
Valid prediction for GlimmerHMM_glimmerT_10828-T1
Valid prediction for snap_scaffold_4-snap.3272-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 GlimmerHMM_glimmerT_10842-T1
Valid prediction for snap_scaffold_4-snap.3264-T1
Valid prediction for pasa_asmbl_43150.p1
Valid prediction for CodingQuarry_transcript_49269-T1
Valid prediction for Augustus_model.g7097.t1
Valid prediction for Augustus_model.g7102.t1
Valid prediction for GlimmerHMM_glimmerT_10823-T1
Valid prediction for GlimmerHMM_glimmerT_10829-T1
Valid prediction for Augustus_model.g7105.t1
Valid prediction for GlimmerHMM_glimmerT_10819-T1
Valid prediction for snap_scaffold_4-snap.3255-T1
Valid prediction for Augustus_model.g7099.t1
Valid prediction for GlimmerHMM_glimmerT_10847-T1
Valid prediction for snap_scaffold_4-snap.3285-T1
Valid prediction for snap_scaffold_4-snap.3270-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3301-T1
Valid prediction for HiQ_model.g7103.t1
Couldn't classify 124299, 124754
Sorry, prediction pasa_asmbl_43148.p1 fails validation.
(CGG)	 AC	124299-124754	AG	AGA
Valid prediction for snap_scaffold_4-snap.3260-T1
Valid prediction for snap_scaffold_4-snap.3279-T1
Valid prediction for snap_scaffold_4-snap.3293-T1
Valid prediction for snap_scaffold_4-snap.3258-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10841-T1
Couldn't classify 114393, 114460
Sorry, prediction pasa_asmbl_43569.p1 fails validation.
(ATG)	 GG	113301-113514	GT	AGG
(CCA)	 AG	114393-114460	TG	GCT
-recovered pasa_asmbl_43569.p1, initial, 113301, 113514
Valid prediction for snap_scaffold_4-snap.3274-T1
Valid prediction for snap_scaffold_4-snap.3286-T1
Valid prediction for snap_scaffold_4-snap.3282-T1
Couldn't classify 8623, 8748
Sorry, prediction pasa_asmbl_43156.p1 fails validation.
(AGT)	 AG	8623-8748	GT	AGG
(GGC)	 AG	10428-10538	GT	AGG
(GCT)	 AG	11042-11239	AG	GAA
-recovered pasa_asmbl_43156.p1, terminal, 11042, 11239
-recovered pasa_asmbl_43156.p1, internal, 8623, 8748
-recovered pasa_asmbl_43156.p1, internal, 10428, 10538
Valid prediction for snap_scaffold_4-snap.3292-T1
Valid prediction for snap_scaffold_4-snap.3283-T1
Valid prediction for GlimmerHMM_glimmerT_10840-T1
Valid prediction for snap_scaffold_4-snap.3261-T1
Valid prediction for snap_scaffold_4-snap.3296-T1
Valid prediction for snap_scaffold_4-snap.3280-T1
Valid prediction for GlimmerHMM_glimmerT_10846-T1
Couldn't classify 4509, 4514
Couldn't classify 4539, 4685
Sorry, prediction CodingQuarry_transcript_49270-T1 fails validation.
(ATG)	 TG	4509-4514	CT	TGC
(ATG)	 TG	4539-4685	GG	GAG
Valid prediction for snap_scaffold_4-snap.3267-T1
Valid prediction for Augustus_model.g7106.t1
Valid prediction for GlimmerHMM_glimmerT_10833-T1
Valid prediction for GlimmerHMM_glimmerT_10843-T1
Valid prediction for snap_scaffold_4-snap.3299-T1
Valid prediction for snap_scaffold_4-snap.3287-T1
Valid prediction for GlimmerHMM_glimmerT_10821-T1
Valid prediction for snap_scaffold_4-snap.3268-T1
Valid prediction for snap_scaffold_4-snap.3298-T1
Valid prediction for GlimmerHMM_glimmerT_10820-T1
Valid prediction for snap_scaffold_4-snap.3291-T1
Couldn't classify 6902, 7216
Couldn't classify 7915, 7968
Sorry, prediction pasa_asmbl_43157.p1 fails validation.
(TCA)	 CC	6902-7216	GT	CAG
(TCC)	 AG	7497-7652	GT	AGG
(GTT)	 AG	7915-7968	GG	TGG
-recovered pasa_asmbl_43157.p1, internal, 7497, 7652
Valid prediction for CodingQuarry_transcript_49268-T1
Valid prediction for Augustus_model.g7098.t1
Couldn't classify 4964, 5578
Couldn't classify 6164, 6871
Sorry, prediction pasa_asmbl_43159.p1 fails validation.
(GAG)	 AG	4964-5578	GT	AGG
(GTG)	 AG	5948-6073	GT	AGG
(GTG)	 AG	6164-6871	CA	ACC
-recovered pasa_asmbl_43159.p1, internal, 4964, 5578
-recovered pasa_asmbl_43159.p1, internal, 5948, 6073
Valid prediction for GlimmerHMM_glimmerT_10844-T1
Valid prediction for snap_scaffold_4-snap.3257-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6000, rend_intergenic: 4806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7277, rend_intergenic: 6287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15142, rend_intergenic: 7929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15733, rend_intergenic: 15536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21219, rend_intergenic: 15763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32126, rend_intergenic: 22704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34909, rend_intergenic: 32224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39179, rend_intergenic: 35092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51087, rend_intergenic: 40163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58274, rend_intergenic: 57455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76659, rend_intergenic: 58279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94139, rend_intergenic: 78459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109291, rend_intergenic: 106212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111087, rend_intergenic: 109381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117116, rend_intergenic: 111883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129212, rend_intergenic: 118906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135915, rend_intergenic: 130576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139735, rend_intergenic: 136527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154010, rend_intergenic: 152601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163363, rend_intergenic: 159443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174979, rend_intergenic: 172565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178311, rend_intergenic: 175120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182344
-exon list size: 426


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 6000, rend_intergenic: 4806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7277, rend_intergenic: 6287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15142, rend_intergenic: 7929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15733, rend_intergenic: 15536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21219, rend_intergenic: 15763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32126, rend_intergenic: 22704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34909, rend_intergenic: 32224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39179, rend_intergenic: 35092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51087, rend_intergenic: 40163  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58274, rend_intergenic: 57455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76659, rend_intergenic: 58279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94139, rend_intergenic: 78459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109291, rend_intergenic: 106212  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111087, rend_intergenic: 109381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117116, rend_intergenic: 111883  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129212, rend_intergenic: 118906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135915, rend_intergenic: 130576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139735, rend_intergenic: 136527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154010, rend_intergenic: 152601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163363, rend_intergenic: 159443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174979, rend_intergenic: 172565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178311, rend_intergenic: 175120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support