-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_4809350-4942070

-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 GeneMark_model.701_t
Valid prediction for GeneMark_model.721_t
Valid prediction for GlimmerHMM_glimmerT_574-T1
Valid prediction for snap_scaffold_1-snap.728-T1
Valid prediction for snap_scaffold_1-snap.743-T1
Valid prediction for GeneMark_model.697_t
Valid prediction for GlimmerHMM_glimmerT_585-T1
Valid prediction for GeneMark_model.710_t
Valid prediction for Augustus_model.g439.t1
Valid prediction for GeneMark_model.723_t
Couldn't classify 100782, 100892
Sorry, prediction pasa_asmbl_2786.p1 fails validation.
(CCC)	 CC	100782-100892	GT	AGG
(CGT)	 AG	101049-101132	GT	AGG
(GAC)	 AG	103311-103400	GT	AGG
(GAA)	 AG	104765-104823	GT	AGG
(CAC)	 AG	105775-105935	GT	AGG
(GCC)	 AG	106218-106332	GT	AGG
(GCC)	 AG	106503-106624	GT	AGG
(GGA)	 AG	106915-107015	GT	AGG
(AAG)	 AG	107202-107282	GA	AGG
-recovered pasa_asmbl_2786.p1, terminal, 107202, 107282
-recovered pasa_asmbl_2786.p1, internal, 101049, 101132
-recovered pasa_asmbl_2786.p1, internal, 103311, 103400
-recovered pasa_asmbl_2786.p1, internal, 104765, 104823
-recovered pasa_asmbl_2786.p1, internal, 105775, 105935
-recovered pasa_asmbl_2786.p1, internal, 106218, 106332
-recovered pasa_asmbl_2786.p1, internal, 106503, 106624
-recovered pasa_asmbl_2786.p1, internal, 106915, 107015
Valid prediction for GeneMark_model.707_t
Valid prediction for GeneMark_model.728_t
Valid prediction for GeneMark_model.711_t
Valid prediction for GeneMark_model.719_t
Valid prediction for Augustus_model.g444.t1
Valid prediction for Augustus_model.g449.t1
Valid prediction for GeneMark_model.726_t
Valid prediction for GlimmerHMM_glimmerT_589-T1
Valid prediction for Augustus_model.g441.t1
Valid prediction for GeneMark_model.699_t
Valid prediction for Augustus_model.g438.t1
Valid prediction for snap_scaffold_1-snap.722-T1
Valid prediction for GeneMark_model.715_t
Valid prediction for GlimmerHMM_glimmerT_586-T1
Valid prediction for snap_scaffold_1-snap.723-T1
Valid prediction for GeneMark_model.717_t
Valid prediction for GeneMark_model.705_t
Valid prediction for GlimmerHMM_glimmerT_582-T1
Valid prediction for CodingQuarry_transcript_2596-T1
Valid prediction for snap_scaffold_1-snap.742-T1
Valid prediction for Augustus_model.g451.t1
Valid prediction for GlimmerHMM_glimmerT_575-T1
Valid prediction for Augustus_model.g447.t1
Valid prediction for snap_scaffold_1-snap.745-T1
Valid prediction for snap_scaffold_1-snap.749-T1
Valid prediction for GeneMark_model.702_t
Valid prediction for snap_scaffold_1-snap.726-T1
Valid prediction for GeneMark_model.713_t
Valid prediction for snap_scaffold_1-snap.733-T1
Valid prediction for snap_scaffold_1-snap.740-T1
Valid prediction for GlimmerHMM_glimmerT_583-T1
Valid prediction for GlimmerHMM_glimmerT_578-T1
Valid prediction for GlimmerHMM_glimmerT_587-T1
Valid prediction for GeneMark_model.709_t
Valid prediction for snap_scaffold_1-snap.725-T1
Valid prediction for snap_scaffold_1-snap.746-T1
Couldn't classify 59666, 60170
Couldn't classify 61008, 61117
Sorry, prediction pasa_asmbl_1685.p2 fails validation.
(GAG)	 TC	59666-60170	GT	AGG
(GCG)	 AG	60605-60700	GT	AGG
(GTC)	 AG	61008-61117	CT	CCC
-recovered pasa_asmbl_1685.p2, internal, 60605, 60700
Valid prediction for GeneMark_model.695_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 CodingQuarry_transcript_2597-T1
Valid prediction for Augustus_model.g454.t1
Valid prediction for snap_scaffold_1-snap.741-T1
Valid prediction for GlimmerHMM_glimmerT_577-T1
Valid prediction for GeneMark_model.727_t
Valid prediction for snap_scaffold_1-snap.735-T1
Valid prediction for GeneMark_model.708_t
Valid prediction for GlimmerHMM_glimmerT_576-T1
Valid prediction for GeneMark_model.696_t
Valid prediction for GlimmerHMM_glimmerT_573-T1
Valid prediction for snap_scaffold_1-snap.736-T1
Valid prediction for GeneMark_model.718_t
Valid prediction for snap_scaffold_1-snap.729-T1
Valid prediction for GlimmerHMM_glimmerT_592-T1
Valid prediction for snap_scaffold_1-snap.739-T1
Valid prediction for snap_scaffold_1-snap.747-T1
Valid prediction for GeneMark_model.714_t
Valid prediction for GeneMark_model.700_t
Valid prediction for snap_scaffold_1-snap.750-T1
Valid prediction for GlimmerHMM_glimmerT_580-T1
Valid prediction for CodingQuarry_transcript_2593-T1
Couldn't classify 19555, 19600
Sorry, prediction pasa_asmbl_229.p1 fails validation.
(TAC)	 CG	19555-19600	GT	CGG
(AGG)	 AG	19693-19811	GT	AGG
(TAT)	 AG	20133-20261	GT	TGG
(ATT)	 AG	20592-20769	GT	AGG
(TCA)	 AG	20968-21103	GT	TGG
(GAA)	 AG	21183-21286	GT	AGG
(GGG)	 AG	21414-21653	GT	AGG
(CTC)	 AG	21917-21976	GT	AGG
(GTT)	 AG	22169-22378	GT	AGG
(TCA)	 AG	22631-22788	GT	AGG
(GTT)	 AG	23204-23340	GT	AGG
(GAT)	 AG	23763-23916	AC	AGA
-recovered pasa_asmbl_229.p1, terminal, 23763, 23916
-recovered pasa_asmbl_229.p1, internal, 19693, 19811
-recovered pasa_asmbl_229.p1, internal, 20133, 20261
-recovered pasa_asmbl_229.p1, internal, 20592, 20769
-recovered pasa_asmbl_229.p1, internal, 20968, 21103
-recovered pasa_asmbl_229.p1, internal, 21183, 21286
-recovered pasa_asmbl_229.p1, internal, 21414, 21653
-recovered pasa_asmbl_229.p1, internal, 21917, 21976
-recovered pasa_asmbl_229.p1, internal, 22169, 22378
-recovered pasa_asmbl_229.p1, internal, 22631, 22788
-recovered pasa_asmbl_229.p1, internal, 23204, 23340
Valid prediction for GlimmerHMM_glimmerT_579-T1
Valid prediction for GeneMark_model.720_t
Couldn't classify 68704, 68782
Sorry, prediction pasa_asmbl_223.p1 fails validation.
(ATG)	 GC	66208-66276	GT	AGG
(GTT)	 AG	66601-66695	GT	AGG
(GCT)	 AG	66872-66965	GT	AGG
(GAT)	 AG	67147-67286	GT	AGG
(GTT)	 AG	68704-68782	GT	AGG
-recovered pasa_asmbl_223.p1, initial, 66208, 66276
-recovered pasa_asmbl_223.p1, internal, 66601, 66695
-recovered pasa_asmbl_223.p1, internal, 66872, 66965
-recovered pasa_asmbl_223.p1, internal, 67147, 67286
-recovered pasa_asmbl_223.p1, internal, 68704, 68782
Valid prediction for Augustus_model.g442.t1
Valid prediction for GeneMark_model.724_t
Valid prediction for snap_scaffold_1-snap.724-T1
Valid prediction for snap_scaffold_1-snap.721-T1
Valid prediction for Augustus_model.g440.t1
Valid prediction for snap_scaffold_1-snap.727-T1
Valid prediction for GeneMark_model.729_t
Valid prediction for GlimmerHMM_glimmerT_584-T1
Valid prediction for snap_scaffold_1-snap.734-T1
Valid prediction for snap_scaffold_1-snap.748-T1
Valid prediction for snap_scaffold_1-snap.732-T1
Valid prediction for HiQ_model.g453.t1
Valid prediction for GeneMark_model.712_t
Valid prediction for snap_scaffold_1-snap.737-T1
Valid prediction for GeneMark_model.694_t
Valid prediction for GlimmerHMM_glimmerT_590-T1
Valid prediction for Augustus_model.g446.t1
Valid prediction for GeneMark_model.716_t
Valid prediction for CodingQuarry_transcript_2595-T1
Valid prediction for GeneMark_model.704_t
Valid prediction for snap_scaffold_1-snap.731-T1
Couldn't classify 13337, 13825
Sorry, prediction pasa_asmbl_233.p1 fails validation.
(TCT)	 TC	13337-13825	CG	AGC
Valid prediction for Augustus_model.g445.t1
Valid prediction for Augustus_model.g448.t1
Valid prediction for GeneMark_model.703_t
Valid prediction for pasa_asmbl_230.p1
Valid prediction for snap_scaffold_1-snap.730-T1
Valid prediction for Augustus_model.g452.t1
Valid prediction for GlimmerHMM_glimmerT_591-T1
Valid prediction for Augustus_model.g450.t1
Valid prediction for GeneMark_model.693_t
Valid prediction for snap_scaffold_1-snap.738-T1
Valid prediction for GeneMark_model.698_t
Valid prediction for Augustus_model.g443.t1
Valid prediction for GlimmerHMM_glimmerT_588-T1
Valid prediction for snap_scaffold_1-snap.744-T1
Valid prediction for GeneMark_model.722_t
Couldn't classify 8044, 8135
Sorry, prediction pasa_asmbl_1236.p1 fails validation.
(CAG)	 CG	8044-8135	GT	GGG
(CTG)	 AG	8347-8442	GT	GGG
(GTG)	 AG	8607-8781	GT	GGG
(CTC)	 AG	8983-9052	GT	GGG
(AGA)	 AG	9208-9292	GT	GGG
(GTT)	 AG	9439-9567	GT	CTG
(GGA)	 AG	9738-9810	GT	AGG
(CAA)	 AG	9936-10007	GT	AAG
(ATC)	 AG	10254-10342	GT	AGG
(GGA)	 AG	10457-10616	GT	TGG
(GCT)	 AG	10777-10910	GT	AAG
(AGA)	 AG	11071-11211	GT	AGG
(GCT)	 AG	11299-11419	GT	AGG
(GTG)	 AG	11537-11641	GT	AGG
(TTT)	 AG	11815-11911	GT	GGG
(GGA)	 AG	12340-12416	GT	GAG
-recovered pasa_asmbl_1236.p1, terminal, 12340, 12416
-recovered pasa_asmbl_1236.p1, internal, 8347, 8442
-recovered pasa_asmbl_1236.p1, internal, 8607, 8781
-recovered pasa_asmbl_1236.p1, internal, 8983, 9052
-recovered pasa_asmbl_1236.p1, internal, 9208, 9292
-recovered pasa_asmbl_1236.p1, internal, 9439, 9567
-recovered pasa_asmbl_1236.p1, internal, 9738, 9810
-recovered pasa_asmbl_1236.p1, internal, 9936, 10007
-recovered pasa_asmbl_1236.p1, internal, 10254, 10342
-recovered pasa_asmbl_1236.p1, internal, 10457, 10616
-recovered pasa_asmbl_1236.p1, internal, 10777, 10910
-recovered pasa_asmbl_1236.p1, internal, 11071, 11211
-recovered pasa_asmbl_1236.p1, internal, 11299, 11419
-recovered pasa_asmbl_1236.p1, internal, 11537, 11641
-recovered pasa_asmbl_1236.p1, internal, 11815, 11911
-recovered pasa_asmbl_1236.p1, internal, 12340, 12416
Valid prediction for GeneMark_model.706_t
Valid prediction for GlimmerHMM_glimmerT_581-T1
Couldn't classify 7504, 7645
Sorry, prediction pasa_asmbl_234.p1 fails validation.
(ATG)	 CC	5854-5878	GT	TGG
(TCC)	 AG	6094-6235	GT	GTG
(AAT)	 AG	6460-6584	GT	ATG
(TGT)	 AG	7074-7205	GT	CGG
(CTG)	 AG	7329-7377	GT	AGG
(GTC)	 AG	7504-7645	CC	GGC
-recovered pasa_asmbl_234.p1, initial, 5854, 5878
-recovered pasa_asmbl_234.p1, internal, 6094, 6235
-recovered pasa_asmbl_234.p1, internal, 6460, 6584
-recovered pasa_asmbl_234.p1, internal, 7074, 7205
-recovered pasa_asmbl_234.p1, internal, 7329, 7377

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 107282, rend_intergenic: 107279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22981, rend_intergenic: 19452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37333, rend_intergenic: 34548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81336, rend_intergenic: 79265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101227, rend_intergenic: 98452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121835, rend_intergenic: 118897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 132721
-exon list size: 482


building trellis

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-found 24 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 107282, rend_intergenic: 107279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22981, rend_intergenic: 19452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37333, rend_intergenic: 34548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81336, rend_intergenic: 79265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101227, rend_intergenic: 98452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121835, rend_intergenic: 118897  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