-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_17986884-18136316

-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.3651_t
Couldn't classify 42390, 42398
Couldn't classify 43125, 43484
Sorry, prediction CodingQuarry_transcript_2975-T1 fails validation.
(ATG)	 AA	42390-42398	CT	ACC
(CTT)	 AC	43125-43484	CC	GAC
Valid prediction for GlimmerHMM_glimmerT_2482-T1
Valid prediction for GeneMark_model.3664_t
Valid prediction for snap_scaffold_1-snap.3307-T1
Valid prediction for GlimmerHMM_glimmerT_2480-T1
Valid prediction for snap_scaffold_1-snap.3295-T1
Valid prediction for GlimmerHMM_glimmerT_2496-T1
Valid prediction for Augustus_model.g1792.t1
Valid prediction for GeneMark_model.3632_t
Valid prediction for snap_scaffold_1-snap.3315-T1
Valid prediction for GeneMark_model.3653_t
Valid prediction for GeneMark_model.3660_t
Valid prediction for GlimmerHMM_glimmerT_2488-T1
Valid prediction for snap_scaffold_1-snap.3305-T1
Valid prediction for snap_scaffold_1-snap.3316-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.3641_t
Valid prediction for GeneMark_model.3636_t
Valid prediction for GeneMark_model.3634_t
Valid prediction for GeneMark_model.3642_t
Valid prediction for GeneMark_model.3666_t
Valid prediction for GlimmerHMM_glimmerT_2476-T1
Valid prediction for GeneMark_model.3638_t
Valid prediction for GeneMark_model.3662_t
Valid prediction for snap_scaffold_1-snap.3299-T1
Valid prediction for GeneMark_model.3658_t
Valid prediction for snap_scaffold_1-snap.3308-T1
Valid prediction for GeneMark_model.3669_t
Valid prediction for GeneMark_model.3646_t
Valid prediction for snap_scaffold_1-snap.3320-T1
Valid prediction for GlimmerHMM_glimmerT_2492-T1
Valid prediction for Augustus_model.g1785.t1
Valid prediction for Augustus_model.g1786.t1
Valid prediction for GeneMark_model.3648_t
Couldn't classify 33327, 33396
Sorry, prediction GeneMark_model.3640_t fails validation.
(GTC)	 AG	33327-33396	GT	GAG
(ACA)	 AG	34022-34048	GT	CGG
(AGA)	 AG	34074-34094	GT	GGG
(TTA)	 AG	36898-36901	AG	AAA
add_exon() Sorry, GeneMark_model.3640_t 33327-33396-terminal-3 is invalid.
-recovered GeneMark_model.3640_t, terminal, 33327, 33396
-recovered GeneMark_model.3640_t, terminal, 36898, 36901
-recovered GeneMark_model.3640_t, internal, 33327, 33396
-recovered GeneMark_model.3640_t, internal, 34022, 34048
-recovered GeneMark_model.3640_t, internal, 34074, 34094
Valid prediction for GeneMark_model.3668_t
Valid prediction for GeneMark_model.3654_t
Valid prediction for snap_scaffold_1-snap.3310-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.3652_t
Valid prediction for GlimmerHMM_glimmerT_2489-T1
Valid prediction for Augustus_model.g1790.t1
Valid prediction for Augustus_model.g1791.t1
Valid prediction for Augustus_model.g1794.t1
Valid prediction for GeneMark_model.3655_t
Valid prediction for GlimmerHMM_glimmerT_2493-T1
Valid prediction for Augustus_model.g1795.t1
Valid prediction for snap_scaffold_1-snap.3303-T1
Couldn't classify 101366, 101908
Sorry, prediction pasa_asmbl_1081.p1 fails validation.
(GTG)	 GG	101366-101908	GA	AGG
Valid prediction for GeneMark_model.3656_t
Valid prediction for Augustus_model.g1798.t1
Valid prediction for CodingQuarry_transcript_2982-T1
Valid prediction for HiQ_model.g1793.t1
Valid prediction for GeneMark_model.3643_t
Couldn't classify 91211, 91339
Sorry, prediction pasa_asmbl_1082.p1 fails validation.
(AAA)	 AG	91211-91339	GT	AGG
(GGG)	 AG	91490-91666	GT	CAG
(AAA)	 AG	91811-91932	GT	GAG
(GCT)	 AG	92237-92463	GT	TGG
(GGT)	 AG	92856-92888	GT	GAG
(AAC)	 AG	93389-93553	GT	AGG
(TTC)	 AG	93720-93797	GT	AGG
(TGA)	 AG	94044-94148	GT	CGG
(AGC)	 AG	94534-94711	GT	AGG
(GCT)	 AG	94893-95038	GT	AGG
(CTG)	 AG	95206-95287	GT	AGG
(GTC)	 AG	95404-95515	CT	AAC
-recovered pasa_asmbl_1082.p1, terminal, 92856, 92888
add_exon() Sorry, pasa_asmbl_1082.p1 94893-95038-terminal-2 is invalid.
-recovered pasa_asmbl_1082.p1, terminal, 94893, 95038
-recovered pasa_asmbl_1082.p1, terminal, 95404, 95515
-recovered pasa_asmbl_1082.p1, internal, 91211, 91339
-recovered pasa_asmbl_1082.p1, internal, 91490, 91666
-recovered pasa_asmbl_1082.p1, internal, 91811, 91932
-recovered pasa_asmbl_1082.p1, internal, 92237, 92463
-recovered pasa_asmbl_1082.p1, internal, 92856, 92888
-recovered pasa_asmbl_1082.p1, internal, 93389, 93553
-recovered pasa_asmbl_1082.p1, internal, 93720, 93797
-recovered pasa_asmbl_1082.p1, internal, 94044, 94148
-recovered pasa_asmbl_1082.p1, internal, 94534, 94711
-recovered pasa_asmbl_1082.p1, internal, 94893, 95038
-recovered pasa_asmbl_1082.p1, internal, 95206, 95287
Valid prediction for CodingQuarry_transcript_2979-T1
Valid prediction for Augustus_model.g1788.t1
Valid prediction for GeneMark_model.3633_t
Valid prediction for GeneMark_model.3645_t
Valid prediction for GeneMark_model.3670_t
Valid prediction for CodingQuarry_transcript_2976-T1
Valid prediction for snap_scaffold_1-snap.3313-T1
Valid prediction for GeneMark_model.3657_t
Valid prediction for GlimmerHMM_glimmerT_2491-T1
Valid prediction for snap_scaffold_1-snap.3318-T1
Valid prediction for GeneMark_model.3644_t
Valid prediction for GeneMark_model.3667_t
Valid prediction for snap_scaffold_1-snap.3302-T1
Valid prediction for GlimmerHMM_glimmerT_2479-T1
Couldn't classify 39609, 40667
Sorry, prediction pasa_asmbl_1091.p1 fails validation.
(CAG)	 TG	39609-40667	GT	AGG
Valid prediction for Augustus_model.g1799.t1
Valid prediction for GlimmerHMM_glimmerT_2486-T1
Valid prediction for GlimmerHMM_glimmerT_2484-T1
Valid prediction for snap_scaffold_1-snap.3306-T1
Valid prediction for HiQ_model.g1787.t1
Couldn't classify 124596, 124685
Sorry, prediction GeneMark_model.3639_t fails validation.
(GTG)	 AG	124596-124685	GT	GTG
(AGC)	 AG	124723-124768	CG	AAC
-recovered GeneMark_model.3639_t, terminal, 124723, 124768
-recovered GeneMark_model.3639_t, internal, 124596, 124685
Valid prediction for GlimmerHMM_glimmerT_2481-T1
Valid prediction for GlimmerHMM_glimmerT_2495-T1
Valid prediction for snap_scaffold_1-snap.3296-T1
Valid prediction for snap_scaffold_1-snap.3311-T1
Valid prediction for GeneMark_model.3650_t
Valid prediction for GeneMark_model.3647_t
Valid prediction for snap_scaffold_1-snap.3312-T1
Valid prediction for CodingQuarry_transcript_2980-T1
Valid prediction for GlimmerHMM_glimmerT_2478-T1
Valid prediction for snap_scaffold_1-snap.3301-T1
Valid prediction for GeneMark_model.3637_t
Valid prediction for CodingQuarry_transcript_2977-T1
Valid prediction for GlimmerHMM_glimmerT_2487-T1
Valid prediction for snap_scaffold_1-snap.3304-T1
Valid prediction for GeneMark_model.3649_t
Valid prediction for snap_scaffold_1-snap.3297-T1
Valid prediction for GeneMark_model.3635_t
Valid prediction for GeneMark_model.3663_t
Valid prediction for snap_scaffold_1-snap.3298-T1
Valid prediction for Augustus_model.g1789.t1
Valid prediction for snap_scaffold_1-snap.3294-T1
Valid prediction for pasa_asmbl_1076.p1
Valid prediction for GeneMark_model.3661_t
Valid prediction for Augustus_model.g1796.t1
Valid prediction for Augustus_model.g1797.t1
Valid prediction for GlimmerHMM_glimmerT_2483-T1
Valid prediction for snap_scaffold_1-snap.3319-T1
Valid prediction for pasa_asmbl_1086.p1
Valid prediction for GeneMark_model.3665_t
Valid prediction for snap_scaffold_1-snap.3309-T1
Valid prediction for GlimmerHMM_glimmerT_2475-T1
Valid prediction for GeneMark_model.3659_t
Valid prediction for GlimmerHMM_glimmerT_2485-T1
Valid prediction for GlimmerHMM_glimmerT_2494-T1
Valid prediction for snap_scaffold_1-snap.3317-T1
Valid prediction for GlimmerHMM_glimmerT_2477-T1
Valid prediction for CodingQuarry_transcript_2983-T1
Valid prediction for GlimmerHMM_glimmerT_2490-T1
Valid prediction for snap_scaffold_1-snap.3300-T1
Couldn't classify 36387, 36599
Sorry, prediction pasa_asmbl_1093.p1 fails validation.
(ATG)	 AG	33232-33471	GT	AGG
(GCG)	 AG	36387-36599	GT	AGG
-recovered pasa_asmbl_1093.p1, initial, 33232, 33471
-recovered pasa_asmbl_1093.p1, internal, 33232, 33471
-recovered pasa_asmbl_1093.p1, internal, 36387, 36599
Valid prediction for snap_scaffold_1-snap.3314-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14866, rend_intergenic: 7704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73102, rend_intergenic: 70125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73585, rend_intergenic: 73265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86857, rend_intergenic: 74219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127706, rend_intergenic: 121530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135656, rend_intergenic: 127724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147938, rend_intergenic: 143327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149433
-exon list size: 546


building trellis

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99.3    
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99.8    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 14866, rend_intergenic: 7704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73102, rend_intergenic: 70125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73585, rend_intergenic: 73265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86857, rend_intergenic: 74219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127706, rend_intergenic: 121530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135656, rend_intergenic: 127724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147938, rend_intergenic: 143327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support