-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_20195494-20409160

-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_1-snap.3786-T1
Valid prediction for pasa_asmbl_2613.p1
Valid prediction for GeneMark_model.4299_t
Valid prediction for Augustus_model.g1962.t1
Valid prediction for GeneMark_model.4314_t
Couldn't classify 193450, 193627
Sorry, prediction pasa_asmbl_2618.p1 fails validation.
(CGC)	 AG	193450-193627	GT	GGG
(TGT)	 AG	193722-193901	GT	AGG
(GAG)	 AG	194114-194242	GT	CAG
(TGC)	 AG	194345-194424	GT	AGG
(GCT)	 AG	194617-194809	GT	AGG
(ATG)	 AG	195357-195653	GT	ACG
(TTG)	 AG	195841-196161	GT	AGG
(ACT)	 AG	196302-196306	AG	GAA
add_exon() Sorry, pasa_asmbl_2618.p1 195357-195653-initial-1 is invalid.
-recovered pasa_asmbl_2618.p1, initial, 195357, 195653
-recovered pasa_asmbl_2618.p1, terminal, 196302, 196306
-recovered pasa_asmbl_2618.p1, internal, 193450, 193627
-recovered pasa_asmbl_2618.p1, internal, 193722, 193901
-recovered pasa_asmbl_2618.p1, internal, 194114, 194242
-recovered pasa_asmbl_2618.p1, internal, 194345, 194424
-recovered pasa_asmbl_2618.p1, internal, 194617, 194809
-recovered pasa_asmbl_2618.p1, internal, 195357, 195653
-recovered pasa_asmbl_2618.p1, internal, 195841, 196161
Valid prediction for GeneMark_model.4303_t
Valid prediction for snap_scaffold_1-snap.3821-T1
Valid prediction for snap_scaffold_1-snap.3823-T1
Valid prediction for GlimmerHMM_glimmerT_2781-T1
Valid prediction for snap_scaffold_1-snap.3808-T1
Valid prediction for GeneMark_model.4302_t
Valid prediction for snap_scaffold_1-snap.3819-T1
Valid prediction for snap_scaffold_1-snap.3814-T1
Valid prediction for snap_scaffold_1-snap.3816-T1
Valid prediction for snap_scaffold_1-snap.3817-T1
Valid prediction for GeneMark_model.4279_t
Valid prediction for GlimmerHMM_glimmerT_2784-T1
Valid prediction for GlimmerHMM_glimmerT_2796-T1
Valid prediction for GeneMark_model.4328_t
Valid prediction for GeneMark_model.4322_t
Valid prediction for snap_scaffold_1-snap.3818-T1
Valid prediction for snap_scaffold_1-snap.3793-T1
Valid prediction for snap_scaffold_1-snap.3815-T1
Valid prediction for CodingQuarry_transcript_3020-T1
Valid prediction for GeneMark_model.4326_t
Valid prediction for HiQ_model.g1958.t1
Valid prediction for snap_scaffold_1-snap.3803-T1
Valid prediction for GlimmerHMM_glimmerT_2794-T1
Valid prediction for snap_scaffold_1-snap.3825-T1
Valid prediction for GeneMark_model.4323_t
Valid prediction for snap_scaffold_1-snap.3813-T1
Valid prediction for snap_scaffold_1-snap.3810-T1
Valid prediction for snap_scaffold_1-snap.3809-T1
Valid prediction for GlimmerHMM_glimmerT_2789-T1
Valid prediction for GeneMark_model.4284_t
Valid prediction for GlimmerHMM_glimmerT_2785-T1
Valid prediction for Augustus_model.g1960.t1
Valid prediction for GlimmerHMM_glimmerT_2795-T1
Valid prediction for snap_scaffold_1-snap.3806-T1
Valid prediction for GeneMark_model.4312_t
Valid prediction for CodingQuarry_transcript_3024-T1
Couldn't classify 190127, 190178
Couldn't classify 192655, 192947
Sorry, prediction pasa_asmbl_2617.p1 fails validation.
(TCA)	 CG	190127-190178	GT	TGG
(CGT)	 AG	191192-191307	GT	AGG
(CTC)	 AG	192336-192477	GT	AGG
(ACA)	 AG	192655-192947	GG	TTG
-recovered pasa_asmbl_2617.p1, internal, 191192, 191307
-recovered pasa_asmbl_2617.p1, internal, 192336, 192477
Valid prediction for GeneMark_model.4296_t
Valid prediction for Augustus_model.g1953.t1
Valid prediction for GeneMark_model.4316_t
Valid prediction for GeneMark_model.4306_t
Valid prediction for GeneMark_model.4318_t
Valid prediction for GeneMark_model.4320_t
Couldn't classify 171299, 171610
Sorry, prediction pasa_asmbl_2760.p1 fails validation.
(TCA)	 TT	171299-171610	GG	CAG
Valid prediction for CodingQuarry_transcript_3019-T1
Valid prediction for snap_scaffold_1-snap.3801-T1
Valid prediction for GeneMark_model.4282_t
Valid prediction for Augustus_model.g1961.t1
Valid prediction for GlimmerHMM_glimmerT_2791-T1
Valid prediction for CodingQuarry_transcript_3018-T1
Valid prediction for GeneMark_model.4324_t
Valid prediction for CodingQuarry_transcript_3021-T1
Valid prediction for GeneMark_model.4304_t
Valid prediction for GeneMark_model.4325_t
Valid prediction for CodingQuarry_transcript_3022-T1
Valid prediction for pasa_asmbl_2606.p1
Valid prediction for GlimmerHMM_glimmerT_2787-T1
Valid prediction for GeneMark_model.4327_t
Valid prediction for GlimmerHMM_glimmerT_2797-T1
Valid prediction for snap_scaffold_1-snap.3790-T1
Valid prediction for HiQ_model.g1959.t1
Valid prediction for GlimmerHMM_glimmerT_2780-T1
Valid prediction for GeneMark_model.4321_t
Valid prediction for snap_scaffold_1-snap.3800-T1
Valid prediction for snap_scaffold_1-snap.3795-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g1957.t1
Valid prediction for Augustus_model.g1955.t1
Valid prediction for GlimmerHMM_glimmerT_2786-T1
Valid prediction for snap_scaffold_1-snap.3824-T1
Valid prediction for snap_scaffold_1-snap.3787-T1
Valid prediction for GeneMark_model.4294_t
Valid prediction for GeneMark_model.4330_t
Valid prediction for Augustus_model.g1956.t1
Valid prediction for CodingQuarry_transcript_3023-T1
Valid prediction for GeneMark_model.4289_t
Valid prediction for snap_scaffold_1-snap.3796-T1
Valid prediction for snap_scaffold_1-snap.3812-T1
Valid prediction for snap_scaffold_1-snap.3797-T1
Valid prediction for GlimmerHMM_glimmerT_2782-T1
Valid prediction for GeneMark_model.4297_t
Valid prediction for GeneMark_model.4310_t
Valid prediction for Augustus_model.g1954.t1
Valid prediction for GeneMark_model.4292_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 GeneMark_model.4285_t
Valid prediction for GlimmerHMM_glimmerT_2790-T1
Valid prediction for GeneMark_model.4280_t
Valid prediction for GeneMark_model.4301_t
Valid prediction for GeneMark_model.4298_t
Valid prediction for snap_scaffold_1-snap.3802-T1
Valid prediction for snap_scaffold_1-snap.3794-T1
Couldn't classify 81848, 82165
Sorry, prediction pasa_asmbl_2598.p1 fails validation.
(ATG)	 GT	81848-82165	AC	CGA
Valid prediction for GeneMark_model.4315_t
Valid prediction for snap_scaffold_1-snap.3798-T1
Valid prediction for GeneMark_model.4307_t
Valid prediction for GeneMark_model.4283_t
Valid prediction for snap_scaffold_1-snap.3785-T1
Valid prediction for GeneMark_model.4319_t
Valid prediction for GeneMark_model.4293_t
Valid prediction for GeneMark_model.4291_t
Valid prediction for snap_scaffold_1-snap.3789-T1
Valid prediction for snap_scaffold_1-snap.3792-T1
Valid prediction for snap_scaffold_1-snap.3799-T1
Valid prediction for GeneMark_model.4281_t
Valid prediction for snap_scaffold_1-snap.3791-T1
Valid prediction for snap_scaffold_1-snap.3820-T1
Valid prediction for snap_scaffold_1-snap.3784-T1
Valid prediction for snap_scaffold_1-snap.3807-T1
Valid prediction for snap_scaffold_1-snap.3804-T1
Valid prediction for GeneMark_model.4295_t
Valid prediction for snap_scaffold_1-snap.3805-T1
Valid prediction for GeneMark_model.4313_t
Valid prediction for GlimmerHMM_glimmerT_2792-T1
Valid prediction for GeneMark_model.4300_t
Valid prediction for GeneMark_model.4309_t
Valid prediction for snap_scaffold_1-snap.3811-T1
Valid prediction for GeneMark_model.4329_t
Valid prediction for GeneMark_model.4277_t
Valid prediction for GlimmerHMM_glimmerT_2783-T1
Valid prediction for snap_scaffold_1-snap.3788-T1
Valid prediction for snap_scaffold_1-snap.3822-T1
Valid prediction for GeneMark_model.4290_t
Valid prediction for GlimmerHMM_glimmerT_2788-T1
Valid prediction for GeneMark_model.4287_t
Valid prediction for GeneMark_model.4317_t
Valid prediction for GlimmerHMM_glimmerT_2793-T1
Valid prediction for GeneMark_model.4311_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14593, rend_intergenic: 7210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18022, rend_intergenic: 16802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28015, rend_intergenic: 27305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38422, rend_intergenic: 32149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52815, rend_intergenic: 48822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69841, rend_intergenic: 61944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77738, rend_intergenic: 71795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84170, rend_intergenic: 83462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88341, rend_intergenic: 87083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101492, rend_intergenic: 91933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131761, rend_intergenic: 123903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147921, rend_intergenic: 147010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195431, rend_intergenic: 191263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213667
-exon list size: 636


building trellis

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-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 14593, rend_intergenic: 7210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18022, rend_intergenic: 16802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28015, rend_intergenic: 27305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38422, rend_intergenic: 32149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52815, rend_intergenic: 48822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69841, rend_intergenic: 61944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77738, rend_intergenic: 71795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84170, rend_intergenic: 83462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88341, rend_intergenic: 87083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101492, rend_intergenic: 91933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131761, rend_intergenic: 123903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147921, rend_intergenic: 147010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195431, rend_intergenic: 191263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support