-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_20954937-21135519

-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.4507_t
Valid prediction for snap_scaffold_1-snap.3969-T1
Valid prediction for GeneMark_model.4544_t
Valid prediction for GlimmerHMM_glimmerT_2876-T1
Valid prediction for snap_scaffold_1-snap.3979-T1
Valid prediction for snap_scaffold_1-snap.3991-T1
Valid prediction for GlimmerHMM_glimmerT_2886-T1
Valid prediction for HiQ_model.g2010.t1
Valid prediction for snap_scaffold_1-snap.3976-T1
Valid prediction for GeneMark_model.4528_t
Valid prediction for snap_scaffold_1-snap.3981-T1
Valid prediction for snap_scaffold_1-snap.4001-T1
Valid prediction for GeneMark_model.4546_t
Valid prediction for GeneMark_model.4502_t
Valid prediction for snap_scaffold_1-snap.3989-T1
Valid prediction for GeneMark_model.4533_t
Valid prediction for snap_scaffold_1-snap.3993-T1
Couldn't classify 18983, 19339
Sorry, prediction pasa_asmbl_1205.p1 fails validation.
(CTC)	 TC	18983-19339	TT	TTT
Valid prediction for snap_scaffold_1-snap.3971-T1
Valid prediction for GlimmerHMM_glimmerT_2897-T1
Valid prediction for snap_scaffold_1-snap.3963-T1
Valid prediction for GlimmerHMM_glimmerT_2872-T1
Valid prediction for GeneMark_model.4516_t
Valid prediction for snap_scaffold_1-snap.4004-T1
Valid prediction for GeneMark_model.4553_t
Valid prediction for snap_scaffold_1-snap.3967-T1
Valid prediction for GeneMark_model.4548_t
Valid prediction for GeneMark_model.4550_t
Valid prediction for snap_scaffold_1-snap.3983-T1
Valid prediction for GlimmerHMM_glimmerT_2894-T1
Valid prediction for snap_scaffold_1-snap.3980-T1
Valid prediction for snap_scaffold_1-snap.3997-T1
Valid prediction for GeneMark_model.4521_t
Valid prediction for GlimmerHMM_glimmerT_2885-T1
Valid prediction for pasa_asmbl_2653.p1
Valid prediction for snap_scaffold_1-snap.3965-T1
Valid prediction for GeneMark_model.4526_t
Valid prediction for GeneMark_model.4503_t
Valid prediction for GeneMark_model.4512_t
Valid prediction for GeneMark_model.4536_t
Valid prediction for GeneMark_model.4555_t
Valid prediction for GeneMark_model.4517_t
Valid prediction for Augustus_model.g2009.t1
Valid prediction for GeneMark_model.4518_t
Valid prediction for Augustus_model.g2012.t1
Valid prediction for snap_scaffold_1-snap.3994-T1
Valid prediction for snap_scaffold_1-snap.3973-T1
Valid prediction for GeneMark_model.4511_t
Valid prediction for snap_scaffold_1-snap.4000-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2887-T1
Valid prediction for GlimmerHMM_glimmerT_2883-T1
Valid prediction for GeneMark_model.4541_t
Valid prediction for CodingQuarry_transcript_3041-T1
Valid prediction for snap_scaffold_1-snap.3960-T1
Valid prediction for Augustus_model.g2014.t1
Valid prediction for GeneMark_model.4501_t
Valid prediction for CodingQuarry_transcript_3039-T1
Valid prediction for GeneMark_model.4519_t
Valid prediction for GeneMark_model.4543_t
Valid prediction for Augustus_model.g2013.t1
Valid prediction for snap_scaffold_1-snap.3959-T1
Valid prediction for GeneMark_model.4510_t
Valid prediction for GlimmerHMM_glimmerT_2877-T1
Valid prediction for GeneMark_model.4557_t
Valid prediction for GlimmerHMM_glimmerT_2873-T1
Valid prediction for snap_scaffold_1-snap.3987-T1
Valid prediction for GeneMark_model.4552_t
Valid prediction for snap_scaffold_1-snap.3998-T1
Valid prediction for snap_scaffold_1-snap.3970-T1
Valid prediction for GlimmerHMM_glimmerT_2898-T1
Valid prediction for GeneMark_model.4500_t
Valid prediction for GlimmerHMM_glimmerT_2896-T1
Valid prediction for GlimmerHMM_glimmerT_2879-T1
Valid prediction for GlimmerHMM_glimmerT_2892-T1
Valid prediction for GeneMark_model.4514_t
Valid prediction for GeneMark_model.4524_t
Valid prediction for GeneMark_model.4506_t
Valid prediction for GlimmerHMM_glimmerT_2884-T1
Valid prediction for GeneMark_model.4499_t
Valid prediction for snap_scaffold_1-snap.3974-T1
Valid prediction for snap_scaffold_1-snap.3996-T1
Valid prediction for GlimmerHMM_glimmerT_2875-T1
Valid prediction for CodingQuarry_transcript_3038-T1
Couldn't classify 35799, 35984
Sorry, prediction pasa_asmbl_2657.p2 fails validation.
(ATG)	 GC	33883-34041	GT	AGG
(GTG)	 AG	35799-35984	AT	TCA
-recovered pasa_asmbl_2657.p2, initial, 33883, 34041
Valid prediction for GlimmerHMM_glimmerT_2878-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_2890-T1
Valid prediction for snap_scaffold_1-snap.3995-T1
Valid prediction for GeneMark_model.4532_t
Valid prediction for snap_scaffold_1-snap.3975-T1
Valid prediction for GeneMark_model.4531_t
Valid prediction for snap_scaffold_1-snap.3990-T1
Valid prediction for GeneMark_model.4520_t
Valid prediction for Augustus_model.g2020.t1
Valid prediction for GeneMark_model.4556_t
Valid prediction for GlimmerHMM_glimmerT_2881-T1
Valid prediction for GeneMark_model.4504_t
Valid prediction for GeneMark_model.4551_t
Valid prediction for GlimmerHMM_glimmerT_2902-T1
Valid prediction for GlimmerHMM_glimmerT_2889-T1
Valid prediction for GeneMark_model.4515_t
Valid prediction for GeneMark_model.4549_t
Valid prediction for GeneMark_model.4545_t
Valid prediction for GeneMark_model.4538_t
Valid prediction for Augustus_model.g2019.t1
Valid prediction for GeneMark_model.4527_t
Valid prediction for GeneMark_model.4542_t
Valid prediction for snap_scaffold_1-snap.3966-T1
Valid prediction for Augustus_model.g2021.t1
Valid prediction for GeneMark_model.4535_t
Valid prediction for GeneMark_model.4547_t
Valid prediction for GlimmerHMM_glimmerT_2901-T1
Valid prediction for GlimmerHMM_glimmerT_2874-T1
Valid prediction for snap_scaffold_1-snap.3999-T1
Valid prediction for snap_scaffold_1-snap.3986-T1
Valid prediction for Augustus_model.g2015.t1
Valid prediction for GeneMark_model.4530_t
Valid prediction for Augustus_model.g2018.t1
Valid prediction for GlimmerHMM_glimmerT_2893-T1
Valid prediction for GlimmerHMM_glimmerT_2880-T1
Valid prediction for Augustus_model.g2022.t1
Valid prediction for GlimmerHMM_glimmerT_2899-T1
Valid prediction for GeneMark_model.4508_t
Valid prediction for Augustus_model.g2011.t1
Valid prediction for GeneMark_model.4513_t
Valid prediction for snap_scaffold_1-snap.3961-T1
Valid prediction for GeneMark_model.4534_t
Valid prediction for GeneMark_model.4540_t
Valid prediction for snap_scaffold_1-snap.3962-T1
Valid prediction for GeneMark_model.4529_t
Valid prediction for snap_scaffold_1-snap.3984-T1
Valid prediction for snap_scaffold_1-snap.3988-T1
Valid prediction for snap_scaffold_1-snap.3972-T1
Valid prediction for Augustus_model.g2016.t1
Valid prediction for GeneMark_model.4523_t
Valid prediction for GlimmerHMM_glimmerT_2895-T1
Valid prediction for snap_scaffold_1-snap.3992-T1
Valid prediction for GlimmerHMM_glimmerT_2891-T1
Valid prediction for GeneMark_model.4525_t
Valid prediction for snap_scaffold_1-snap.3978-T1
Valid prediction for GlimmerHMM_glimmerT_2882-T1
Valid prediction for GeneMark_model.4537_t
Valid prediction for snap_scaffold_1-snap.3982-T1
Valid prediction for GlimmerHMM_glimmerT_2888-T1
Valid prediction for snap_scaffold_1-snap.4002-T1
Valid prediction for snap_scaffold_1-snap.3977-T1
Valid prediction for snap_scaffold_1-snap.3964-T1
Valid prediction for snap_scaffold_1-snap.3985-T1
Valid prediction for GlimmerHMM_glimmerT_2900-T1
Valid prediction for Augustus_model.g2017.t1
Valid prediction for snap_scaffold_1-snap.3968-T1
Valid prediction for GeneMark_model.4554_t
Valid prediction for GeneMark_model.4509_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16512, rend_intergenic: 12273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25481, rend_intergenic: 20503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34423, rend_intergenic: 32775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75039, rend_intergenic: 72523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83791, rend_intergenic: 81360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98400, rend_intergenic: 91522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100885, rend_intergenic: 98738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101899, rend_intergenic: 101584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107540, rend_intergenic: 104327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128517, rend_intergenic: 124008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128718, rend_intergenic: 128551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130966, rend_intergenic: 129033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134873, rend_intergenic: 131080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140227, rend_intergenic: 138900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149916, rend_intergenic: 145559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158649, rend_intergenic: 151327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161865, rend_intergenic: 158779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172131, rend_intergenic: 162475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180583
-exon list size: 725


building trellis

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96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 16512, rend_intergenic: 12273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25481, rend_intergenic: 20503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34423, rend_intergenic: 32775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75039, rend_intergenic: 72523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83791, rend_intergenic: 81360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98400, rend_intergenic: 91522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100885, rend_intergenic: 98738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101899, rend_intergenic: 101584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107540, rend_intergenic: 104327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128517, rend_intergenic: 124008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128718, rend_intergenic: 128551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130966, rend_intergenic: 129033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134873, rend_intergenic: 131080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140227, rend_intergenic: 138900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149916, rend_intergenic: 145559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158649, rend_intergenic: 151327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161865, rend_intergenic: 158779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172131, rend_intergenic: 162475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support