-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_12072457-12243861

-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_14-snap.2516-T1
Valid prediction for GeneMark_model.60963_t
Valid prediction for CodingQuarry_transcript_15821-T1
Valid prediction for GlimmerHMM_glimmerT_35565-T1
Valid prediction for GeneMark_model.60975_t
Valid prediction for GeneMark_model.60962_t
Valid prediction for Augustus_model.g23932.t1
Valid prediction for GlimmerHMM_glimmerT_35554-T1
Valid prediction for Augustus_model.g23939.t1
Couldn't classify 90370, 90614
Sorry, prediction pasa_asmbl_12402.p1 fails validation.
(CGT)	 TG	90370-90614	GT	TGG
(GCT)	 AG	90736-90955	AG	GAA
-recovered pasa_asmbl_12402.p1, terminal, 90736, 90955
Valid prediction for GeneMark_model.60984_t
Valid prediction for GeneMark_model.60960_t
Valid prediction for snap_scaffold_14-snap.2501-T1
Valid prediction for GeneMark_model.60979_t
Valid prediction for GlimmerHMM_glimmerT_35561-T1
Valid prediction for GeneMark_model.60987_t
Valid prediction for snap_scaffold_14-snap.2511-T1
Valid prediction for GeneMark_model.60973_t
Valid prediction for GeneMark_model.60969_t
Valid prediction for snap_scaffold_14-snap.2485-T1
Valid prediction for GlimmerHMM_glimmerT_35556-T1
Valid prediction for GlimmerHMM_glimmerT_35553-T1
Valid prediction for GeneMark_model.60980_t
Valid prediction for GeneMark_model.60965_t
Valid prediction for GeneMark_model.60961_t
Valid prediction for GlimmerHMM_glimmerT_35552-T1
Valid prediction for GeneMark_model.60976_t
Valid prediction for snap_scaffold_14-snap.2518-T1
Valid prediction for snap_scaffold_14-snap.2490-T1
Valid prediction for snap_scaffold_14-snap.2492-T1
Valid prediction for snap_scaffold_14-snap.2499-T1
Valid prediction for GeneMark_model.60994_t
Valid prediction for snap_scaffold_14-snap.2515-T1
Valid prediction for GeneMark_model.60989_t
Valid prediction for snap_scaffold_14-snap.2522-T1
Valid prediction for snap_scaffold_14-snap.2510-T1
Valid prediction for snap_scaffold_14-snap.2502-T1
Valid prediction for GlimmerHMM_glimmerT_35549-T1
Valid prediction for snap_scaffold_14-snap.2498-T1
Valid prediction for GeneMark_model.60986_t
Valid prediction for snap_scaffold_14-snap.2497-T1
Valid prediction for GlimmerHMM_glimmerT_35564-T1
Valid prediction for pasa_asmbl_12397.p1
Valid prediction for snap_scaffold_14-snap.2495-T1
Valid prediction for GeneMark_model.60972_t
Valid prediction for snap_scaffold_14-snap.2500-T1
Valid prediction for GeneMark_model.60992_t
Valid prediction for snap_scaffold_14-snap.2491-T1
Valid prediction for pasa_asmbl_12401.p1
Valid prediction for GeneMark_model.60978_t
Valid prediction for snap_scaffold_14-snap.2507-T1
Valid prediction for GlimmerHMM_glimmerT_35558-T1
Valid prediction for Augustus_model.g23933.t1
Valid prediction for HiQ_model.g23934.t1
Valid prediction for GlimmerHMM_glimmerT_35557-T1
Valid prediction for GlimmerHMM_glimmerT_35555-T1
Valid prediction for snap_scaffold_14-snap.2486-T1
Valid prediction for Augustus_model.g23937.t1
Valid prediction for GlimmerHMM_glimmerT_35548-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_35563-T1
Valid prediction for Augustus_model.g23941.t1
Valid prediction for Augustus_model.g23943.t1
Valid prediction for GlimmerHMM_glimmerT_35568-T1
Valid prediction for GeneMark_model.60977_t
Valid prediction for Augustus_model.g23935.t1
Valid prediction for Augustus_model.g23944.t1
Valid prediction for snap_scaffold_14-snap.2508-T1
Valid prediction for snap_scaffold_14-snap.2503-T1
Valid prediction for Augustus_model.g23938.t1
Valid prediction for GlimmerHMM_glimmerT_35547-T1
Valid prediction for snap_scaffold_14-snap.2488-T1
Valid prediction for Augustus_model.g23931.t1
Valid prediction for snap_scaffold_14-snap.2521-T1
Valid prediction for GeneMark_model.60974_t
Valid prediction for snap_scaffold_14-snap.2489-T1
Valid prediction for GlimmerHMM_glimmerT_35566-T1
Valid prediction for Augustus_model.g23936.t1
Valid prediction for snap_scaffold_14-snap.2514-T1
Valid prediction for Augustus_model.g23940.t1
Valid prediction for GlimmerHMM_glimmerT_35562-T1
Valid prediction for GlimmerHMM_glimmerT_35567-T1
Valid prediction for snap_scaffold_14-snap.2504-T1
Valid prediction for GeneMark_model.60993_t
Valid prediction for snap_scaffold_14-snap.2496-T1
Valid prediction for GlimmerHMM_glimmerT_35569-T1
Valid prediction for GeneMark_model.60964_t
Valid prediction for GeneMark_model.60990_t
Couldn't classify 72695, 72813
Couldn't classify 73190, 73442
Sorry, prediction pasa_asmbl_13539.p1 fails validation.
(CAC)	 TC	72695-72813	GT	AGG
(TGC)	 AG	73190-73442	AG	CCA
Valid prediction for GeneMark_model.60966_t
Valid prediction for GeneMark_model.60985_t
Valid prediction for GeneMark_model.60995_t
Valid prediction for GeneMark_model.60970_t
Valid prediction for snap_scaffold_14-snap.2517-T1
Valid prediction for GeneMark_model.60983_t
Valid prediction for GeneMark_model.60967_t
Valid prediction for snap_scaffold_14-snap.2493-T1
Valid prediction for GeneMark_model.60968_t
Couldn't classify 18183, 18668
Sorry, prediction pasa_asmbl_13544.p2 fails validation.
(ATG)	 CT	18183-18668	GG	CAG
Valid prediction for GlimmerHMM_glimmerT_35560-T1
Valid prediction for GeneMark_model.60971_t
Valid prediction for Augustus_model.g23930.t1
Valid prediction for GeneMark_model.60981_t
Valid prediction for snap_scaffold_14-snap.2519-T1
Valid prediction for GlimmerHMM_glimmerT_35550-T1
Couldn't classify 73793, 74042
Sorry, prediction pasa_asmbl_13538.p2 fails validation.
(GGA)	 GG	73793-74042	GT	AGG
(ATG)	 AG	76303-76371	GT	AGG
(GCT)	 AG	77068-77115	GT	AGG
(GCG)	 AG	77734-77906	GT	AGG
(GTG)	 AG	79056-79157	GT	AGG
(GTG)	 AG	79292-79519	TG	AAT
-recovered pasa_asmbl_13538.p2, initial, 76303, 76371
-recovered pasa_asmbl_13538.p2, terminal, 79292, 79519
-recovered pasa_asmbl_13538.p2, internal, 76303, 76371
-recovered pasa_asmbl_13538.p2, internal, 77068, 77115
-recovered pasa_asmbl_13538.p2, internal, 77734, 77906
-recovered pasa_asmbl_13538.p2, internal, 79056, 79157
Valid prediction for snap_scaffold_14-snap.2505-T1
Valid prediction for snap_scaffold_14-snap.2487-T1
Valid prediction for GeneMark_model.60982_t
Valid prediction for GlimmerHMM_glimmerT_35571-T1
Valid prediction for GeneMark_model.60991_t
Valid prediction for snap_scaffold_14-snap.2512-T1
Valid prediction for snap_scaffold_14-snap.2523-T1
Valid prediction for snap_scaffold_14-snap.2513-T1
Valid prediction for GlimmerHMM_glimmerT_35570-T1
Valid prediction for snap_scaffold_14-snap.2484-T1
Valid prediction for GlimmerHMM_glimmerT_35559-T1
Valid prediction for Augustus_model.g23942.t1
Valid prediction for snap_scaffold_14-snap.2494-T1
Valid prediction for GlimmerHMM_glimmerT_35551-T1
Valid prediction for snap_scaffold_14-snap.2506-T1
Valid prediction for snap_scaffold_14-snap.2483-T1
Valid prediction for GeneMark_model.60988_t
Valid prediction for snap_scaffold_14-snap.2520-T1
Valid prediction for snap_scaffold_14-snap.2509-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18002, rend_intergenic: 11410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31484, rend_intergenic: 26824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137834, rend_intergenic: 135074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143886, rend_intergenic: 142616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149016, rend_intergenic: 147018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156482, rend_intergenic: 152618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166366, rend_intergenic: 165313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171405
-exon list size: 512


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 18002, rend_intergenic: 11410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31484, rend_intergenic: 26824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137834, rend_intergenic: 135074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143886, rend_intergenic: 142616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149016, rend_intergenic: 147018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156482, rend_intergenic: 152618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166366, rend_intergenic: 165313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support