-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_3295573-3444901

-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.66652_t
Valid prediction for GeneMark_model.66644_t
Valid prediction for snap_scaffold_16-snap.642-T1
Valid prediction for GeneMark_model.66610_t
Valid prediction for Augustus_model.g26122.t1
Valid prediction for snap_scaffold_16-snap.619-T1
Valid prediction for snap_scaffold_16-snap.627-T1
Valid prediction for snap_scaffold_16-snap.632-T1
Valid prediction for GlimmerHMM_glimmerT_38919-T1
Valid prediction for GeneMark_model.66648_t
Valid prediction for snap_scaffold_16-snap.640-T1
Valid prediction for snap_scaffold_16-snap.628-T1
Valid prediction for Augustus_model.g26118.t1
Valid prediction for GeneMark_model.66640_t
Valid prediction for snap_scaffold_16-snap.634-T1
Valid prediction for snap_scaffold_16-snap.620-T1
Valid prediction for GeneMark_model.66653_t
Valid prediction for GeneMark_model.66647_t
Valid prediction for GeneMark_model.66606_t
Valid prediction for Augustus_model.g26130.t1
Valid prediction for GlimmerHMM_glimmerT_38898-T1
Valid prediction for snap_scaffold_16-snap.631-T1
Valid prediction for GlimmerHMM_glimmerT_38907-T1
Valid prediction for GlimmerHMM_glimmerT_38902-T1
Valid prediction for GeneMark_model.66624_t
Valid prediction for snap_scaffold_16-snap.647-T1
Valid prediction for snap_scaffold_16-snap.654-T1
Valid prediction for GlimmerHMM_glimmerT_38904-T1
Valid prediction for GeneMark_model.66605_t
Valid prediction for GeneMark_model.66631_t
Valid prediction for GeneMark_model.66633_t
Valid prediction for snap_scaffold_16-snap.652-T1
Valid prediction for GlimmerHMM_glimmerT_38918-T1
Valid prediction for Augustus_model.g26124.t1
Valid prediction for GlimmerHMM_glimmerT_38913-T1
Valid prediction for GeneMark_model.66645_t
Valid prediction for Augustus_model.g26128.t1
Valid prediction for Augustus_model.g26127.t1
Valid prediction for GeneMark_model.66650_t
Valid prediction for GeneMark_model.66622_t
Valid prediction for GeneMark_model.66617_t
Valid prediction for GeneMark_model.66608_t
Valid prediction for GlimmerHMM_glimmerT_38901-T1
Valid prediction for GlimmerHMM_glimmerT_38911-T1
Valid prediction for snap_scaffold_16-snap.648-T1
Valid prediction for GlimmerHMM_glimmerT_38914-T1
Valid prediction for GlimmerHMM_glimmerT_38915-T1
Valid prediction for GlimmerHMM_glimmerT_38899-T1
Valid prediction for GeneMark_model.66615_t
Valid prediction for GlimmerHMM_glimmerT_38923-T1
Valid prediction for GeneMark_model.66658_t
Valid prediction for Augustus_model.g26117.t1
Valid prediction for snap_scaffold_16-snap.622-T1
Valid prediction for GeneMark_model.66613_t
Valid prediction for GeneMark_model.66629_t
Valid prediction for GeneMark_model.66643_t
Valid prediction for GeneMark_model.66619_t
Valid prediction for snap_scaffold_16-snap.646-T1
Valid prediction for Augustus_model.g26119.t1
Valid prediction for GlimmerHMM_glimmerT_38912-T1
Valid prediction for GeneMark_model.66636_t
Valid prediction for GeneMark_model.66638_t
Valid prediction for GeneMark_model.66655_t
Valid prediction for snap_scaffold_16-snap.643-T1
Valid prediction for snap_scaffold_16-snap.618-T1
Valid prediction for GeneMark_model.66612_t
Valid prediction for GeneMark_model.66626_t
Valid prediction for snap_scaffold_16-snap.623-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 Augustus_model.g26125.t1
Valid prediction for GeneMark_model.66639_t
Valid prediction for GeneMark_model.66630_t
Valid prediction for GlimmerHMM_glimmerT_38906-T1
Valid prediction for GeneMark_model.66618_t
Valid prediction for GeneMark_model.66634_t
Valid prediction for GeneMark_model.66637_t
Valid prediction for snap_scaffold_16-snap.630-T1
Valid prediction for GlimmerHMM_glimmerT_38897-T1
Valid prediction for GlimmerHMM_glimmerT_38910-T1
Valid prediction for snap_scaffold_16-snap.637-T1
Valid prediction for GeneMark_model.66659_t
Valid prediction for snap_scaffold_16-snap.629-T1
Valid prediction for GeneMark_model.66651_t
Valid prediction for GlimmerHMM_glimmerT_38916-T1
Valid prediction for GeneMark_model.66656_t
Valid prediction for snap_scaffold_16-snap.655-T1
Valid prediction for GeneMark_model.66621_t
Valid prediction for snap_scaffold_16-snap.644-T1
Valid prediction for GeneMark_model.66642_t
Valid prediction for GeneMark_model.66607_t
Valid prediction for snap_scaffold_16-snap.649-T1
Valid prediction for GlimmerHMM_glimmerT_38920-T1
Valid prediction for snap_scaffold_16-snap.650-T1
Valid prediction for GeneMark_model.66646_t
Valid prediction for snap_scaffold_16-snap.626-T1
Valid prediction for GeneMark_model.66627_t
Valid prediction for Augustus_model.g26120.t1
Valid prediction for snap_scaffold_16-snap.633-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.617-T1
Valid prediction for snap_scaffold_16-snap.625-T1
Valid prediction for GeneMark_model.66635_t
Valid prediction for GeneMark_model.66628_t
Valid prediction for Augustus_model.g26121.t1
Valid prediction for snap_scaffold_16-snap.636-T1
Valid prediction for snap_scaffold_16-snap.653-T1
Valid prediction for GlimmerHMM_glimmerT_38905-T1
Couldn't classify 141116, 141210
Sorry, prediction pasa_asmbl_16152.p1 fails validation.
(GAA)	 TG	141116-141210	GT	CGG
(CTC)	 AG	141353-141444	GT	AGG
(CCC)	 AG	142302-142481	GT	AGG
(GTT)	 AG	142804-142902	GT	AGG
(GTC)	 AG	143391-143483	GT	AGG
(GAT)	 AG	143624-143780	GT	AGG
(GTT)	 AG	143900-144015	GT	CGG
(GCC)	 AG	144236-144312	GG	GAG
-recovered pasa_asmbl_16152.p1, terminal, 144236, 144312
-recovered pasa_asmbl_16152.p1, internal, 141353, 141444
-recovered pasa_asmbl_16152.p1, internal, 142302, 142481
-recovered pasa_asmbl_16152.p1, internal, 142804, 142902
-recovered pasa_asmbl_16152.p1, internal, 143391, 143483
-recovered pasa_asmbl_16152.p1, internal, 143624, 143780
-recovered pasa_asmbl_16152.p1, internal, 143900, 144015
Valid prediction for snap_scaffold_16-snap.641-T1
Valid prediction for GlimmerHMM_glimmerT_38921-T1
Valid prediction for snap_scaffold_16-snap.624-T1
Valid prediction for GeneMark_model.66623_t
Valid prediction for GeneMark_model.66641_t
Valid prediction for GlimmerHMM_glimmerT_38903-T1
Valid prediction for GeneMark_model.66649_t
Valid prediction for GeneMark_model.66625_t
Valid prediction for GlimmerHMM_glimmerT_38900-T1
Valid prediction for snap_scaffold_16-snap.645-T1
Valid prediction for snap_scaffold_16-snap.651-T1
Valid prediction for GlimmerHMM_glimmerT_38908-T1
Valid prediction for Augustus_model.g26123.t1
Valid prediction for GeneMark_model.66614_t
Valid prediction for GlimmerHMM_glimmerT_38922-T1
Valid prediction for GeneMark_model.66620_t
Valid prediction for Augustus_model.g26132.t1
Valid prediction for Augustus_model.g26126.t1
Valid prediction for snap_scaffold_16-snap.621-T1
Valid prediction for snap_scaffold_16-snap.638-T1
Valid prediction for Augustus_model.g26131.t1
Valid prediction for GeneMark_model.66611_t
Valid prediction for GeneMark_model.66616_t
Valid prediction for Augustus_model.g26116.t1
Valid prediction for GeneMark_model.66654_t
Valid prediction for snap_scaffold_16-snap.635-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g26129.t1
Valid prediction for GeneMark_model.66632_t
Valid prediction for GlimmerHMM_glimmerT_38917-T1
Valid prediction for snap_scaffold_16-snap.639-T1
Valid prediction for GlimmerHMM_glimmerT_38909-T1
Valid prediction for GeneMark_model.66609_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9618, rend_intergenic: 7780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19902, rend_intergenic: 17132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29178, rend_intergenic: 23727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40119, rend_intergenic: 32570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52980, rend_intergenic: 41621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56967, rend_intergenic: 53571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62305, rend_intergenic: 58814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64013, rend_intergenic: 62867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72930, rend_intergenic: 64308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95301, rend_intergenic: 93752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103498, rend_intergenic: 100498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116533, rend_intergenic: 106117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136167, rend_intergenic: 134238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141110, rend_intergenic: 137316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142926, rend_intergenic: 141571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149075, rend_intergenic: 144942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149329
-exon list size: 693


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 9618, rend_intergenic: 7780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19902, rend_intergenic: 17132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29178, rend_intergenic: 23727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40119, rend_intergenic: 32570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52980, rend_intergenic: 41621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56967, rend_intergenic: 53571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62305, rend_intergenic: 58814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64013, rend_intergenic: 62867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72930, rend_intergenic: 64308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95301, rend_intergenic: 93752  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103498, rend_intergenic: 100498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116533, rend_intergenic: 106117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136167, rend_intergenic: 134238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141110, rend_intergenic: 137316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142926, rend_intergenic: 141571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149075, rend_intergenic: 144942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support