-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_4474333-4773587

-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_9-snap.959-T1
Valid prediction for snap_scaffold_9-snap.990-T1
Valid prediction for GlimmerHMM_glimmerT_22020-T1
Valid prediction for Augustus_model.g14653.t1
Valid prediction for Augustus_model.g14635.t1
Valid prediction for Augustus_model.g14644.t1
Valid prediction for snap_scaffold_9-snap.980-T1
Valid prediction for snap_scaffold_9-snap.977-T1
Valid prediction for Augustus_model.g14646.t1
Valid prediction for snap_scaffold_9-snap.964-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.960-T1
Valid prediction for Augustus_model.g14639.t1
Valid prediction for GlimmerHMM_glimmerT_22034-T1
Valid prediction for GlimmerHMM_glimmerT_22044-T1
Valid prediction for GlimmerHMM_glimmerT_22033-T1
Valid prediction for snap_scaffold_9-snap.968-T1
Valid prediction for snap_scaffold_9-snap.970-T1
Valid prediction for GlimmerHMM_glimmerT_22022-T1
Valid prediction for GlimmerHMM_glimmerT_22041-T1
Valid prediction for GlimmerHMM_glimmerT_22053-T1
Couldn't classify 199001, 199176
Couldn't classify 200486, 201134
Sorry, prediction pasa_asmbl_53953.p1 fails validation.
(CCC)	 CC	199001-199176	GT	TGG
(GTG)	 AG	200486-201134	GA	ACG
Valid prediction for snap_scaffold_9-snap.987-T1
Valid prediction for snap_scaffold_9-snap.967-T1
Valid prediction for snap_scaffold_9-snap.981-T1
Valid prediction for snap_scaffold_9-snap.973-T1
Valid prediction for snap_scaffold_9-snap.956-T1
Valid prediction for snap_scaffold_9-snap.983-T1
Valid prediction for snap_scaffold_9-snap.988-T1
Valid prediction for snap_scaffold_9-snap.958-T1
Valid prediction for GlimmerHMM_glimmerT_22031-T1
Valid prediction for GlimmerHMM_glimmerT_22026-T1
Valid prediction for GlimmerHMM_glimmerT_22025-T1
Valid prediction for snap_scaffold_9-snap.985-T1
Valid prediction for GlimmerHMM_glimmerT_22023-T1
Valid prediction for GlimmerHMM_glimmerT_22042-T1
Valid prediction for Augustus_model.g14636.t1
Valid prediction for snap_scaffold_9-snap.992-T1
Valid prediction for snap_scaffold_9-snap.962-T1
Valid prediction for pasa_asmbl_53952.p1
Valid prediction for snap_scaffold_9-snap.974-T1
Valid prediction for snap_scaffold_9-snap.965-T1
Valid prediction for GlimmerHMM_glimmerT_22032-T1
Valid prediction for snap_scaffold_9-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_22038-T1
Valid prediction for CodingQuarry_transcript_62154-T1
Valid prediction for snap_scaffold_9-snap.952-T1
Valid prediction for snap_scaffold_9-snap.954-T1
Valid prediction for GlimmerHMM_glimmerT_22018-T1
Valid prediction for GlimmerHMM_glimmerT_22036-T1
Valid prediction for GlimmerHMM_glimmerT_22043-T1
Couldn't classify 144392, 144542
Sorry, prediction pasa_asmbl_53950.p1 fails validation.
(CCG)	 AT	144392-144542	GT	AGG
(CTG)	 AG	145119-145400	GT	CTG
(GCC)	 AG	145583-145673	GT	AGG
(ATG)	 AG	145943-145988	AC	AGA
-recovered pasa_asmbl_53950.p1, terminal, 145943, 145988
-recovered pasa_asmbl_53950.p1, internal, 145119, 145400
-recovered pasa_asmbl_53950.p1, internal, 145583, 145673
Valid prediction for Augustus_model.g14637.t1
Valid prediction for snap_scaffold_9-snap.978-T1
Valid prediction for snap_scaffold_9-snap.961-T1
Valid prediction for snap_scaffold_9-snap.984-T1
Valid prediction for snap_scaffold_9-snap.950-T1
Valid prediction for GlimmerHMM_glimmerT_22050-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.g14650.t1
Valid prediction for snap_scaffold_9-snap.976-T1
Valid prediction for snap_scaffold_9-snap.991-T1
Valid prediction for CodingQuarry_transcript_62155-T1
Valid prediction for GlimmerHMM_glimmerT_22040-T1
Valid prediction for snap_scaffold_9-snap.955-T1
Valid prediction for Augustus_model.g14642.t1
Valid prediction for snap_scaffold_9-snap.982-T1
Valid prediction for GlimmerHMM_glimmerT_22048-T1
Valid prediction for GlimmerHMM_glimmerT_22024-T1
Valid prediction for snap_scaffold_9-snap.972-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_22047-T1
Valid prediction for Augustus_model.g14647.t1
Valid prediction for Augustus_model.g14638.t1
Valid prediction for snap_scaffold_9-snap.963-T1
Valid prediction for snap_scaffold_9-snap.993-T1
Valid prediction for snap_scaffold_9-snap.994-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.953-T1
Valid prediction for snap_scaffold_9-snap.969-T1
Valid prediction for GlimmerHMM_glimmerT_22021-T1
Valid prediction for Augustus_model.g14640.t1
Couldn't classify 242242, 242355
Couldn't classify 244014, 244223
Sorry, prediction pasa_asmbl_54968.p1 fails validation.
(ATC)	 TG	242242-242355	GT	AGG
(GGC)	 AG	244014-244223	GT	AGG
-recovered pasa_asmbl_54968.p1, internal, 244014, 244223
Valid prediction for snap_scaffold_9-snap.966-T1
Valid prediction for Augustus_model.g14652.t1
Valid prediction for snap_scaffold_9-snap.951-T1
Valid prediction for pasa_asmbl_55727.p1
Valid prediction for GlimmerHMM_glimmerT_22054-T1
Valid prediction for snap_scaffold_9-snap.975-T1
Valid prediction for Augustus_model.g14641.t1
Valid prediction for GlimmerHMM_glimmerT_22039-T1
Valid prediction for Augustus_model.g14648.t1
Valid prediction for GlimmerHMM_glimmerT_22030-T1
Valid prediction for GlimmerHMM_glimmerT_22052-T1
Valid prediction for GlimmerHMM_glimmerT_22028-T1
Valid prediction for GlimmerHMM_glimmerT_22045-T1
Valid prediction for Augustus_model.g14651.t1
Valid prediction for GlimmerHMM_glimmerT_22029-T1
Valid prediction for snap_scaffold_9-snap.989-T1
Valid prediction for GlimmerHMM_glimmerT_22019-T1
Valid prediction for GlimmerHMM_glimmerT_22037-T1
Valid prediction for GlimmerHMM_glimmerT_22049-T1
Valid prediction for snap_scaffold_9-snap.971-T1
Valid prediction for snap_scaffold_9-snap.979-T1
Valid prediction for Augustus_model.g14643.t1
Valid prediction for GlimmerHMM_glimmerT_22051-T1
Valid prediction for Augustus_model.g14645.t1
Valid prediction for HiQ_model.g14649.t1
Valid prediction for Augustus_model.g14654.t1
Valid prediction for GlimmerHMM_glimmerT_22035-T1
Valid prediction for snap_scaffold_9-snap.986-T1
Valid prediction for GlimmerHMM_glimmerT_22046-T1
Valid prediction for GlimmerHMM_glimmerT_22027-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10823, rend_intergenic: 1608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33544, rend_intergenic: 20999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41273, rend_intergenic: 37110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101979, rend_intergenic: 41317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110995, rend_intergenic: 102229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140134, rend_intergenic: 111039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153740, rend_intergenic: 147567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161301, rend_intergenic: 153865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187229, rend_intergenic: 162265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195973, rend_intergenic: 188924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201340, rend_intergenic: 196307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216789, rend_intergenic: 210472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230941, rend_intergenic: 217794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238032, rend_intergenic: 232326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250224, rend_intergenic: 242798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256918, rend_intergenic: 250553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262023, rend_intergenic: 257126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 271673, rend_intergenic: 262029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272427, rend_intergenic: 272329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 275771, rend_intergenic: 274327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 286870, rend_intergenic: 276333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 299255
-exon list size: 550


building trellis

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99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 10823, rend_intergenic: 1608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33544, rend_intergenic: 20999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41273, rend_intergenic: 37110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101979, rend_intergenic: 41317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110995, rend_intergenic: 102229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140134, rend_intergenic: 111039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153740, rend_intergenic: 147567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161301, rend_intergenic: 153865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187229, rend_intergenic: 162265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195973, rend_intergenic: 188924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201340, rend_intergenic: 196307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216789, rend_intergenic: 210472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230941, rend_intergenic: 217794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238032, rend_intergenic: 232326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250224, rend_intergenic: 242798  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256918, rend_intergenic: 250553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262023, rend_intergenic: 257126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 271673, rend_intergenic: 262029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272427, rend_intergenic: 272329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 275771, rend_intergenic: 274327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 286870, rend_intergenic: 276333  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