-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_18558778-18815402

-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 GlimmerHMM_glimmerT_11163-T1
Valid prediction for snap_scaffold_4-snap.3820-T1
Valid prediction for snap_scaffold_4-snap.3841-T1
Valid prediction for Augustus_model.g7319.t1
Valid prediction for snap_scaffold_4-snap.3834-T1
Valid prediction for snap_scaffold_4-snap.3848-T1
Valid prediction for Augustus_model.g7318.t1
Valid prediction for snap_scaffold_4-snap.3823-T1
Couldn't classify 213929, 214018
Couldn't classify 219935, 219982
Sorry, prediction pasa_asmbl_42108.p1 fails validation.
(CGA)	 CT	213929-214018	GT	GGG
(TAC)	 AG	214352-214422	GT	AGG
(AGA)	 AG	215144-215207	GT	AGG
(CCA)	 AG	217474-217593	GT	AGG
(ATC)	 AG	219338-219391	GT	CTG
(GAC)	 AG	219935-219982	AT	AGA
-recovered pasa_asmbl_42108.p1, internal, 214352, 214422
-recovered pasa_asmbl_42108.p1, internal, 215144, 215207
-recovered pasa_asmbl_42108.p1, internal, 217474, 217593
-recovered pasa_asmbl_42108.p1, internal, 219338, 219391
Valid prediction for Augustus_model.g7323.t1
Valid prediction for Augustus_model.g7325.t1
Valid prediction for GlimmerHMM_glimmerT_11162-T1
Couldn't classify 240222, 240904
Sorry, prediction pasa_asmbl_42110.p1 fails validation.
(ATG)	 CG	234223-234276	GT	AGG
(GAG)	 AG	234410-234482	GT	AGG
(TAC)	 AG	236818-237051	GT	AGG
(GTG)	 AG	237910-237933	GT	GGG
(AGG)	 AG	238854-238906	GT	AGG
(GAA)	 AG	239015-239122	GT	TGG
(GCA)	 AG	239312-239546	GT	AGG
(CCA)	 AG	240222-240904	AA	AGA
-recovered pasa_asmbl_42110.p1, initial, 234223, 234276
-recovered pasa_asmbl_42110.p1, internal, 234410, 234482
-recovered pasa_asmbl_42110.p1, internal, 236818, 237051
-recovered pasa_asmbl_42110.p1, internal, 237910, 237933
-recovered pasa_asmbl_42110.p1, internal, 238854, 238906
-recovered pasa_asmbl_42110.p1, internal, 239015, 239122
-recovered pasa_asmbl_42110.p1, internal, 239312, 239546
Valid prediction for Augustus_model.g7326.t1
Valid prediction for Augustus_model.g7321.t1
Valid prediction for snap_scaffold_4-snap.3858-T1
Valid prediction for GlimmerHMM_glimmerT_11147-T1
Valid prediction for snap_scaffold_4-snap.3830-T1
Valid prediction for HiQ_model.g7322.t1
Couldn't classify 211957, 212280
Sorry, prediction pasa_asmbl_42106.p1 fails validation.
(CTG)	 GT	211957-212280	CA	GAC
Valid prediction for snap_scaffold_4-snap.3809-T1
Valid prediction for GlimmerHMM_glimmerT_11140-T1
Valid prediction for GlimmerHMM_glimmerT_11154-T1
Valid prediction for snap_scaffold_4-snap.3815-T1
Valid prediction for snap_scaffold_4-snap.3826-T1
Valid prediction for GlimmerHMM_glimmerT_11152-T1
Valid prediction for GlimmerHMM_glimmerT_11157-T1
Valid prediction for snap_scaffold_4-snap.3813-T1
Valid prediction for HiQ_model.g7324.t1
Valid prediction for GlimmerHMM_glimmerT_11164-T1
Valid prediction for GlimmerHMM_glimmerT_11149-T1
Valid prediction for GlimmerHMM_glimmerT_11143-T1
Valid prediction for snap_scaffold_4-snap.3851-T1
Valid prediction for snap_scaffold_4-snap.3812-T1
Valid prediction for snap_scaffold_4-snap.3817-T1
Valid prediction for snap_scaffold_4-snap.3810-T1
Valid prediction for snap_scaffold_4-snap.3831-T1
Valid prediction for snap_scaffold_4-snap.3847-T1
Valid prediction for snap_scaffold_4-snap.3843-T1
Valid prediction for GlimmerHMM_glimmerT_11159-T1
Valid prediction for snap_scaffold_4-snap.3832-T1
Valid prediction for snap_scaffold_4-snap.3827-T1
Valid prediction for snap_scaffold_4-snap.3814-T1
Valid prediction for GlimmerHMM_glimmerT_11148-T1
Valid prediction for snap_scaffold_4-snap.3838-T1
Valid prediction for GlimmerHMM_glimmerT_11141-T1
Valid prediction for snap_scaffold_4-snap.3825-T1
Valid prediction for snap_scaffold_4-snap.3845-T1
Valid prediction for snap_scaffold_4-snap.3849-T1
Valid prediction for GlimmerHMM_glimmerT_11142-T1
Valid prediction for GlimmerHMM_glimmerT_11160-T1
Valid prediction for GlimmerHMM_glimmerT_11161-T1
Valid prediction for snap_scaffold_4-snap.3855-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 snap_scaffold_4-snap.3836-T1
Valid prediction for HiQ_model.g7320.t1
Valid prediction for GlimmerHMM_glimmerT_11156-T1
Valid prediction for snap_scaffold_4-snap.3853-T1
Valid prediction for snap_scaffold_4-snap.3846-T1
Valid prediction for snap_scaffold_4-snap.3857-T1
Valid prediction for GlimmerHMM_glimmerT_11144-T1
Valid prediction for snap_scaffold_4-snap.3816-T1
Valid prediction for snap_scaffold_4-snap.3819-T1
Valid prediction for snap_scaffold_4-snap.3835-T1
Valid prediction for snap_scaffold_4-snap.3808-T1
Valid prediction for snap_scaffold_4-snap.3854-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3828-T1
Valid prediction for GlimmerHMM_glimmerT_11146-T1
Valid prediction for snap_scaffold_4-snap.3837-T1
Valid prediction for snap_scaffold_4-snap.3821-T1
Valid prediction for snap_scaffold_4-snap.3818-T1
Couldn't classify 248327, 248522
Couldn't classify 250244, 250353
Sorry, prediction pasa_asmbl_43648.p1 fails validation.
(GAG)	 CC	248327-248522	GT	CTG
(CTA)	 AG	248907-248972	GT	TGG
(GCT)	 AG	249854-249976	GT	AGG
(ATG)	 AG	250244-250353	CT	TGC
-recovered pasa_asmbl_43648.p1, internal, 248907, 248972
-recovered pasa_asmbl_43648.p1, internal, 249854, 249976
Valid prediction for GlimmerHMM_glimmerT_11153-T1
Valid prediction for pasa_asmbl_43386.p1
Valid prediction for snap_scaffold_4-snap.3811-T1
Valid prediction for snap_scaffold_4-snap.3856-T1
Valid prediction for GlimmerHMM_glimmerT_11150-T1
Valid prediction for CodingQuarry_transcript_49377-T1
Valid prediction for snap_scaffold_4-snap.3842-T1
Valid prediction for GlimmerHMM_glimmerT_11151-T1
Valid prediction for snap_scaffold_4-snap.3840-T1
Valid prediction for Augustus_model.g7316.t1
Valid prediction for GlimmerHMM_glimmerT_11158-T1
Valid prediction for GlimmerHMM_glimmerT_11145-T1
Valid prediction for snap_scaffold_4-snap.3833-T1
Valid prediction for Augustus_model.g7317.t1
Valid prediction for snap_scaffold_4-snap.3829-T1
Valid prediction for snap_scaffold_4-snap.3844-T1
Valid prediction for snap_scaffold_4-snap.3822-T1
Valid prediction for snap_scaffold_4-snap.3852-T1
Valid prediction for GlimmerHMM_glimmerT_11139-T1
Valid prediction for snap_scaffold_4-snap.3850-T1
Valid prediction for snap_scaffold_4-snap.3839-T1
Valid prediction for snap_scaffold_4-snap.3824-T1
Valid prediction for GlimmerHMM_glimmerT_11155-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 62912, rend_intergenic: 62909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10696, rend_intergenic: 4767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19817, rend_intergenic: 11281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34512, rend_intergenic: 20346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57458, rend_intergenic: 56265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61059, rend_intergenic: 59108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62840, rend_intergenic: 62080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80079, rend_intergenic: 62909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85394, rend_intergenic: 80829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101566, rend_intergenic: 85557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116208, rend_intergenic: 101802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138085, rend_intergenic: 116710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142252, rend_intergenic: 138511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151410, rend_intergenic: 148546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158279, rend_intergenic: 151500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171681, rend_intergenic: 158302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174559, rend_intergenic: 171985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187166, rend_intergenic: 174589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194057, rend_intergenic: 193922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199544, rend_intergenic: 194131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203798, rend_intergenic: 201469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204159, rend_intergenic: 203964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207643, rend_intergenic: 204271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219953, rend_intergenic: 211714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230434, rend_intergenic: 222319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242796, rend_intergenic: 234097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255531, rend_intergenic: 244070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256625
-exon list size: 398


building trellis

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48.5    
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99.0    
99.2    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 62912, rend_intergenic: 62909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10696, rend_intergenic: 4767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19817, rend_intergenic: 11281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34512, rend_intergenic: 20346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57458, rend_intergenic: 56265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61059, rend_intergenic: 59108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62840, rend_intergenic: 62080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80079, rend_intergenic: 62909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85394, rend_intergenic: 80829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101566, rend_intergenic: 85557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116208, rend_intergenic: 101802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138085, rend_intergenic: 116710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142252, rend_intergenic: 138511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151410, rend_intergenic: 148546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158279, rend_intergenic: 151500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171681, rend_intergenic: 158302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174559, rend_intergenic: 171985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187166, rend_intergenic: 174589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194057, rend_intergenic: 193922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199544, rend_intergenic: 194131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203798, rend_intergenic: 201469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204159, rend_intergenic: 203964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207643, rend_intergenic: 204271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219953, rend_intergenic: 211714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230434, rend_intergenic: 222319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 242796, rend_intergenic: 234097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 255531, rend_intergenic: 244070  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