-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_5136336-5332475

-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.63559_t
Valid prediction for pasa_asmbl_14130.p1
Valid prediction for GeneMark_model.63550_t
Valid prediction for GlimmerHMM_glimmerT_36914-T1
Valid prediction for snap_scaffold_15-snap.1150-T1
Valid prediction for GeneMark_model.63522_t
Valid prediction for Augustus_model.g24786.t1
Valid prediction for GeneMark_model.63544_t
Valid prediction for snap_scaffold_15-snap.1137-T1
Valid prediction for snap_scaffold_15-snap.1135-T1
Valid prediction for Augustus_model.g24785.t1
Valid prediction for GeneMark_model.63513_t
Valid prediction for snap_scaffold_15-snap.1138-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.63551_t
Valid prediction for GeneMark_model.63547_t
Valid prediction for Augustus_model.g24783.t1
Valid prediction for snap_scaffold_15-snap.1147-T1
Valid prediction for GeneMark_model.63515_t
Valid prediction for CodingQuarry_transcript_17957-T1
Valid prediction for snap_scaffold_15-snap.1152-T1
Valid prediction for snap_scaffold_15-snap.1149-T1
Valid prediction for snap_scaffold_15-snap.1122-T1
Valid prediction for CodingQuarry_transcript_17958-T1
Valid prediction for GlimmerHMM_glimmerT_36929-T1
Valid prediction for snap_scaffold_15-snap.1121-T1
Valid prediction for GeneMark_model.63533_t
Valid prediction for snap_scaffold_15-snap.1130-T1
Couldn't classify 94845, 95414
Sorry, prediction pasa_asmbl_14137.p1 fails validation.
(GGT)	 CT	94845-95414	AC	AAA
Valid prediction for GeneMark_model.63517_t
Valid prediction for GeneMark_model.63519_t
Valid prediction for Augustus_model.g24777.t1
Valid prediction for Augustus_model.g24778.t1
Valid prediction for snap_scaffold_15-snap.1131-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.63538_t
Valid prediction for Augustus_model.g24781.t1
Valid prediction for snap_scaffold_15-snap.1124-T1
Valid prediction for Augustus_model.g24775.t1
Valid prediction for GeneMark_model.63557_t
Valid prediction for GlimmerHMM_glimmerT_36941-T1
Valid prediction for GeneMark_model.63528_t
Valid prediction for GlimmerHMM_glimmerT_36924-T1
Valid prediction for snap_scaffold_15-snap.1133-T1
Valid prediction for GeneMark_model.63514_t
Valid prediction for GlimmerHMM_glimmerT_36919-T1
Valid prediction for GeneMark_model.63549_t
Valid prediction for GlimmerHMM_glimmerT_36917-T1
Valid prediction for Augustus_model.g24773.t1
Valid prediction for GeneMark_model.63530_t
Valid prediction for Augustus_model.g24780.t1
Valid prediction for GlimmerHMM_glimmerT_36930-T1
Valid prediction for GlimmerHMM_glimmerT_36934-T1
Valid prediction for GlimmerHMM_glimmerT_36915-T1
Valid prediction for GlimmerHMM_glimmerT_36932-T1
Valid prediction for GlimmerHMM_glimmerT_36918-T1
Valid prediction for GeneMark_model.63555_t
Valid prediction for GeneMark_model.63542_t
Valid prediction for snap_scaffold_15-snap.1120-T1
Valid prediction for GeneMark_model.63534_t
Valid prediction for snap_scaffold_15-snap.1139-T1
Valid prediction for snap_scaffold_15-snap.1145-T1
Valid prediction for GeneMark_model.63536_t
Valid prediction for GeneMark_model.63560_t
Valid prediction for snap_scaffold_15-snap.1144-T1
Valid prediction for GlimmerHMM_glimmerT_36940-T1
Valid prediction for GeneMark_model.63546_t
Valid prediction for GeneMark_model.63539_t
Valid prediction for HiQ_model.g24774.t1
Valid prediction for GlimmerHMM_glimmerT_36921-T1
Valid prediction for GeneMark_model.63553_t
Valid prediction for Augustus_model.g24776.t1
Valid prediction for GlimmerHMM_glimmerT_36936-T1
Valid prediction for snap_scaffold_15-snap.1126-T1
Valid prediction for snap_scaffold_15-snap.1132-T1
Valid prediction for snap_scaffold_15-snap.1141-T1
Valid prediction for pasa_asmbl_14133.p1
Valid prediction for GeneMark_model.63525_t

-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 GeneMark_model.63562_t
Valid prediction for GeneMark_model.63518_t
Couldn't classify 149499, 149602
Sorry, prediction pasa_asmbl_15201.p1 fails validation.
(ATG)	 TC	147155-147163	GT	AGG
(CCC)	 AG	147764-147999	GT	CTG
(ACA)	 AG	148178-148259	GT	ATG
(GTG)	 AG	148384-148515	GC	AGG
(GAG)	 AG	148654-148759	GT	AGG
(GTG)	 AG	148850-148907	GT	AGG
(CCT)	 AG	149149-149318	GT	AGG
(ACA)	 AG	149499-149602	AC	CCA
-recovered pasa_asmbl_15201.p1, initial, 147155, 147163
-recovered pasa_asmbl_15201.p1, internal, 147764, 147999
-recovered pasa_asmbl_15201.p1, internal, 148178, 148259
-recovered pasa_asmbl_15201.p1, internal, 148384, 148515
-recovered pasa_asmbl_15201.p1, internal, 148654, 148759
-recovered pasa_asmbl_15201.p1, internal, 148850, 148907
-recovered pasa_asmbl_15201.p1, internal, 149149, 149318
Valid prediction for GlimmerHMM_glimmerT_36927-T1
Valid prediction for GlimmerHMM_glimmerT_36923-T1
Valid prediction for snap_scaffold_15-snap.1154-T1
Valid prediction for Augustus_model.g24782.t1
Valid prediction for GeneMark_model.63543_t
Valid prediction for GlimmerHMM_glimmerT_36922-T1
Valid prediction for snap_scaffold_15-snap.1142-T1
Valid prediction for GeneMark_model.63554_t
Valid prediction for snap_scaffold_15-snap.1155-T1
Valid prediction for GlimmerHMM_glimmerT_36939-T1
Valid prediction for GlimmerHMM_glimmerT_36933-T1
Valid prediction for GeneMark_model.63561_t
Couldn't classify 12881, 13143
Sorry, prediction pasa_asmbl_15203.p1 fails validation.
(ATG)	 CA	8076-8083	GT	TTG
(TCC)	 AG	9016-9186	GT	AGG
(GAT)	 AG	9705-9771	GT	AGG
(AAC)	 AG	9873-9954	GT	AGG
(GTG)	 AG	10066-10175	GT	GGG
(GCT)	 AG	10310-10363	GT	AGG
(ATT)	 AG	10520-10631	GT	TGG
(GTT)	 AG	10871-10960	GT	ACG
(GAC)	 AG	11867-12005	GT	TGG
(GGA)	 AG	12153-12225	GT	GGG
(GTG)	 AG	12364-12484	GT	GGG
(GCC)	 AG	12881-13143	AA	TCA
-recovered pasa_asmbl_15203.p1, initial, 8076, 8083
-recovered pasa_asmbl_15203.p1, internal, 9016, 9186
-recovered pasa_asmbl_15203.p1, internal, 9705, 9771
-recovered pasa_asmbl_15203.p1, internal, 9873, 9954
-recovered pasa_asmbl_15203.p1, internal, 10066, 10175
-recovered pasa_asmbl_15203.p1, internal, 10310, 10363
-recovered pasa_asmbl_15203.p1, internal, 10520, 10631
-recovered pasa_asmbl_15203.p1, internal, 10871, 10960
-recovered pasa_asmbl_15203.p1, internal, 11867, 12005
-recovered pasa_asmbl_15203.p1, internal, 12153, 12225
-recovered pasa_asmbl_15203.p1, internal, 12364, 12484
Valid prediction for Augustus_model.g24784.t1
Valid prediction for GeneMark_model.63529_t
Valid prediction for GeneMark_model.63556_t
Valid prediction for GlimmerHMM_glimmerT_36916-T1
Valid prediction for GeneMark_model.63548_t
Valid prediction for Augustus_model.g24779.t1
Valid prediction for snap_scaffold_15-snap.1125-T1
Valid prediction for snap_scaffold_15-snap.1153-T1
Valid prediction for GlimmerHMM_glimmerT_36935-T1
Valid prediction for snap_scaffold_15-snap.1123-T1
Valid prediction for GeneMark_model.63545_t
Valid prediction for snap_scaffold_15-snap.1140-T1
Valid prediction for snap_scaffold_15-snap.1151-T1
Valid prediction for GlimmerHMM_glimmerT_36926-T1
Valid prediction for Augustus_model.g24787.t1
Valid prediction for GeneMark_model.63521_t
Valid prediction for GeneMark_model.63526_t
Valid prediction for GlimmerHMM_glimmerT_36920-T1
Valid prediction for GeneMark_model.63523_t
Valid prediction for GlimmerHMM_glimmerT_36938-T1
Valid prediction for snap_scaffold_15-snap.1136-T1
Valid prediction for GlimmerHMM_glimmerT_36942-T1
Valid prediction for snap_scaffold_15-snap.1146-T1
Valid prediction for snap_scaffold_15-snap.1129-T1
Valid prediction for GeneMark_model.63524_t
Valid prediction for snap_scaffold_15-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_36928-T1
Valid prediction for GlimmerHMM_glimmerT_36931-T1
Valid prediction for GeneMark_model.63558_t
Valid prediction for Augustus_model.g24788.t1
Valid prediction for snap_scaffold_15-snap.1134-T1
Valid prediction for GlimmerHMM_glimmerT_36925-T1
Valid prediction for GeneMark_model.63540_t
Valid prediction for snap_scaffold_15-snap.1143-T1
Valid prediction for pasa_asmbl_15204.p1
Valid prediction for GeneMark_model.63516_t
Valid prediction for GeneMark_model.63527_t
Valid prediction for snap_scaffold_15-snap.1127-T1
Valid prediction for GeneMark_model.63520_t
Valid prediction for CodingQuarry_transcript_17959-T1
Valid prediction for GeneMark_model.63552_t
Valid prediction for GeneMark_model.63535_t
Valid prediction for Augustus_model.g24789.t1
Valid prediction for GeneMark_model.63537_t
Valid prediction for snap_scaffold_15-snap.1148-T1
Valid prediction for GlimmerHMM_glimmerT_36937-T1
Valid prediction for GeneMark_model.63531_t
Valid prediction for GeneMark_model.63541_t
Valid prediction for GeneMark_model.63532_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27567, rend_intergenic: 22892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35217, rend_intergenic: 28565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40143, rend_intergenic: 36482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80054, rend_intergenic: 56779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90715, rend_intergenic: 90098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113591, rend_intergenic: 109442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117914, rend_intergenic: 114228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118732, rend_intergenic: 118107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130114, rend_intergenic: 128148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140308, rend_intergenic: 134144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148888, rend_intergenic: 143005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196140
-exon list size: 688


building trellis

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96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 27567, rend_intergenic: 22892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35217, rend_intergenic: 28565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40143, rend_intergenic: 36482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80054, rend_intergenic: 56779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90715, rend_intergenic: 90098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113591, rend_intergenic: 109442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117914, rend_intergenic: 114228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118732, rend_intergenic: 118107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130114, rend_intergenic: 128148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140308, rend_intergenic: 134144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148888, rend_intergenic: 143005  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