-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_5191787-5343462

-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 pasa_asmbl_24413.p1
Valid prediction for Augustus_model.g2529.t1
Valid prediction for HiQ_model.g2533.t1
Couldn't classify 51165, 51584
Sorry, prediction pasa_asmbl_24409.p1 fails validation.
(GAG)	 TG	51165-51584	GA	ACG
Valid prediction for GlimmerHMM_glimmerT_3785-T1
Valid prediction for snap_scaffold_2-snap.1200-T1
Valid prediction for snap_scaffold_2-snap.1193-T1
Valid prediction for snap_scaffold_2-snap.1177-T1
Valid prediction for snap_scaffold_2-snap.1191-T1
Valid prediction for snap_scaffold_2-snap.1179-T1
Valid prediction for snap_scaffold_2-snap.1205-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3793-T1
Couldn't classify 6826, 6845
Couldn't classify 7714, 7837
Sorry, prediction pasa_asmbl_24395.p1 fails validation.
(CTA)	 CA	6826-6845	GT	AGG
(GGA)	 AG	7011-7137	GT	AGG
(GAC)	 AG	7500-7606	GT	GAG
(GGA)	 AG	7714-7837	AC	AGA
-recovered pasa_asmbl_24395.p1, internal, 7011, 7137
-recovered pasa_asmbl_24395.p1, internal, 7500, 7606
Valid prediction for GlimmerHMM_glimmerT_3790-T1
Valid prediction for Augustus_model.g2538.t1
Valid prediction for snap_scaffold_2-snap.1183-T1
Valid prediction for GlimmerHMM_glimmerT_3792-T1
Valid prediction for GlimmerHMM_glimmerT_3791-T1
Valid prediction for snap_scaffold_2-snap.1202-T1
Valid prediction for GlimmerHMM_glimmerT_3783-T1
Couldn't classify 20447, 20499
Couldn't classify 21718, 21734
Sorry, prediction pasa_asmbl_24404.p1 fails validation.
(CGC)	 GG	20447-20499	GT	AGG
(TGA)	 AG	20780-20923	GT	GGG
(GGA)	 AG	21045-21081	GT	AGG
(GTG)	 AG	21251-21413	GT	GCG
(AGC)	 AG	21718-21734	GT	GTG
-recovered pasa_asmbl_24404.p1, internal, 20780, 20923
-recovered pasa_asmbl_24404.p1, internal, 21045, 21081
-recovered pasa_asmbl_24404.p1, internal, 21251, 21413
-recovered pasa_asmbl_24404.p1, internal, 21718, 21734
Valid prediction for Augustus_model.g2536.t1
Couldn't classify 18428, 18449
Couldn't classify 19697, 19843
Sorry, prediction pasa_asmbl_24403.p1 fails validation.
(TCC)	 AC	18428-18449	GT	TGG
(GTT)	 AG	18722-18915	GT	CAG
(GTG)	 AG	19095-19174	GT	AGG
(GGT)	 AG	19436-19583	GT	ATG
(TCT)	 AG	19697-19843	GA	CCG
-recovered pasa_asmbl_24403.p1, internal, 18722, 18915
-recovered pasa_asmbl_24403.p1, internal, 19095, 19174
-recovered pasa_asmbl_24403.p1, internal, 19436, 19583
Valid prediction for snap_scaffold_2-snap.1197-T1
Valid prediction for GlimmerHMM_glimmerT_3796-T1
Valid prediction for HiQ_model.g2528.t1
Valid prediction for snap_scaffold_2-snap.1204-T1
Valid prediction for snap_scaffold_2-snap.1201-T1
Valid prediction for GlimmerHMM_glimmerT_3789-T1
Valid prediction for snap_scaffold_2-snap.1182-T1
Valid prediction for snap_scaffold_2-snap.1176-T1
Valid prediction for snap_scaffold_2-snap.1188-T1
Valid prediction for snap_scaffold_2-snap.1185-T1
Valid prediction for Augustus_model.g2532.t1
Valid prediction for GlimmerHMM_glimmerT_3784-T1
Valid prediction for snap_scaffold_2-snap.1171-T1
Valid prediction for GlimmerHMM_glimmerT_3786-T1
Valid prediction for snap_scaffold_2-snap.1170-T1
Valid prediction for GlimmerHMM_glimmerT_3787-T1
Valid prediction for snap_scaffold_2-snap.1207-T1
Valid prediction for snap_scaffold_2-snap.1192-T1
Valid prediction for snap_scaffold_2-snap.1172-T1
Couldn't classify 23511, 23729
Sorry, prediction pasa_asmbl_24405.p1 fails validation.
(TTG)	 GC	23511-23729	GT	AGG
(GCC)	 AG	24206-24369	GT	GGG
(CTA)	 AG	26433-26616	CT	AGC
-recovered pasa_asmbl_24405.p1, terminal, 26433, 26616
-recovered pasa_asmbl_24405.p1, internal, 24206, 24369
Valid prediction for snap_scaffold_2-snap.1206-T1
Valid prediction for GlimmerHMM_glimmerT_3794-T1
Valid prediction for Augustus_model.g2527.t1
Valid prediction for HiQ_model.g2534.t1
Valid prediction for snap_scaffold_2-snap.1181-T1
Valid prediction for Augustus_model.g2530.t1
Valid prediction for snap_scaffold_2-snap.1173-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_3795-T1
Valid prediction for Augustus_model.g2531.t1
Valid prediction for snap_scaffold_2-snap.1195-T1
Valid prediction for GlimmerHMM_glimmerT_3799-T1
Valid prediction for Augustus_model.g2540.t1
Valid prediction for GlimmerHMM_glimmerT_3788-T1
Valid prediction for snap_scaffold_2-snap.1187-T1
Valid prediction for CodingQuarry_transcript_28552-T1
Valid prediction for snap_scaffold_2-snap.1174-T1
Valid prediction for snap_scaffold_2-snap.1198-T1
Valid prediction for snap_scaffold_2-snap.1178-T1
Valid prediction for snap_scaffold_2-snap.1175-T1
Valid prediction for Augustus_model.g2539.t1
Valid prediction for snap_scaffold_2-snap.1190-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3802-T1
Valid prediction for snap_scaffold_2-snap.1196-T1
Valid prediction for GlimmerHMM_glimmerT_3800-T1
Valid prediction for Augustus_model.g2542.t1
Valid prediction for snap_scaffold_2-snap.1184-T1
Valid prediction for Augustus_model.g2537.t1
Valid prediction for pasa_asmbl_23142.p1
Valid prediction for snap_scaffold_2-snap.1194-T1
Valid prediction for snap_scaffold_2-snap.1199-T1
Valid prediction for GlimmerHMM_glimmerT_3801-T1
Valid prediction for Augustus_model.g2541.t1
Valid prediction for snap_scaffold_2-snap.1189-T1
Valid prediction for GlimmerHMM_glimmerT_3797-T1
Valid prediction for snap_scaffold_2-snap.1186-T1
Valid prediction for snap_scaffold_2-snap.1203-T1
Valid prediction for Augustus_model.g2535.t1
Valid prediction for snap_scaffold_2-snap.1180-T1
Valid prediction for GlimmerHMM_glimmerT_3798-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24810, rend_intergenic: 16584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36283, rend_intergenic: 29928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42739, rend_intergenic: 36592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45378, rend_intergenic: 44970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47107, rend_intergenic: 45424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65478, rend_intergenic: 58558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72012, rend_intergenic: 68084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83957, rend_intergenic: 75408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96840, rend_intergenic: 84973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105063, rend_intergenic: 97300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110186, rend_intergenic: 108856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121075, rend_intergenic: 114095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124550, rend_intergenic: 122988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150275, rend_intergenic: 124556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151676
-exon list size: 507


building trellis

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98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 24810, rend_intergenic: 16584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36283, rend_intergenic: 29928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42739, rend_intergenic: 36592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45378, rend_intergenic: 44970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47107, rend_intergenic: 45424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65478, rend_intergenic: 58558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72012, rend_intergenic: 68084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83957, rend_intergenic: 75408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96840, rend_intergenic: 84973  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105063, rend_intergenic: 97300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110186, rend_intergenic: 108856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121075, rend_intergenic: 114095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124550, rend_intergenic: 122988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150275, rend_intergenic: 124556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support