-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_6048554-6234403

-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: +)Couldn't classify 140705, 141224
Sorry, prediction pasa_asmbl_45409.p1 fails validation.
(TTC)	 CC	140705-141224	GT	AGG
(GTG)	 AG	141532-141702	GT	CGG
(GTA)	 AG	141820-142000	GT	AGG
(CCG)	 AG	142163-142196	GC	GAG
-recovered pasa_asmbl_45409.p1, terminal, 142163, 142196
-recovered pasa_asmbl_45409.p1, internal, 141532, 141702
-recovered pasa_asmbl_45409.p1, internal, 141820, 142000
-recovered pasa_asmbl_45409.p1, internal, 142163, 142196
Valid prediction for GlimmerHMM_glimmerT_12026-T1
Valid prediction for Augustus_model.g7890.t1
Couldn't classify 169809, 170502
Couldn't classify 171661, 171752
Sorry, prediction pasa_asmbl_45413.p1 fails validation.
(CGT)	 TC	169809-170502	GT	AGG
(GAA)	 AG	171661-171752	GT	TGG
-recovered pasa_asmbl_45413.p1, internal, 171661, 171752
Valid prediction for snap_scaffold_5-snap.1214-T1
Valid prediction for GlimmerHMM_glimmerT_12035-T1
Valid prediction for snap_scaffold_5-snap.1194-T1
Valid prediction for snap_scaffold_5-snap.1213-T1
Valid prediction for GlimmerHMM_glimmerT_12034-T1
Valid prediction for snap_scaffold_5-snap.1192-T1
Valid prediction for snap_scaffold_5-snap.1201-T1
Couldn't classify 117877, 117927
Couldn't classify 119819, 119917
Sorry, prediction pasa_asmbl_45402.p1 fails validation.
(AGG)	 TC	117877-117927	GT	AAG
(GCT)	 AG	118449-118573	GT	AGG
(AAG)	 AG	119014-119113	GT	CTG
(CTT)	 AG	119819-119917	GT	TGG
-recovered pasa_asmbl_45402.p1, internal, 118449, 118573
-recovered pasa_asmbl_45402.p1, internal, 119014, 119113
-recovered pasa_asmbl_45402.p1, internal, 119819, 119917
Valid prediction for GlimmerHMM_glimmerT_12025-T1
Valid prediction for snap_scaffold_5-snap.1218-T1
Valid prediction for snap_scaffold_5-snap.1195-T1
Valid prediction for GlimmerHMM_glimmerT_12031-T1
Valid prediction for Augustus_model.g7892.t1
Valid prediction for snap_scaffold_5-snap.1204-T1
Valid prediction for snap_scaffold_5-snap.1187-T1
Valid prediction for snap_scaffold_5-snap.1180-T1
Valid prediction for snap_scaffold_5-snap.1207-T1
Valid prediction for GlimmerHMM_glimmerT_12040-T1
Valid prediction for snap_scaffold_5-snap.1215-T1
Valid prediction for GlimmerHMM_glimmerT_12042-T1
Valid prediction for Augustus_model.g7884.t1
Valid prediction for CodingQuarry_transcript_52086-T1
Valid prediction for CodingQuarry_transcript_52085-T1
Valid prediction for GlimmerHMM_glimmerT_12023-T1
Couldn't classify 4063, 4080
Sorry, prediction pasa_asmbl_45396.p1 fails validation.
(AGA)	 TG	4063-4080	GT	AGG
(GTG)	 AG	4174-4389	GT	CTG
(ATC)	 AG	4568-4678	GT	CAG
(GTG)	 AG	4826-4927	GT	AGG
(GAC)	 AG	5240-5315	GT	CAG
(GTC)	 AG	5581-5708	GT	AGG
(AAA)	 AG	5937-6158	GA	GAG
-recovered pasa_asmbl_45396.p1, terminal, 5937, 6158
-recovered pasa_asmbl_45396.p1, internal, 4174, 4389
-recovered pasa_asmbl_45396.p1, internal, 4568, 4678
-recovered pasa_asmbl_45396.p1, internal, 4826, 4927
-recovered pasa_asmbl_45396.p1, internal, 5240, 5315
-recovered pasa_asmbl_45396.p1, internal, 5581, 5708
Valid prediction for snap_scaffold_5-snap.1190-T1
Valid prediction for GlimmerHMM_glimmerT_12033-T1
Valid prediction for pasa_asmbl_45397.p1
Valid prediction for snap_scaffold_5-snap.1211-T1
Valid prediction for snap_scaffold_5-snap.1205-T1
Valid prediction for snap_scaffold_5-snap.1186-T1
Valid prediction for Augustus_model.g7899.t1
Valid prediction for Augustus_model.g7898.t1
Valid prediction for Augustus_model.g7893.t1
Valid prediction for snap_scaffold_5-snap.1210-T1
Valid prediction for snap_scaffold_5-snap.1202-T1
Couldn't classify 139142, 139509
Couldn't classify 140504, 140608
Sorry, prediction pasa_asmbl_45407.p1 fails validation.
(CAG)	 AC	139142-139509	GT	CGG
(GTT)	 AG	140180-140402	GT	CGG
(AAA)	 AG	140504-140608	GT	CCG
-recovered pasa_asmbl_45407.p1, internal, 140180, 140402
-recovered pasa_asmbl_45407.p1, internal, 140504, 140608
Valid prediction for Augustus_model.g7888.t1
Valid prediction for CodingQuarry_transcript_52087-T1
Valid prediction for GlimmerHMM_glimmerT_12022-T1
Valid prediction for Augustus_model.g7887.t1
Valid prediction for snap_scaffold_5-snap.1203-T1
Couldn't classify 135417, 135579
Couldn't classify 138131, 138397
Sorry, prediction pasa_asmbl_45405.p1 fails validation.
(GGG)	 AG	135417-135579	GT	CTG
(TGG)	 AG	135799-135891	GT	CAG
(CCT)	 AG	136922-137121	GT	CGG
(ATG)	 AG	137608-137769	GT	AGG
(AAG)	 AG	137856-137969	GT	AGG
(GAG)	 AG	138131-138397	CC	CTC
-recovered pasa_asmbl_45405.p1, initial, 137608, 137769
-recovered pasa_asmbl_45405.p1, internal, 135417, 135579
-recovered pasa_asmbl_45405.p1, internal, 135799, 135891
-recovered pasa_asmbl_45405.p1, internal, 136922, 137121
-recovered pasa_asmbl_45405.p1, internal, 137608, 137769
-recovered pasa_asmbl_45405.p1, internal, 137856, 137969
Valid prediction for snap_scaffold_5-snap.1178-T1
Valid prediction for Augustus_model.g7894.t1
Valid prediction for GlimmerHMM_glimmerT_12029-T1
Valid prediction for GlimmerHMM_glimmerT_12046-T1
Valid prediction for HiQ_model.g7895.t1
Valid prediction for HiQ_model.g7882.t1
Valid prediction for Augustus_model.g7897.t1
Valid prediction for snap_scaffold_5-snap.1183-T1
Valid prediction for snap_scaffold_5-snap.1216-T1
Valid prediction for snap_scaffold_5-snap.1200-T1
Valid prediction for GlimmerHMM_glimmerT_12044-T1
Valid prediction for snap_scaffold_5-snap.1189-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_12032-T1
Valid prediction for snap_scaffold_5-snap.1196-T1
Valid prediction for snap_scaffold_5-snap.1181-T1
Valid prediction for snap_scaffold_5-snap.1193-T1
Valid prediction for snap_scaffold_5-snap.1212-T1
Valid prediction for snap_scaffold_5-snap.1191-T1
Valid prediction for snap_scaffold_5-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_12038-T1
Valid prediction for snap_scaffold_5-snap.1197-T1
Valid prediction for snap_scaffold_5-snap.1199-T1
Valid prediction for Augustus_model.g7885.t1
Valid prediction for GlimmerHMM_glimmerT_12041-T1
Valid prediction for GlimmerHMM_glimmerT_12045-T1
Valid prediction for snap_scaffold_5-snap.1185-T1
Valid prediction for snap_scaffold_5-snap.1182-T1
Valid prediction for snap_scaffold_5-snap.1198-T1
Valid prediction for GlimmerHMM_glimmerT_12024-T1
Valid prediction for snap_scaffold_5-snap.1206-T1
Valid prediction for snap_scaffold_5-snap.1209-T1
Valid prediction for GlimmerHMM_glimmerT_12037-T1
Valid prediction for Augustus_model.g7883.t1
Valid prediction for GlimmerHMM_glimmerT_12036-T1
Valid prediction for GlimmerHMM_glimmerT_12043-T1
Valid prediction for snap_scaffold_5-snap.1184-T1
Valid prediction for GlimmerHMM_glimmerT_12030-T1
Valid prediction for Augustus_model.g7889.t1
Valid prediction for snap_scaffold_5-snap.1217-T1
Valid prediction for GlimmerHMM_glimmerT_12027-T1
Valid prediction for Augustus_model.g7896.t1
Valid prediction for snap_scaffold_5-snap.1208-T1
Valid prediction for Augustus_model.g7891.t1
Valid prediction for snap_scaffold_5-snap.1179-T1
Valid prediction for Augustus_model.g7886.t1
Valid prediction for GlimmerHMM_glimmerT_12039-T1
Valid prediction for GlimmerHMM_glimmerT_12028-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30389, rend_intergenic: 29165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40110, rend_intergenic: 31243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72589, rend_intergenic: 72563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77074, rend_intergenic: 73153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84868, rend_intergenic: 83391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113029, rend_intergenic: 87943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153742, rend_intergenic: 151050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156714, rend_intergenic: 154805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161850, rend_intergenic: 157143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182695, rend_intergenic: 173237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185850
-exon list size: 360


building trellis

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90.3    
90.6    
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93.1    
93.4    
93.6    
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97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 30389, rend_intergenic: 29165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40110, rend_intergenic: 31243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72589, rend_intergenic: 72563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77074, rend_intergenic: 73153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84868, rend_intergenic: 83391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113029, rend_intergenic: 87943  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153742, rend_intergenic: 151050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156714, rend_intergenic: 154805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161850, rend_intergenic: 157143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182695, rend_intergenic: 173237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support