-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_6001143-6208003

-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 Augustus_model.g31893.t1
Valid prediction for pasa_asmbl_28617.p1
Valid prediction for Augustus_model.g31886.t1
Valid prediction for Augustus_model.g31901.t1
Valid prediction for GlimmerHMM_glimmerT_47797-T1
Valid prediction for snap_scaffold_21-snap.1239-T1
Valid prediction for snap_scaffold_21-snap.1224-T1
Valid prediction for GlimmerHMM_glimmerT_47803-T1
Valid prediction for snap_scaffold_21-snap.1214-T1
Valid prediction for GlimmerHMM_glimmerT_47812-T1
Valid prediction for Augustus_model.g31892.t1
Couldn't classify 50445, 50629
Couldn't classify 50713, 50836
Sorry, prediction pasa_asmbl_28979.p1 fails validation.
(AAG)	 AG	50445-50629	GT	TGG
(CAT)	 AG	50713-50836	AT	ACA
-recovered pasa_asmbl_28979.p1, internal, 50445, 50629
Couldn't classify 111600, 111767
Couldn't classify 113342, 113362
Sorry, prediction pasa_asmbl_28613.p1 fails validation.
(ATT)	 TG	111600-111767	GT	AGG
(GAG)	 AG	111912-112097	GT	AGG
(GGT)	 AG	112200-112311	GT	AGG
(AAA)	 AG	112406-112565	GT	AGG
(GTG)	 AG	112763-112851	GT	CGG
(AGG)	 AG	112949-113076	GT	AAG
(ACC)	 AG	113342-113362	TT	ACT
-recovered pasa_asmbl_28613.p1, internal, 111912, 112097
-recovered pasa_asmbl_28613.p1, internal, 112200, 112311
-recovered pasa_asmbl_28613.p1, internal, 112406, 112565
-recovered pasa_asmbl_28613.p1, internal, 112763, 112851
-recovered pasa_asmbl_28613.p1, internal, 112949, 113076
Valid prediction for GlimmerHMM_glimmerT_47789-T1
Valid prediction for Augustus_model.g31891.t1
Valid prediction for snap_scaffold_21-snap.1221-T1
Valid prediction for snap_scaffold_21-snap.1238-T1
Valid prediction for snap_scaffold_21-snap.1237-T1
Valid prediction for CodingQuarry_transcript_32565-T1
Valid prediction for Augustus_model.g31896.t1
Valid prediction for snap_scaffold_21-snap.1205-T1
Valid prediction for HiQ_model.g31907.t1
Valid prediction for Augustus_model.g31885.t1
Valid prediction for GlimmerHMM_glimmerT_47816-T1
Valid prediction for GlimmerHMM_glimmerT_47792-T1
Valid prediction for Augustus_model.g31883.t1
Valid prediction for GlimmerHMM_glimmerT_47807-T1
Valid prediction for snap_scaffold_21-snap.1225-T1
Valid prediction for snap_scaffold_21-snap.1250-T1
Valid prediction for Augustus_model.g31905.t1
Valid prediction for snap_scaffold_21-snap.1245-T1
Valid prediction for snap_scaffold_21-snap.1211-T1
Valid prediction for GlimmerHMM_glimmerT_47799-T1
Valid prediction for pasa_asmbl_28615.p1
Valid prediction for snap_scaffold_21-snap.1252-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g31906.t1
Valid prediction for Augustus_model.g31904.t1
Valid prediction for snap_scaffold_21-snap.1209-T1
Valid prediction for snap_scaffold_21-snap.1232-T1
Valid prediction for snap_scaffold_21-snap.1219-T1
Valid prediction for Augustus_model.g31899.t1
Valid prediction for snap_scaffold_21-snap.1242-T1
Valid prediction for GlimmerHMM_glimmerT_47806-T1
Valid prediction for GlimmerHMM_glimmerT_47817-T1
Valid prediction for Augustus_model.g31881.t1
Couldn't classify 126081, 126135
Couldn't classify 127093, 127518
Sorry, prediction pasa_asmbl_28616.p1 fails validation.
(TTC)	 GT	126081-126135	GT	TGG
(ATA)	 AG	126858-127006	GT	AGG
(CCC)	 AG	127093-127518	CC	CCC
-recovered pasa_asmbl_28616.p1, internal, 126858, 127006
Valid prediction for CodingQuarry_transcript_32564-T1
Valid prediction for snap_scaffold_21-snap.1253-T1
Valid prediction for GlimmerHMM_glimmerT_47819-T1
Valid prediction for CodingQuarry_transcript_32569-T1
Valid prediction for GlimmerHMM_glimmerT_47813-T1
Valid prediction for GlimmerHMM_glimmerT_47791-T1
Valid prediction for Augustus_model.g31884.t1
Valid prediction for snap_scaffold_21-snap.1246-T1
Valid prediction for GlimmerHMM_glimmerT_47810-T1
Valid prediction for Augustus_model.g31888.t1
Valid prediction for snap_scaffold_21-snap.1234-T1
Valid prediction for snap_scaffold_21-snap.1247-T1
Valid prediction for Augustus_model.g31887.t1
Valid prediction for snap_scaffold_21-snap.1235-T1
Valid prediction for Augustus_model.g31894.t1
Valid prediction for snap_scaffold_21-snap.1206-T1
Valid prediction for Augustus_model.g31897.t1
Valid prediction for snap_scaffold_21-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_47805-T1
Valid prediction for Augustus_model.g31890.t1
Valid prediction for pasa_asmbl_28621.p1
Valid prediction for Augustus_model.g31889.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_47821-T1
Valid prediction for GlimmerHMM_glimmerT_47795-T1
Valid prediction for GlimmerHMM_glimmerT_47788-T1
Valid prediction for snap_scaffold_21-snap.1254-T1
Valid prediction for GlimmerHMM_glimmerT_47815-T1
Valid prediction for pasa_asmbl_27715.p1
Valid prediction for snap_scaffold_21-snap.1223-T1
Valid prediction for GlimmerHMM_glimmerT_47801-T1
Valid prediction for snap_scaffold_21-snap.1244-T1
Valid prediction for GlimmerHMM_glimmerT_47809-T1
Valid prediction for snap_scaffold_21-snap.1208-T1
Valid prediction for snap_scaffold_21-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_47793-T1
Couldn't classify 8426, 9028
Sorry, prediction pasa_asmbl_27716.p2 fails validation.
(GCC)	 TG	8426-9028	AG	AAA
Valid prediction for GlimmerHMM_glimmerT_47808-T1
Valid prediction for GlimmerHMM_glimmerT_47822-T1
Valid prediction for GlimmerHMM_glimmerT_47804-T1
Valid prediction for GlimmerHMM_glimmerT_47800-T1
Valid prediction for snap_scaffold_21-snap.1217-T1
Valid prediction for snap_scaffold_21-snap.1231-T1
Valid prediction for GlimmerHMM_glimmerT_47790-T1
Valid prediction for Augustus_model.g31908.t1
Valid prediction for snap_scaffold_21-snap.1243-T1
Valid prediction for CodingQuarry_transcript_32566-T1
Valid prediction for GlimmerHMM_glimmerT_47798-T1
Valid prediction for snap_scaffold_21-snap.1249-T1
Valid prediction for snap_scaffold_21-snap.1222-T1
Valid prediction for snap_scaffold_21-snap.1233-T1
Valid prediction for Augustus_model.g31900.t1
Valid prediction for snap_scaffold_21-snap.1228-T1
Valid prediction for GlimmerHMM_glimmerT_47820-T1
Valid prediction for snap_scaffold_21-snap.1226-T1
Couldn't classify 203840, 204283
Sorry, prediction pasa_asmbl_28607.p1 fails validation.
(ATG)	 CC	203840-204283	CT	ACC
Valid prediction for GlimmerHMM_glimmerT_47787-T1
Valid prediction for Augustus_model.g31882.t1
Valid prediction for snap_scaffold_21-snap.1213-T1
Valid prediction for GlimmerHMM_glimmerT_47814-T1
Valid prediction for snap_scaffold_21-snap.1220-T1
Valid prediction for snap_scaffold_21-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_47818-T1
Valid prediction for GlimmerHMM_glimmerT_47811-T1
Valid prediction for snap_scaffold_21-snap.1227-T1
Valid prediction for snap_scaffold_21-snap.1230-T1
Valid prediction for GlimmerHMM_glimmerT_47796-T1
Valid prediction for Augustus_model.g31903.t1
Valid prediction for snap_scaffold_21-snap.1241-T1
Valid prediction for snap_scaffold_21-snap.1248-T1
Valid prediction for snap_scaffold_21-snap.1210-T1
Valid prediction for GlimmerHMM_glimmerT_47802-T1
Valid prediction for Augustus_model.g31898.t1
Valid prediction for snap_scaffold_21-snap.1240-T1
Valid prediction for snap_scaffold_21-snap.1216-T1
Valid prediction for GlimmerHMM_glimmerT_47794-T1
Valid prediction for snap_scaffold_21-snap.1207-T1
Valid prediction for snap_scaffold_21-snap.1215-T1
Valid prediction for Augustus_model.g31895.t1
Valid prediction for snap_scaffold_21-snap.1236-T1
Valid prediction for snap_scaffold_21-snap.1229-T1
Valid prediction for Augustus_model.g31902.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16740, rend_intergenic: 7793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20607, rend_intergenic: 17701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35966, rend_intergenic: 26634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39016, rend_intergenic: 35978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55402, rend_intergenic: 39676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72478, rend_intergenic: 62904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73271, rend_intergenic: 72960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78068, rend_intergenic: 73533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79565, rend_intergenic: 78173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98965, rend_intergenic: 88583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136328, rend_intergenic: 132393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150826, rend_intergenic: 145774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155901, rend_intergenic: 153213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162569, rend_intergenic: 158794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167485, rend_intergenic: 163046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173189, rend_intergenic: 169215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176018, rend_intergenic: 173601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 146819, rend_intergenic: 146816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206861
-exon list size: 518


building trellis

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99.2    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 16740, rend_intergenic: 7793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20607, rend_intergenic: 17701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35966, rend_intergenic: 26634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39016, rend_intergenic: 35978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55402, rend_intergenic: 39676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72478, rend_intergenic: 62904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73271, rend_intergenic: 72960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78068, rend_intergenic: 73533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79565, rend_intergenic: 78173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98965, rend_intergenic: 88583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136328, rend_intergenic: 132393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150826, rend_intergenic: 145774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155901, rend_intergenic: 153213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162569, rend_intergenic: 158794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167485, rend_intergenic: 163046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173189, rend_intergenic: 169215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176018, rend_intergenic: 173601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 146819, rend_intergenic: 146816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support