-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_6953728-7134567

-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 98006, 98212
Sorry, prediction pasa_asmbl_31668.p1 fails validation.
(ATG)	 AA	95608-95729	GT	GGG
(AGA)	 AG	96195-96363	GT	CTG
(GCT)	 AG	97215-97313	GT	AGG
(GCT)	 AG	97588-97752	GT	AGG
(GTG)	 AG	98006-98212	CT	GTC
-recovered pasa_asmbl_31668.p1, initial, 95608, 95729
-recovered pasa_asmbl_31668.p1, internal, 96195, 96363
-recovered pasa_asmbl_31668.p1, internal, 97215, 97313
-recovered pasa_asmbl_31668.p1, internal, 97588, 97752
Valid prediction for pasa_asmbl_31669.p1
Valid prediction for HiQ_model.g34276.t1
Valid prediction for snap_scaffold_23-snap.1281-T1
Valid prediction for snap_scaffold_23-snap.1293-T1
Valid prediction for snap_scaffold_23-snap.1291-T1
Valid prediction for snap_scaffold_23-snap.1279-T1
Valid prediction for HiQ_model.g34271.t1
Valid prediction for snap_scaffold_23-snap.1277-T1
Valid prediction for GlimmerHMM_glimmerT_51239-T1
Valid prediction for GlimmerHMM_glimmerT_51225-T1
Valid prediction for GlimmerHMM_glimmerT_51236-T1
Valid prediction for Augustus_model.g34280.t1
Valid prediction for snap_scaffold_23-snap.1258-T1
Couldn't classify 126083, 126212
Sorry, prediction pasa_asmbl_31672.p1 fails validation.
(CCT)	 GC	126083-126212	GT	TGG
(GTT)	 AG	126714-126976	AT	AGA
-recovered pasa_asmbl_31672.p1, terminal, 126714, 126976
Valid prediction for GlimmerHMM_glimmerT_51238-T1
Valid prediction for Augustus_model.g34281.t1
Valid prediction for snap_scaffold_23-snap.1264-T1
Valid prediction for snap_scaffold_23-snap.1269-T1
Couldn't classify 66419, 66475
Sorry, prediction pasa_asmbl_31664.p1 fails validation.
(CAG)	 TC	66419-66475	GT	AGG
(GAG)	 AG	67103-67242	GT	AGG
(TTC)	 AG	68043-68202	GT	GGG
(GTC)	 AG	68635-68745	GT	AGG
(GAA)	 AG	68907-68987	GT	AGG
(GAC)	 AG	69340-69528	AG	AGA
-recovered pasa_asmbl_31664.p1, terminal, 69340, 69528
-recovered pasa_asmbl_31664.p1, internal, 67103, 67242
-recovered pasa_asmbl_31664.p1, internal, 68043, 68202
-recovered pasa_asmbl_31664.p1, internal, 68635, 68745
-recovered pasa_asmbl_31664.p1, internal, 68907, 68987
Valid prediction for Augustus_model.g34270.t1
Valid prediction for snap_scaffold_23-snap.1285-T1
Valid prediction for snap_scaffold_23-snap.1287-T1
Valid prediction for Augustus_model.g34275.t1
Valid prediction for Augustus_model.g34285.t1
Valid prediction for GlimmerHMM_glimmerT_51240-T1
Valid prediction for Augustus_model.g34284.t1
Couldn't classify 158945, 159364
Sorry, prediction pasa_asmbl_31673.p2 fails validation.
(ATG)	 CC	158945-159364	GG	CTG
Valid prediction for snap_scaffold_23-snap.1271-T1
Valid prediction for snap_scaffold_23-snap.1267-T1
Valid prediction for GlimmerHMM_glimmerT_51227-T1
Valid prediction for GlimmerHMM_glimmerT_51249-T1
Valid prediction for GlimmerHMM_glimmerT_51247-T1
Valid prediction for Augustus_model.g34278.t1
Valid prediction for GlimmerHMM_glimmerT_51241-T1
Valid prediction for GlimmerHMM_glimmerT_51226-T1
Valid prediction for snap_scaffold_23-snap.1283-T1
Valid prediction for snap_scaffold_23-snap.1273-T1
Valid prediction for snap_scaffold_23-snap.1262-T1
Valid prediction for snap_scaffold_23-snap.1259-T1
Valid prediction for snap_scaffold_23-snap.1255-T1
Valid prediction for GlimmerHMM_glimmerT_51248-T1
Valid prediction for GlimmerHMM_glimmerT_51233-T1
Valid prediction for Augustus_model.g34277.t1
Valid prediction for snap_scaffold_23-snap.1260-T1
Valid prediction for GlimmerHMM_glimmerT_51251-T1
Valid prediction for CodingQuarry_transcript_35708-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 CodingQuarry_transcript_35705-T1
Valid prediction for snap_scaffold_23-snap.1284-T1
Valid prediction for snap_scaffold_23-snap.1265-T1
Couldn't classify 8632, 8774
Sorry, prediction pasa_asmbl_31017.p1 fails validation.
(ATG)	 CT	1782-1838	GT	AGG
(GAT)	 AG	4710-4787	GT	CGG
(GGA)	 AG	5017-5124	GT	AGG
(GAG)	 AG	6396-6507	GT	AGG
(GCA)	 AG	7094-7222	GT	GTG
(TCC)	 AG	8632-8774	CT	CCC
-recovered pasa_asmbl_31017.p1, initial, 1782, 1838
-recovered pasa_asmbl_31017.p1, internal, 4710, 4787
-recovered pasa_asmbl_31017.p1, internal, 5017, 5124
-recovered pasa_asmbl_31017.p1, internal, 6396, 6507
-recovered pasa_asmbl_31017.p1, internal, 7094, 7222
Valid prediction for CodingQuarry_transcript_35706-T1
Valid prediction for CodingQuarry_transcript_35702-T1
Valid prediction for Augustus_model.g34286.t1
Valid prediction for snap_scaffold_23-snap.1257-T1
Valid prediction for Augustus_model.g34282.t1
Valid prediction for pasa_asmbl_31012.p1
Valid prediction for snap_scaffold_23-snap.1288-T1
Valid prediction for GlimmerHMM_glimmerT_51235-T1
Valid prediction for GlimmerHMM_glimmerT_51230-T1
Valid prediction for GlimmerHMM_glimmerT_51244-T1
Valid prediction for snap_scaffold_23-snap.1272-T1
Valid prediction for pasa_asmbl_31008.p1
Valid prediction for pasa_asmbl_31011.p1
Valid prediction for snap_scaffold_23-snap.1256-T1
Valid prediction for GlimmerHMM_glimmerT_51224-T1
Valid prediction for CodingQuarry_transcript_35703-T1
Couldn't classify 103549, 103639
Couldn't classify 106026, 106208
Sorry, prediction pasa_asmbl_31010.p1 fails validation.
(GAG)	 AC	103549-103639	GT	AGG
(CTG)	 AG	104334-104503	GT	AGG
(ATG)	 AG	104755-104920	GT	TGG
(AGC)	 AG	105260-105447	GT	AGG
(GAA)	 AG	105604-105678	GT	AGG
(GGA)	 AG	105771-105860	GT	AGG
(CAC)	 AG	106026-106208	GG	GGG
-recovered pasa_asmbl_31010.p1, initial, 104755, 104920
-recovered pasa_asmbl_31010.p1, internal, 104334, 104503
-recovered pasa_asmbl_31010.p1, internal, 104755, 104920
-recovered pasa_asmbl_31010.p1, internal, 105260, 105447
-recovered pasa_asmbl_31010.p1, internal, 105604, 105678
-recovered pasa_asmbl_31010.p1, internal, 105771, 105860
Valid prediction for snap_scaffold_23-snap.1274-T1
Valid prediction for Augustus_model.g34273.t1
Valid prediction for Augustus_model.g34268.t1
Valid prediction for snap_scaffold_23-snap.1275-T1
Valid prediction for GlimmerHMM_glimmerT_51242-T1
Valid prediction for GlimmerHMM_glimmerT_51229-T1
Valid prediction for snap_scaffold_23-snap.1292-T1
Valid prediction for snap_scaffold_23-snap.1266-T1
Valid prediction for GlimmerHMM_glimmerT_51234-T1
Valid prediction for GlimmerHMM_glimmerT_51223-T1
Valid prediction for HiQ_model.g34269.t1
Valid prediction for CodingQuarry_transcript_35704-T1
Valid prediction for GlimmerHMM_glimmerT_51231-T1
Valid prediction for HiQ_model.g34267.t1
Couldn't classify 106416, 106536
Sorry, prediction pasa_asmbl_31009.p1 fails validation.
(GCG)	 AA	106416-106536	GT	AGG
(CGA)	 AG	106995-107314	TA	AGT
-recovered pasa_asmbl_31009.p1, terminal, 106995, 107314
Valid prediction for GlimmerHMM_glimmerT_51246-T1
Valid prediction for GlimmerHMM_glimmerT_51237-T1
Valid prediction for snap_scaffold_23-snap.1270-T1
Valid prediction for Augustus_model.g34279.t1
Valid prediction for snap_scaffold_23-snap.1286-T1
Valid prediction for GlimmerHMM_glimmerT_51245-T1
Valid prediction for GlimmerHMM_glimmerT_51232-T1
Valid prediction for CodingQuarry_transcript_35710-T1
Valid prediction for snap_scaffold_23-snap.1280-T1
Valid prediction for snap_scaffold_23-snap.1278-T1
Valid prediction for snap_scaffold_23-snap.1290-T1
Valid prediction for snap_scaffold_23-snap.1282-T1
Valid prediction for HiQ_model.g34274.t1
Valid prediction for snap_scaffold_23-snap.1263-T1
Valid prediction for GlimmerHMM_glimmerT_51228-T1
Valid prediction for snap_scaffold_23-snap.1261-T1
Valid prediction for GlimmerHMM_glimmerT_51252-T1
Valid prediction for GlimmerHMM_glimmerT_51250-T1
Valid prediction for snap_scaffold_23-snap.1268-T1
Valid prediction for Augustus_model.g34272.t1
Valid prediction for snap_scaffold_23-snap.1276-T1
Valid prediction for pasa_asmbl_31003.p1
Valid prediction for Augustus_model.g34283.t1
Valid prediction for GlimmerHMM_glimmerT_51243-T1
Valid prediction for pasa_asmbl_30996.p1
Valid prediction for HiQ_model.g34266.t1
Valid prediction for Augustus_model.g34265.t1
Valid prediction for snap_scaffold_23-snap.1289-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13223, rend_intergenic: 3027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25936, rend_intergenic: 13428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27872, rend_intergenic: 25984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32607, rend_intergenic: 27935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41486, rend_intergenic: 38904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52399, rend_intergenic: 49517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69528, rend_intergenic: 63202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77431, rend_intergenic: 73527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80336, rend_intergenic: 77708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86928, rend_intergenic: 80940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106957, rend_intergenic: 103345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111331, rend_intergenic: 107531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126976, rend_intergenic: 115749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141007, rend_intergenic: 136499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165157, rend_intergenic: 147196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167783, rend_intergenic: 165865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176858, rend_intergenic: 173993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180840
-exon list size: 393


building trellis

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34.7    
34.9    
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35.9    
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39.5    
39.7    
40.0    
40.3    
40.5    
40.8    
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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 13223, rend_intergenic: 3027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25936, rend_intergenic: 13428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27872, rend_intergenic: 25984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32607, rend_intergenic: 27935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41486, rend_intergenic: 38904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52399, rend_intergenic: 49517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69528, rend_intergenic: 63202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77431, rend_intergenic: 73527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80336, rend_intergenic: 77708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86928, rend_intergenic: 80940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106957, rend_intergenic: 103345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111331, rend_intergenic: 107531  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126976, rend_intergenic: 115749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141007, rend_intergenic: 136499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165157, rend_intergenic: 147196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167783, rend_intergenic: 165865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176858, rend_intergenic: 173993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support