-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_6971855-7119634

-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.85210_t
Valid prediction for snap_scaffold_21-snap.1467-T1
Valid prediction for snap_scaffold_21-snap.1464-T1
Valid prediction for GlimmerHMM_glimmerT_49187-T1
Valid prediction for snap_scaffold_21-snap.1473-T1
Valid prediction for snap_scaffold_21-snap.1463-T1
Valid prediction for GeneMark_model.85217_t
Valid prediction for GeneMark_model.85193_t
Couldn't classify 21486, 21537
Sorry, prediction pasa_asmbl_28725.p1 fails validation.
(CTG)	 CG	21486-21537	GT	AGG
(TGT)	 AG	21789-21931	GT	AGG
(GAG)	 AG	22070-22165	GT	AGG
(GAG)	 AG	22309-22445	GT	ACG
(CAA)	 AG	23152-23235	GT	ACG
(TAC)	 AG	23362-23468	GT	AGG
(TCT)	 AG	23563-23714	GT	TGG
(GGT)	 AG	23859-23997	GT	AGG
(GTC)	 AG	24125-24198	GT	AGG
(ATG)	 AG	24365-24481	GT	AGG
(AAC)	 AG	24572-24694	GT	GAG
(GAT)	 AG	24924-25115	GT	AGG
(CGA)	 AG	25233-25334	GT	AGG
(ATT)	 AG	25440-25555	GC	AGG
(TCA)	 AG	25672-25799	GT	AGG
(CCC)	 AG	25953-26087	GT	AGG
(GAG)	 AG	26183-26271	GC	GAG
-recovered pasa_asmbl_28725.p1, initial, 24365, 24481
-recovered pasa_asmbl_28725.p1, terminal, 26183, 26271
-recovered pasa_asmbl_28725.p1, internal, 21789, 21931
-recovered pasa_asmbl_28725.p1, internal, 22070, 22165
-recovered pasa_asmbl_28725.p1, internal, 22309, 22445
-recovered pasa_asmbl_28725.p1, internal, 23152, 23235
-recovered pasa_asmbl_28725.p1, internal, 23362, 23468
-recovered pasa_asmbl_28725.p1, internal, 23563, 23714
-recovered pasa_asmbl_28725.p1, internal, 23859, 23997
-recovered pasa_asmbl_28725.p1, internal, 24125, 24198
-recovered pasa_asmbl_28725.p1, internal, 24365, 24481
-recovered pasa_asmbl_28725.p1, internal, 24572, 24694
-recovered pasa_asmbl_28725.p1, internal, 24924, 25115
-recovered pasa_asmbl_28725.p1, internal, 25233, 25334
-recovered pasa_asmbl_28725.p1, internal, 25440, 25555
-recovered pasa_asmbl_28725.p1, internal, 25672, 25799
-recovered pasa_asmbl_28725.p1, internal, 25953, 26087
-recovered pasa_asmbl_28725.p1, internal, 26183, 26271
Valid prediction for snap_scaffold_21-snap.1460-T1
Couldn't classify 143451, 143512
Sorry, prediction pasa_asmbl_28729.p1 fails validation.
(AAG)	 AG	143451-143512	GT	TGG
(GAT)	 AG	143623-143818	GT	AGG
(TAT)	 AG	143992-144114	GT	AGG
(GTG)	 AG	144590-144792	GT	AGG
(GGA)	 AG	145173-145294	GT	AGG
(GTG)	 AG	145472-145608	GT	AGG
(GTG)	 AG	145719-145901	CC	GAC
-recovered pasa_asmbl_28729.p1, terminal, 145719, 145901
-recovered pasa_asmbl_28729.p1, internal, 143451, 143512
-recovered pasa_asmbl_28729.p1, internal, 143623, 143818
-recovered pasa_asmbl_28729.p1, internal, 143992, 144114
-recovered pasa_asmbl_28729.p1, internal, 144590, 144792
-recovered pasa_asmbl_28729.p1, internal, 145173, 145294
-recovered pasa_asmbl_28729.p1, internal, 145472, 145608
Valid prediction for GeneMark_model.85216_t
Valid prediction for GeneMark_model.85191_t
Valid prediction for GeneMark_model.85223_t
Valid prediction for GeneMark_model.85225_t
Valid prediction for snap_scaffold_21-snap.1456-T1
Valid prediction for GeneMark_model.85218_t
Valid prediction for snap_scaffold_21-snap.1475-T1
Valid prediction for snap_scaffold_21-snap.1452-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g32971.t1
Valid prediction for GlimmerHMM_glimmerT_49166-T1
Valid prediction for snap_scaffold_21-snap.1458-T1
Valid prediction for GlimmerHMM_glimmerT_49185-T1
Valid prediction for GeneMark_model.85190_t
Valid prediction for GeneMark_model.85208_t
Valid prediction for GlimmerHMM_glimmerT_49180-T1
Valid prediction for snap_scaffold_21-snap.1468-T1
Valid prediction for Augustus_model.g32965.t1
Valid prediction for snap_scaffold_21-snap.1480-T1
Valid prediction for GlimmerHMM_glimmerT_49178-T1
Valid prediction for GlimmerHMM_glimmerT_49184-T1
Valid prediction for GlimmerHMM_glimmerT_49188-T1
Valid prediction for Augustus_model.g32962.t1
Valid prediction for Augustus_model.g32970.t1
Valid prediction for snap_scaffold_21-snap.1472-T1
Valid prediction for Augustus_model.g32974.t1
Valid prediction for snap_scaffold_21-snap.1449-T1
Valid prediction for Augustus_model.g32972.t1
Valid prediction for snap_scaffold_21-snap.1448-T1
Valid prediction for GeneMark_model.85201_t
Valid prediction for GeneMark_model.85219_t
Valid prediction for GlimmerHMM_glimmerT_49190-T1
Valid prediction for GeneMark_model.85221_t
Valid prediction for Augustus_model.g32957.t1
Valid prediction for GlimmerHMM_glimmerT_49169-T1
Valid prediction for GeneMark_model.85213_t
Valid prediction for GlimmerHMM_glimmerT_49174-T1
Valid prediction for snap_scaffold_21-snap.1455-T1
Valid prediction for GeneMark_model.85199_t
Valid prediction for Augustus_model.g32967.t1
Valid prediction for snap_scaffold_21-snap.1477-T1
Valid prediction for snap_scaffold_21-snap.1479-T1
Valid prediction for Augustus_model.g32959.t1
Couldn't classify 20592, 20672
Couldn't classify 20919, 21434
Sorry, prediction pasa_asmbl_28724.p1 fails validation.
(AAG)	 TA	20592-20672	GT	AGG
(ATC)	 AG	20919-21434	CC	CCC
Valid prediction for GeneMark_model.85205_t
Valid prediction for GlimmerHMM_glimmerT_49173-T1
Valid prediction for Augustus_model.g32963.t1
Valid prediction for Augustus_model.g32964.t1
Valid prediction for GlimmerHMM_glimmerT_49168-T1
Valid prediction for GlimmerHMM_glimmerT_49191-T1
Valid prediction for GeneMark_model.85202_t
Valid prediction for Augustus_model.g32973.t1
Valid prediction for GeneMark_model.85195_t
Valid prediction for snap_scaffold_21-snap.1470-T1
Valid prediction for GeneMark_model.85212_t
Valid prediction for GeneMark_model.85215_t
Valid prediction for GlimmerHMM_glimmerT_49175-T1
Valid prediction for GlimmerHMM_glimmerT_49182-T1
Valid prediction for GlimmerHMM_glimmerT_49189-T1
Valid prediction for GlimmerHMM_glimmerT_49181-T1
Valid prediction for GlimmerHMM_glimmerT_49170-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 GeneMark_model.85192_t
Valid prediction for snap_scaffold_21-snap.1476-T1
Valid prediction for HiQ_model.g32961.t1
Valid prediction for snap_scaffold_21-snap.1459-T1
Valid prediction for Augustus_model.g32968.t1
Valid prediction for Augustus_model.g32958.t1
Valid prediction for snap_scaffold_21-snap.1469-T1
Valid prediction for GlimmerHMM_glimmerT_49186-T1
Valid prediction for HiQ_model.g32960.t1
Valid prediction for GlimmerHMM_glimmerT_49176-T1
Valid prediction for GlimmerHMM_glimmerT_49172-T1
Valid prediction for snap_scaffold_21-snap.1471-T1
Valid prediction for snap_scaffold_21-snap.1466-T1
Valid prediction for snap_scaffold_21-snap.1474-T1
Valid prediction for GeneMark_model.85198_t
Valid prediction for snap_scaffold_21-snap.1447-T1
Valid prediction for GeneMark_model.85203_t
Valid prediction for snap_scaffold_21-snap.1457-T1
Valid prediction for snap_scaffold_21-snap.1453-T1
Valid prediction for GeneMark_model.85200_t
Valid prediction for GeneMark_model.85211_t
Valid prediction for pasa_asmbl_27797.p1
Valid prediction for GlimmerHMM_glimmerT_49177-T1
Valid prediction for Augustus_model.g32966.t1
Valid prediction for GeneMark_model.85197_t
Valid prediction for GeneMark_model.85220_t
Valid prediction for pasa_asmbl_27800.p1
Valid prediction for GeneMark_model.85222_t
Valid prediction for GeneMark_model.85196_t
Valid prediction for GeneMark_model.85214_t
Valid prediction for CodingQuarry_transcript_32550-T1
Valid prediction for snap_scaffold_21-snap.1450-T1
Valid prediction for snap_scaffold_21-snap.1462-T1
Valid prediction for snap_scaffold_21-snap.1478-T1
Valid prediction for GlimmerHMM_glimmerT_49183-T1
Valid prediction for GeneMark_model.85194_t
Valid prediction for GeneMark_model.85209_t
Valid prediction for snap_scaffold_21-snap.1451-T1
Valid prediction for GeneMark_model.85224_t
Valid prediction for Augustus_model.g32969.t1
Valid prediction for GlimmerHMM_glimmerT_49167-T1
Valid prediction for CodingQuarry_transcript_32549-T1
Valid prediction for GlimmerHMM_glimmerT_49171-T1
Couldn't classify 65096, 65235
Sorry, prediction pasa_asmbl_27803.p1 fails validation.
(ATG)	 AG	62644-62854	GT	TGG
(ACT)	 AG	65096-65235	GG	CAG
-recovered pasa_asmbl_27803.p1, initial, 62644, 62854
-recovered pasa_asmbl_27803.p1, internal, 62644, 62854
Valid prediction for GeneMark_model.85206_t
Valid prediction for snap_scaffold_21-snap.1465-T1
Valid prediction for snap_scaffold_21-snap.1446-T1
Valid prediction for snap_scaffold_21-snap.1461-T1
Valid prediction for snap_scaffold_21-snap.1481-T1
Valid prediction for GlimmerHMM_glimmerT_49179-T1
Valid prediction for snap_scaffold_21-snap.1454-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55383, rend_intergenic: 43200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75258, rend_intergenic: 72717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82752, rend_intergenic: 81409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97839, rend_intergenic: 96766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104961, rend_intergenic: 103708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106792, rend_intergenic: 105660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108666, rend_intergenic: 108559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112629, rend_intergenic: 109678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127647, rend_intergenic: 118566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130128, rend_intergenic: 128475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131085, rend_intergenic: 130296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140697, rend_intergenic: 135661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145901, rend_intergenic: 142183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 147780
-exon list size: 578


building trellis

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99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 55383, rend_intergenic: 43200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75258, rend_intergenic: 72717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82752, rend_intergenic: 81409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97839, rend_intergenic: 96766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104961, rend_intergenic: 103708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106792, rend_intergenic: 105660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108666, rend_intergenic: 108559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112629, rend_intergenic: 109678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127647, rend_intergenic: 118566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130128, rend_intergenic: 128475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131085, rend_intergenic: 130296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140697, rend_intergenic: 135661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145901, rend_intergenic: 142183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11709
-exon list size: 17


building trellis

5.3    
10.5    
15.8    
21.1    
26.3    
31.6    
36.8    
42.1    
47.4    
52.6    
57.9    
63.2    
68.4    
73.7    
78.9    
84.2    
89.5    
94.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11012
-exon list size: 14


building trellis

6.2    
12.5    
18.8    
25.0    
31.2    
37.5    
43.8    
50.0    
56.2    
62.5    
68.8    
75.0    
81.2    
87.5    
93.8    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support