-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_11295832-11492559

-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 GlimmerHMM_glimmerT_1567-T1
Valid prediction for GeneMark_model.2072_t
Valid prediction for GeneMark_model.2062_t
Valid prediction for snap_scaffold_1-snap.1995-T1
Valid prediction for snap_scaffold_1-snap.1996-T1
Valid prediction for GlimmerHMM_glimmerT_1564-T1
Valid prediction for snap_scaffold_1-snap.1981-T1
Valid prediction for CodingQuarry_transcript_2776-T1
Couldn't classify 184024, 184051
Sorry, prediction pasa_asmbl_2101.p1 fails validation.
(TGC)	 AA	184024-184051	GT	AGG
(AGG)	 AG	186026-186171	GT	TGG
(TCT)	 AG	188120-188245	GT	ACG
(GTG)	 AG	188988-189275	GG	GAG
-recovered pasa_asmbl_2101.p1, terminal, 188988, 189275
-recovered pasa_asmbl_2101.p1, internal, 186026, 186171
-recovered pasa_asmbl_2101.p1, internal, 188120, 188245
Valid prediction for CodingQuarry_transcript_2774-T1
Valid prediction for snap_scaffold_1-snap.1992-T1
Valid prediction for GeneMark_model.2058_t
Valid prediction for GeneMark_model.2046_t
Valid prediction for Augustus_model.g1124.t1
Valid prediction for GeneMark_model.2065_t
Valid prediction for CodingQuarry_transcript_2773-T1
Valid prediction for snap_scaffold_1-snap.1966-T1
Valid prediction for HiQ_model.g1134.t1
Valid prediction for snap_scaffold_1-snap.1984-T1
Valid prediction for GeneMark_model.2053_t
Valid prediction for GlimmerHMM_glimmerT_1552-T1
Valid prediction for snap_scaffold_1-snap.1994-T1
Valid prediction for GlimmerHMM_glimmerT_1550-T1
Valid prediction for snap_scaffold_1-snap.1976-T1
Valid prediction for GeneMark_model.2064_t
Valid prediction for GeneMark_model.2049_t
Valid prediction for GlimmerHMM_glimmerT_1566-T1
Valid prediction for GeneMark_model.2073_t
Valid prediction for HiQ_model.g1132.t1
Valid prediction for Augustus_model.g1131.t1
Valid prediction for pasa_asmbl_2092.p1
Valid prediction for snap_scaffold_1-snap.1987-T1
Valid prediction for snap_scaffold_1-snap.1983-T1
Valid prediction for GlimmerHMM_glimmerT_1551-T1
Valid prediction for Augustus_model.g1125.t1
Valid prediction for snap_scaffold_1-snap.1986-T1
Valid prediction for snap_scaffold_1-snap.1985-T1
Valid prediction for snap_scaffold_1-snap.1979-T1
Valid prediction for pasa_asmbl_2085.p1
Valid prediction for snap_scaffold_1-snap.1974-T1
Valid prediction for Augustus_model.g1128.t1
Valid prediction for GeneMark_model.2063_t
Valid prediction for GlimmerHMM_glimmerT_1560-T1
Couldn't classify 110131, 110248
Sorry, prediction pasa_asmbl_2087.p1 fails validation.
(GTG)	 AC	110131-110248	GT	GAG
(TTA)	 AG	111192-111259	GT	AAG
(ATT)	 AG	111432-111497	GT	AGG
(ATC)	 AG	111601-111679	GT	AGG
(GCA)	 AG	111799-111930	GT	ATG
(TGT)	 AG	112043-112152	GT	AGG
(CTG)	 AG	112257-112410	GT	AGG
(GTA)	 AG	112578-112738	GT	AGG
(GGC)	 AG	112903-113100	GT	CGG
(GAC)	 AG	113201-113392	GT	ATG
(GTG)	 AG	113530-113606	GT	AGG
(GTA)	 AG	113749-113935	AT	AGA
-recovered pasa_asmbl_2087.p1, terminal, 113749, 113935
-recovered pasa_asmbl_2087.p1, internal, 111192, 111259
-recovered pasa_asmbl_2087.p1, internal, 111432, 111497
-recovered pasa_asmbl_2087.p1, internal, 111601, 111679
-recovered pasa_asmbl_2087.p1, internal, 111799, 111930
-recovered pasa_asmbl_2087.p1, internal, 112043, 112152
-recovered pasa_asmbl_2087.p1, internal, 112257, 112410
-recovered pasa_asmbl_2087.p1, internal, 112578, 112738
-recovered pasa_asmbl_2087.p1, internal, 112903, 113100
-recovered pasa_asmbl_2087.p1, internal, 113201, 113392
-recovered pasa_asmbl_2087.p1, internal, 113530, 113606
Couldn't classify 146093, 146182
Sorry, prediction pasa_asmbl_2097.p1 fails validation.
(ATG)	 GG	142550-142673	GT	GGG
(TAT)	 AG	144692-144808	GT	AGG
(AGT)	 AG	144894-144990	GT	AGG
(ACA)	 AG	145130-145196	GT	CGG
(GTG)	 AG	145314-145388	GT	AGG
(GTG)	 AG	145811-145867	GT	TCG
(CAA)	 AG	146093-146182	TC	ACT
-recovered pasa_asmbl_2097.p1, initial, 142550, 142673
-recovered pasa_asmbl_2097.p1, internal, 144692, 144808
-recovered pasa_asmbl_2097.p1, internal, 144894, 144990
-recovered pasa_asmbl_2097.p1, internal, 145130, 145196
-recovered pasa_asmbl_2097.p1, internal, 145314, 145388
-recovered pasa_asmbl_2097.p1, internal, 145811, 145867
Valid prediction for GeneMark_model.2075_t
Valid prediction for Augustus_model.g1126.t1
Valid prediction for pasa_asmbl_2089.p2
Valid prediction for GeneMark_model.2066_t
Valid prediction for snap_scaffold_1-snap.1978-T1
Valid prediction for snap_scaffold_1-snap.1971-T1
Valid prediction for GlimmerHMM_glimmerT_1556-T1
Valid prediction for GlimmerHMM_glimmerT_1559-T1
Valid prediction for Augustus_model.g1138.t1
Valid prediction for GeneMark_model.2051_t
Valid prediction for Augustus_model.g1133.t1
Valid prediction for GlimmerHMM_glimmerT_1558-T1
Valid prediction for CodingQuarry_transcript_2777-T1
Valid prediction for snap_scaffold_1-snap.1982-T1
Valid prediction for snap_scaffold_1-snap.1980-T1
Valid prediction for HiQ_model.g1130.t1
Valid prediction for GeneMark_model.2074_t
Valid prediction for GeneMark_model.2048_t
Valid prediction for CodingQuarry_transcript_2775-T1
Valid prediction for snap_scaffold_1-snap.1972-T1
Valid prediction for GeneMark_model.2055_t
Valid prediction for GeneMark_model.2056_t
Valid prediction for GeneMark_model.2069_t
Valid prediction for snap_scaffold_1-snap.1969-T1
Couldn't classify 146444, 146635
Sorry, prediction pasa_asmbl_2098.p1 fails validation.
(AAG)	 TT	146444-146635	GT	AGG
(TTT)	 AG	146730-146876	GT	CTG
(GGG)	 AG	146969-147073	GT	AGG
(TCC)	 AG	147334-147463	GT	AGG
(AAG)	 AG	147605-147667	GT	TGG
(GCT)	 AG	147906-147970	GT	AGG
(AAT)	 AG	148312-148371	TA	GAT
-recovered pasa_asmbl_2098.p1, terminal, 148312, 148371
-recovered pasa_asmbl_2098.p1, internal, 146730, 146876
-recovered pasa_asmbl_2098.p1, internal, 146969, 147073
-recovered pasa_asmbl_2098.p1, internal, 147334, 147463
-recovered pasa_asmbl_2098.p1, internal, 147605, 147667
-recovered pasa_asmbl_2098.p1, internal, 147906, 147970
Valid prediction for GlimmerHMM_glimmerT_1568-T1
Valid prediction for GlimmerHMM_glimmerT_1554-T1
Valid prediction for Augustus_model.g1137.t1
Valid prediction for HiQ_model.g1129.t1
Valid prediction for GlimmerHMM_glimmerT_1557-T1
Valid prediction for GeneMark_model.2060_t
Valid prediction for snap_scaffold_1-snap.1993-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 Augustus_model.g1135.t1
Valid prediction for snap_scaffold_1-snap.1990-T1
Valid prediction for GeneMark_model.2067_t
Valid prediction for snap_scaffold_1-snap.1973-T1
Valid prediction for GeneMark_model.2070_t
Valid prediction for GeneMark_model.2045_t
Valid prediction for HiQ_model.g1136.t1
Valid prediction for GlimmerHMM_glimmerT_1555-T1
Valid prediction for GeneMark_model.2059_t
Couldn't classify 44531, 44584
Sorry, prediction pasa_asmbl_624.p1 fails validation.
(AAG)	 GG	44531-44584	GT	TGG
(ACG)	 AG	45429-45547	GT	CGG
(GAG)	 AG	45658-45769	GT	AGG
(GCA)	 AG	45970-46065	GT	AGG
(GGC)	 AG	46166-46336	GT	ATG
(TTC)	 AG	46426-46431	AA	AAA
-recovered pasa_asmbl_624.p1, terminal, 46426, 46431
-recovered pasa_asmbl_624.p1, internal, 45429, 45547
-recovered pasa_asmbl_624.p1, internal, 45658, 45769
-recovered pasa_asmbl_624.p1, internal, 45970, 46065
-recovered pasa_asmbl_624.p1, internal, 46166, 46336
Valid prediction for CodingQuarry_transcript_2779-T1
Valid prediction for GeneMark_model.2068_t
Valid prediction for GlimmerHMM_glimmerT_1553-T1
Valid prediction for Augustus_model.g1127.t1
Valid prediction for snap_scaffold_1-snap.1970-T1
Valid prediction for GlimmerHMM_glimmerT_1563-T1
Valid prediction for GeneMark_model.2071_t
Valid prediction for snap_scaffold_1-snap.1967-T1
Valid prediction for GeneMark_model.2047_t
Valid prediction for GeneMark_model.2061_t
Valid prediction for snap_scaffold_1-snap.1989-T1
Valid prediction for snap_scaffold_1-snap.1977-T1
Valid prediction for GlimmerHMM_glimmerT_1562-T1
Valid prediction for GeneMark_model.2050_t
Valid prediction for snap_scaffold_1-snap.1968-T1
Valid prediction for snap_scaffold_1-snap.1991-T1
Valid prediction for snap_scaffold_1-snap.1988-T1
Valid prediction for GeneMark_model.2052_t
Valid prediction for GeneMark_model.2057_t
Valid prediction for snap_scaffold_1-snap.1975-T1
Valid prediction for GlimmerHMM_glimmerT_1561-T1
Valid prediction for pasa_asmbl_627.p1
Valid prediction for GlimmerHMM_glimmerT_1565-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29027, rend_intergenic: 13071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49828, rend_intergenic: 39302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67723, rend_intergenic: 66709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95412, rend_intergenic: 91850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174613, rend_intergenic: 162771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196728
-exon list size: 576


building trellis

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-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 29027, rend_intergenic: 13071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49828, rend_intergenic: 39302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67723, rend_intergenic: 66709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95412, rend_intergenic: 91850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174613, rend_intergenic: 162771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11749
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 11518
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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