-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_3717833-3930884

-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 snap_scaffold_4-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_9304-T1
Valid prediction for snap_scaffold_4-snap.870-T1
Valid prediction for CodingQuarry_transcript_48820-T1
Valid prediction for HiQ_model.g6050.t1
Valid prediction for GlimmerHMM_glimmerT_9325-T1
Valid prediction for GeneMark_model.15361_t
Valid prediction for GlimmerHMM_glimmerT_9324-T1
Valid prediction for Augustus_model.g6040.t1
Valid prediction for GlimmerHMM_glimmerT_9327-T1
Valid prediction for snap_scaffold_4-snap.878-T1
Valid prediction for GlimmerHMM_glimmerT_9321-T1
Valid prediction for snap_scaffold_4-snap.884-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g6051.t1
Valid prediction for Augustus_model.g6048.t1
Valid prediction for GeneMark_model.15326_t
Valid prediction for snap_scaffold_4-snap.887-T1
Valid prediction for Augustus_model.g6049.t1
Valid prediction for Augustus_model.g6055.t1
Valid prediction for GeneMark_model.15334_t
Valid prediction for GlimmerHMM_glimmerT_9315-T1
Valid prediction for snap_scaffold_4-snap.885-T1
Couldn't classify 116867, 116912
Couldn't classify 120170, 120183
Sorry, prediction pasa_asmbl_42528.p1 fails validation.
(TCA)	 GT	116867-116912	GT	AGG
(ATC)	 AG	118574-118625	GT	AGG
(CGT)	 AG	118715-118787	GT	ACG
(ACC)	 AG	119221-119354	GT	ATG
(GGG)	 AG	119676-119713	GT	AGG
(AGT)	 AG	119859-120053	GT	AGG
(GGA)	 AG	120170-120183	GG	GCG
-recovered pasa_asmbl_42528.p1, internal, 118574, 118625
-recovered pasa_asmbl_42528.p1, internal, 118715, 118787
-recovered pasa_asmbl_42528.p1, internal, 119221, 119354
-recovered pasa_asmbl_42528.p1, internal, 119676, 119713
-recovered pasa_asmbl_42528.p1, internal, 119859, 120053
Valid prediction for snap_scaffold_4-snap.865-T1
Valid prediction for GeneMark_model.15335_t
Valid prediction for pasa_asmbl_42530.p1
Valid prediction for GeneMark_model.15338_t
Valid prediction for Augustus_model.g6037.t1
Valid prediction for GeneMark_model.15329_t
Valid prediction for GeneMark_model.15354_t
Valid prediction for snap_scaffold_4-snap.893-T1
Valid prediction for snap_scaffold_4-snap.858-T1
Valid prediction for pasa_asmbl_42532.p1
Valid prediction for GlimmerHMM_glimmerT_9307-T1
Valid prediction for GlimmerHMM_glimmerT_9332-T1
Valid prediction for GeneMark_model.15342_t
Valid prediction for GeneMark_model.15344_t
Valid prediction for GeneMark_model.15357_t
Valid prediction for snap_scaffold_4-snap.886-T1
Couldn't classify 139991, 140021
Couldn't classify 140540, 140726
Sorry, prediction pasa_asmbl_43584.p1 fails validation.
(GTG)	 GA	139991-140021	GT	GGG
(GTG)	 AG	140173-140356	GT	AAG
(CAT)	 AG	140540-140726	AC	CAA
-recovered pasa_asmbl_43584.p1, internal, 140173, 140356
Valid prediction for GlimmerHMM_glimmerT_9322-T1
Valid prediction for snap_scaffold_4-snap.864-T1
Valid prediction for snap_scaffold_4-snap.856-T1
Valid prediction for GeneMark_model.15346_t
Valid prediction for GlimmerHMM_glimmerT_9312-T1
Valid prediction for Augustus_model.g6043.t1
Valid prediction for GlimmerHMM_glimmerT_9316-T1
Valid prediction for GlimmerHMM_glimmerT_9331-T1
Valid prediction for snap_scaffold_4-snap.850-T1
Valid prediction for snap_scaffold_4-snap.888-T1
Valid prediction for GeneMark_model.15349_t
Valid prediction for GeneMark_model.15341_t
Valid prediction for GeneMark_model.15348_t
Valid prediction for snap_scaffold_4-snap.873-T1
Valid prediction for snap_scaffold_4-snap.871-T1
Valid prediction for snap_scaffold_4-snap.869-T1
Valid prediction for Augustus_model.g6046.t1
Valid prediction for GeneMark_model.15352_t
Valid prediction for GeneMark_model.15350_t
Valid prediction for snap_scaffold_4-snap.881-T1
Valid prediction for GeneMark_model.15332_t
Valid prediction for GeneMark_model.15327_t
Couldn't classify 120442, 120592
Sorry, prediction pasa_asmbl_42529.p1 fails validation.
(CAT)	 GG	120442-120592	GT	AGG
(CCT)	 AG	121244-121330	GT	AAG
(GTT)	 AG	121709-121802	GT	AGG
(AAG)	 AG	122001-122041	GT	AGG
(GCT)	 AG	122146-122253	GT	CGG
(ACT)	 AG	123957-124393	CC	GAC
-recovered pasa_asmbl_42529.p1, terminal, 123957, 124393
-recovered pasa_asmbl_42529.p1, internal, 121244, 121330
-recovered pasa_asmbl_42529.p1, internal, 121709, 121802
-recovered pasa_asmbl_42529.p1, internal, 122001, 122041
-recovered pasa_asmbl_42529.p1, internal, 122146, 122253
Valid prediction for GlimmerHMM_glimmerT_9319-T1
Valid prediction for GeneMark_model.15356_t
Valid prediction for snap_scaffold_4-snap.851-T1
Valid prediction for GlimmerHMM_glimmerT_9310-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_9308-T1
Valid prediction for Augustus_model.g6033.t1
Valid prediction for snap_scaffold_4-snap.848-T1
Valid prediction for GeneMark_model.15355_t
Valid prediction for snap_scaffold_4-snap.866-T1
Valid prediction for GlimmerHMM_glimmerT_9305-T1
Valid prediction for Augustus_model.g6039.t1
Valid prediction for GlimmerHMM_glimmerT_9323-T1
Valid prediction for snap_scaffold_4-snap.859-T1
Valid prediction for snap_scaffold_4-snap.877-T1
Valid prediction for snap_scaffold_4-snap.854-T1
Valid prediction for snap_scaffold_4-snap.855-T1
Valid prediction for snap_scaffold_4-snap.890-T1
Valid prediction for Augustus_model.g6034.t1
Valid prediction for snap_scaffold_4-snap.847-T1
Valid prediction for GeneMark_model.15362_t
Valid prediction for Augustus_model.g6052.t1
Valid prediction for Augustus_model.g6047.t1
Valid prediction for GeneMark_model.15331_t
Valid prediction for Augustus_model.g6035.t1
Valid prediction for snap_scaffold_4-snap.895-T1
Valid prediction for snap_scaffold_4-snap.853-T1
Valid prediction for pasa_asmbl_41204.p1
Valid prediction for GlimmerHMM_glimmerT_9314-T1
Valid prediction for snap_scaffold_4-snap.863-T1
Valid prediction for Augustus_model.g6036.t1
Valid prediction for GlimmerHMM_glimmerT_9329-T1
Valid prediction for GlimmerHMM_glimmerT_9309-T1
Valid prediction for GeneMark_model.15340_t
Valid prediction for snap_scaffold_4-snap.857-T1
Valid prediction for snap_scaffold_4-snap.874-T1
Valid prediction for CodingQuarry_transcript_48825-T1
Valid prediction for snap_scaffold_4-snap.882-T1
Valid prediction for snap_scaffold_4-snap.861-T1
Valid prediction for GeneMark_model.15336_t
Valid prediction for snap_scaffold_4-snap.879-T1
Valid prediction for GlimmerHMM_glimmerT_9318-T1
Valid prediction for Augustus_model.g6041.t1
Valid prediction for snap_scaffold_4-snap.862-T1
Valid prediction for GeneMark_model.15351_t
Valid prediction for GeneMark_model.15343_t
Valid prediction for Augustus_model.g6042.t1
Valid prediction for GlimmerHMM_glimmerT_9326-T1
Valid prediction for snap_scaffold_4-snap.849-T1
Valid prediction for Augustus_model.g6038.t1
Valid prediction for snap_scaffold_4-snap.897-T1
Valid prediction for Augustus_model.g6059.t1
Valid prediction for snap_scaffold_4-snap.892-T1
Valid prediction for snap_scaffold_4-snap.899-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.898-T1
Valid prediction for snap_scaffold_4-snap.876-T1
Valid prediction for GlimmerHMM_glimmerT_9313-T1
Valid prediction for CodingQuarry_transcript_48823-T1
Valid prediction for Augustus_model.g6053.t1
Couldn't classify 18418, 20964
Sorry, prediction pasa_asmbl_41207.p1 fails validation.
(ATG)	 TA	18418-20964	GG	CAG
Valid prediction for GlimmerHMM_glimmerT_9334-T1
Valid prediction for GeneMark_model.15353_t
Valid prediction for snap_scaffold_4-snap.868-T1
Valid prediction for snap_scaffold_4-snap.867-T1
Valid prediction for snap_scaffold_4-snap.860-T1
Valid prediction for GlimmerHMM_glimmerT_9306-T1
Valid prediction for Augustus_model.g6058.t1
Couldn't classify 59780, 60895
Sorry, prediction pasa_asmbl_41199.p1 fails validation.
(AAG)	 CA	59780-60895	AA	AGA
Valid prediction for Augustus_model.g6057.t1
Valid prediction for GeneMark_model.15363_t
Valid prediction for GlimmerHMM_glimmerT_9303-T1
Valid prediction for Augustus_model.g6056.t1
Valid prediction for Augustus_model.g6060.t1
Valid prediction for GlimmerHMM_glimmerT_9311-T1
Valid prediction for GlimmerHMM_glimmerT_9317-T1
Valid prediction for GeneMark_model.15359_t
Valid prediction for snap_scaffold_4-snap.896-T1
Valid prediction for Augustus_model.g6044.t1
Valid prediction for GeneMark_model.15325_t
Valid prediction for Augustus_model.g6045.t1
Valid prediction for snap_scaffold_4-snap.889-T1
Valid prediction for Augustus_model.g6054.t1
Valid prediction for GeneMark_model.15339_t
Valid prediction for GeneMark_model.15358_t
Valid prediction for snap_scaffold_4-snap.880-T1
Couldn't classify 62381, 63598
Sorry, prediction pasa_asmbl_41198.p1 fails validation.
(GTG)	 CA	62381-63598	AG	GAA
Valid prediction for snap_scaffold_4-snap.891-T1
Valid prediction for snap_scaffold_4-snap.872-T1
Valid prediction for GeneMark_model.15330_t
Valid prediction for CodingQuarry_transcript_48824-T1
Valid prediction for Augustus_model.g6032.t1
Valid prediction for GeneMark_model.15337_t
Valid prediction for snap_scaffold_4-snap.852-T1
Valid prediction for snap_scaffold_4-snap.883-T1
Valid prediction for GlimmerHMM_glimmerT_9320-T1
Valid prediction for GlimmerHMM_glimmerT_9335-T1
Valid prediction for GlimmerHMM_glimmerT_9328-T1
Valid prediction for GlimmerHMM_glimmerT_9330-T1
Valid prediction for GeneMark_model.15328_t
Valid prediction for GlimmerHMM_glimmerT_9333-T1
Valid prediction for GeneMark_model.15347_t
Valid prediction for GeneMark_model.15360_t
Valid prediction for GeneMark_model.15345_t
Valid prediction for GlimmerHMM_glimmerT_9336-T1
Valid prediction for snap_scaffold_4-snap.894-T1
Valid prediction for GeneMark_model.15333_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15013, rend_intergenic: 8388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28562, rend_intergenic: 24616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50832, rend_intergenic: 49386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59531, rend_intergenic: 55757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82243, rend_intergenic: 78583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83514, rend_intergenic: 82393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87902, rend_intergenic: 83923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100346, rend_intergenic: 94119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213052
-exon list size: 713


building trellis

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88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 49 predictions from path traversal
Error with prediction: snap lend_intergenic: 15013, rend_intergenic: 8388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28562, rend_intergenic: 24616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50832, rend_intergenic: 49386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59531, rend_intergenic: 55757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82243, rend_intergenic: 78583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83514, rend_intergenic: 82393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87902, rend_intergenic: 83923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100346, rend_intergenic: 94119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 200941 - 213052
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-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