-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_6490251-6717833

-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_17-snap.1334-T1
Valid prediction for snap_scaffold_17-snap.1328-T1
Valid prediction for Augustus_model.g27713.t1
Valid prediction for GlimmerHMM_glimmerT_41367-T1
Valid prediction for GlimmerHMM_glimmerT_41370-T1
Valid prediction for snap_scaffold_17-snap.1332-T1
Valid prediction for Augustus_model.g27703.t1
Valid prediction for GeneMark_model.71200_t
Valid prediction for GeneMark_model.71203_t
Valid prediction for snap_scaffold_17-snap.1327-T1
Valid prediction for snap_scaffold_17-snap.1325-T1
Valid prediction for GlimmerHMM_glimmerT_41381-T1
Valid prediction for GeneMark_model.71208_t
Valid prediction for snap_scaffold_17-snap.1313-T1
Valid prediction for GeneMark_model.71216_t
Valid prediction for snap_scaffold_17-snap.1335-T1
Valid prediction for GeneMark_model.71204_t
Valid prediction for GlimmerHMM_glimmerT_41360-T1
Valid prediction for GeneMark_model.71212_t
Valid prediction for CodingQuarry_transcript_21958-T1
Valid prediction for GlimmerHMM_glimmerT_41377-T1
Valid prediction for Augustus_model.g27709.t1
Valid prediction for snap_scaffold_17-snap.1312-T1
Valid prediction for GeneMark_model.71213_t
Valid prediction for snap_scaffold_17-snap.1321-T1
Valid prediction for snap_scaffold_17-snap.1326-T1
Valid prediction for snap_scaffold_17-snap.1323-T1
Valid prediction for GlimmerHMM_glimmerT_41371-T1
Valid prediction for snap_scaffold_17-snap.1319-T1
Valid prediction for GlimmerHMM_glimmerT_41379-T1
Valid prediction for GlimmerHMM_glimmerT_41355-T1
Valid prediction for snap_scaffold_17-snap.1318-T1
Valid prediction for GeneMark_model.71220_t
Valid prediction for GeneMark_model.71215_t
Couldn't classify 98117, 98206
Couldn't classify 99458, 99593
Sorry, prediction pasa_asmbl_17985.p1 fails validation.
(AGC)	 GG	98117-98206	GT	AGG
(CCA)	 AG	98322-98489	GT	TGG
(ATC)	 AG	98599-98740	GT	AGG
(TGA)	 AG	98833-99011	GT	CGG
(CAA)	 AG	99198-99343	GT	GGG
(GAA)	 AG	99458-99593	CC	AGC
-recovered pasa_asmbl_17985.p1, internal, 98322, 98489
-recovered pasa_asmbl_17985.p1, internal, 98599, 98740
-recovered pasa_asmbl_17985.p1, internal, 98833, 99011
-recovered pasa_asmbl_17985.p1, internal, 99198, 99343
Valid prediction for GeneMark_model.71198_t
Valid prediction for pasa_asmbl_17984.p1
Valid prediction for GlimmerHMM_glimmerT_41365-T1
Valid prediction for snap_scaffold_17-snap.1322-T1
Valid prediction for GlimmerHMM_glimmerT_41359-T1
Valid prediction for GeneMark_model.71217_t
Valid prediction for Augustus_model.g27711.t1
Couldn't classify 100743, 100853
Sorry, prediction pasa_asmbl_17986.p1 fails validation.
(CTG)	 AG	100743-100853	GT	AGG
(GTC)	 AG	101159-101249	GT	AGG
(ATG)	 AG	101463-101547	GT	CGG
(GAT)	 AG	101871-102012	GT	GAG
(ATC)	 AG	102105-102257	GT	AGG
(ATC)	 AG	102402-102578	GT	GGG
(GAT)	 AG	102774-102840	GT	GGG
(TGT)	 AG	102955-103002	GT	AGG
(CCA)	 AG	103112-103267	GT	TGG
(CTA)	 AG	103414-103543	GT	AGG
(GAT)	 AG	103715-103853	GT	TAG
(ATC)	 AG	103956-104003	GA	GAG
-recovered pasa_asmbl_17986.p1, initial, 101463, 101547
-recovered pasa_asmbl_17986.p1, terminal, 103956, 104003
-recovered pasa_asmbl_17986.p1, internal, 100743, 100853
-recovered pasa_asmbl_17986.p1, internal, 101159, 101249
-recovered pasa_asmbl_17986.p1, internal, 101463, 101547
-recovered pasa_asmbl_17986.p1, internal, 101871, 102012
-recovered pasa_asmbl_17986.p1, internal, 102105, 102257
-recovered pasa_asmbl_17986.p1, internal, 102402, 102578
-recovered pasa_asmbl_17986.p1, internal, 102774, 102840
-recovered pasa_asmbl_17986.p1, internal, 102955, 103002
-recovered pasa_asmbl_17986.p1, internal, 103112, 103267
-recovered pasa_asmbl_17986.p1, internal, 103414, 103543
-recovered pasa_asmbl_17986.p1, internal, 103715, 103853
Couldn't classify 113102, 113185
Couldn't classify 116509, 117566
Sorry, prediction pasa_asmbl_17989.p1 fails validation.
(AAC)	 GG	113102-113185	GT	AGG
(GGG)	 AG	113394-113544	GT	AGG
(GTT)	 AG	114611-114701	GT	AGG
(GAA)	 AG	115503-115669	GT	AGG
(GTG)	 AG	116509-117566	GG	CTG
add_exon() Sorry, pasa_asmbl_17989.p1 114611-114701-terminal-3 is invalid.
-recovered pasa_asmbl_17989.p1, terminal, 114611, 114701
-recovered pasa_asmbl_17989.p1, internal, 113394, 113544
-recovered pasa_asmbl_17989.p1, internal, 114611, 114701
-recovered pasa_asmbl_17989.p1, internal, 115503, 115669
Valid prediction for Augustus_model.g27707.t1
Couldn't classify 121142, 121284
Couldn't classify 124350, 124515
Sorry, prediction pasa_asmbl_17990.p1 fails validation.
(GGC)	 CA	121142-121284	GT	CGG
(GAG)	 AG	121453-121686	GT	AGG
(GGG)	 AG	124350-124515	GG	TGG
-recovered pasa_asmbl_17990.p1, internal, 121453, 121686
Valid prediction for Augustus_model.g27708.t1
Valid prediction for pasa_asmbl_17996.p1
Valid prediction for GlimmerHMM_glimmerT_41362-T1
Valid prediction for GlimmerHMM_glimmerT_41375-T1
Valid prediction for snap_scaffold_17-snap.1315-T1
Valid prediction for snap_scaffold_17-snap.1331-T1
Valid prediction for GlimmerHMM_glimmerT_41361-T1
Valid prediction for GeneMark_model.71222_t
Valid prediction for GeneMark_model.71219_t
Valid prediction for Augustus_model.g27712.t1
Valid prediction for snap_scaffold_17-snap.1314-T1
Valid prediction for snap_scaffold_17-snap.1320-T1
Valid prediction for Augustus_model.g27705.t1
Valid prediction for snap_scaffold_17-snap.1309-T1
Valid prediction for HiQ_model.g27719.t1
Valid prediction for pasa_asmbl_17997.p1
Valid prediction for GeneMark_model.71210_t
Valid prediction for HiQ_model.g27718.t1
Valid prediction for Augustus_model.g27722.t1
Valid prediction for GeneMark_model.71221_t
Valid prediction for GeneMark_model.71205_t
Valid prediction for GlimmerHMM_glimmerT_41363-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_41380-T1
Valid prediction for GlimmerHMM_glimmerT_41373-T1
Valid prediction for GlimmerHMM_glimmerT_41358-T1
Valid prediction for snap_scaffold_17-snap.1308-T1
Valid prediction for GlimmerHMM_glimmerT_41368-T1
Valid prediction for GeneMark_model.71195_t
Valid prediction for Augustus_model.g27702.t1
Valid prediction for GlimmerHMM_glimmerT_41376-T1
Valid prediction for Augustus_model.g27710.t1
Valid prediction for GlimmerHMM_glimmerT_41378-T1
Valid prediction for GlimmerHMM_glimmerT_41356-T1
Valid prediction for GlimmerHMM_glimmerT_41353-T1
Valid prediction for Augustus_model.g27704.t1
Valid prediction for GeneMark_model.71218_t
Couldn't classify 29362, 29541
Sorry, prediction pasa_asmbl_19024.p1 fails validation.
(ATG)	 AC	27716-27726	GT	AGG
(GGT)	 AG	28277-28397	GT	AGG
(GAA)	 AG	28513-28635	GT	TGG
(ACA)	 AG	28958-29107	GT	AGG
(GGA)	 AG	29362-29541	AA	GCA
-recovered pasa_asmbl_19024.p1, initial, 27716, 27726
-recovered pasa_asmbl_19024.p1, internal, 28277, 28397
-recovered pasa_asmbl_19024.p1, internal, 28513, 28635
-recovered pasa_asmbl_19024.p1, internal, 28958, 29107
Valid prediction for GeneMark_model.71207_t
Valid prediction for GlimmerHMM_glimmerT_41354-T1
Valid prediction for GeneMark_model.71225_t
Valid prediction for GlimmerHMM_glimmerT_41364-T1
Valid prediction for GeneMark_model.71214_t
Valid prediction for HiQ_model.g27716.t1
Valid prediction for Augustus_model.g27717.t1
Valid prediction for GlimmerHMM_glimmerT_41372-T1
Valid prediction for Augustus_model.g27706.t1
Valid prediction for GeneMark_model.71201_t
Valid prediction for snap_scaffold_17-snap.1317-T1
Valid prediction for snap_scaffold_17-snap.1329-T1
Valid prediction for snap_scaffold_17-snap.1316-T1
Valid prediction for GeneMark_model.71194_t
Valid prediction for GeneMark_model.71192_t
Valid prediction for GeneMark_model.71224_t
Valid prediction for Augustus_model.g27720.t1
Valid prediction for snap_scaffold_17-snap.1310-T1
Valid prediction for GlimmerHMM_glimmerT_41357-T1
Valid prediction for GeneMark_model.71197_t
Valid prediction for GeneMark_model.71211_t
Valid prediction for GeneMark_model.71193_t
Valid prediction for GeneMark_model.71202_t
Valid prediction for GlimmerHMM_glimmerT_41369-T1
Valid prediction for GeneMark_model.71206_t
Valid prediction for Augustus_model.g27714.t1
Valid prediction for Augustus_model.g27721.t1
Valid prediction for GeneMark_model.71223_t
Valid prediction for GeneMark_model.71199_t
Valid prediction for snap_scaffold_17-snap.1330-T1
Valid prediction for GlimmerHMM_glimmerT_41374-T1
Valid prediction for snap_scaffold_17-snap.1324-T1
Valid prediction for snap_scaffold_17-snap.1311-T1
Valid prediction for snap_scaffold_17-snap.1306-T1
Valid prediction for Augustus_model.g27715.t1
Valid prediction for GeneMark_model.71196_t
Valid prediction for GlimmerHMM_glimmerT_41366-T1
Valid prediction for snap_scaffold_17-snap.1307-T1
Valid prediction for GeneMark_model.71209_t
Valid prediction for snap_scaffold_17-snap.1333-T1
Valid prediction for pasa_asmbl_19020.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 104003, rend_intergenic: 98105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184230, rend_intergenic: 181157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222370, rend_intergenic: 218160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227583
-exon list size: 453


building trellis

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38.2    
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88.4    
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89.9    
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90.5    
90.8    
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91.4    
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93.4    
93.6    
93.8    
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95.8    
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97.4    
97.6    
97.8    
98.0    
98.2    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 104003, rend_intergenic: 98105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184230, rend_intergenic: 181157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222370, rend_intergenic: 218160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support