-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_3022316-3194498

-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.70408_t
Valid prediction for GeneMark_model.70413_t
Valid prediction for GeneMark_model.70423_t
Valid prediction for GeneMark_model.70415_t
Valid prediction for GlimmerHMM_glimmerT_40903-T1
Valid prediction for snap_scaffold_17-snap.660-T1
Couldn't classify 167764, 167957
Sorry, prediction pasa_asmbl_17835.p1 fails validation.
(ACC)	 AG	167764-167957	GT	AGG
(TGA)	 AG	170425-170578	CA	GAC
-recovered pasa_asmbl_17835.p1, terminal, 170425, 170578
-recovered pasa_asmbl_17835.p1, internal, 167764, 167957
Valid prediction for snap_scaffold_17-snap.638-T1
Valid prediction for Augustus_model.g27385.t1
Valid prediction for Augustus_model.g27382.t1
Valid prediction for GeneMark_model.70422_t
Valid prediction for GeneMark_model.70440_t
Valid prediction for snap_scaffold_17-snap.668-T1
Valid prediction for snap_scaffold_17-snap.651-T1
Valid prediction for GlimmerHMM_glimmerT_40899-T1
Valid prediction for GeneMark_model.70406_t
Valid prediction for GeneMark_model.70432_t
Valid prediction for GlimmerHMM_glimmerT_40898-T1
Valid prediction for snap_scaffold_17-snap.650-T1
Valid prediction for snap_scaffold_17-snap.671-T1
Valid prediction for snap_scaffold_17-snap.645-T1
Valid prediction for Augustus_model.g27391.t1
Valid prediction for Augustus_model.g27392.t1
Valid prediction for snap_scaffold_17-snap.664-T1
Valid prediction for GlimmerHMM_glimmerT_40907-T1
Valid prediction for snap_scaffold_17-snap.659-T1
Valid prediction for GeneMark_model.70420_t
Valid prediction for GeneMark_model.70434_t
Couldn't classify 895, 1014
Sorry, prediction pasa_asmbl_17828.p1 fails validation.
(GTT)	 AG	895-1014	GT	AGG
(CAC)	 AG	1221-1304	GT	AGG
(AAC)	 AG	1431-1604	GT	TGG
(GCT)	 AG	2063-2144	GT	AGG
(GGT)	 AG	2520-2626	GT	CAG
(GAT)	 AG	2847-2889	GT	TGG
(GCG)	 AG	3003-3162	GT	AGG
(GGC)	 AG	3442-3622	CT	AGC
-recovered pasa_asmbl_17828.p1, terminal, 3442, 3622
-recovered pasa_asmbl_17828.p1, internal, 895, 1014
-recovered pasa_asmbl_17828.p1, internal, 1221, 1304
-recovered pasa_asmbl_17828.p1, internal, 1431, 1604
-recovered pasa_asmbl_17828.p1, internal, 2063, 2144
-recovered pasa_asmbl_17828.p1, internal, 2520, 2626
-recovered pasa_asmbl_17828.p1, internal, 2847, 2889
-recovered pasa_asmbl_17828.p1, internal, 3003, 3162
Valid prediction for GeneMark_model.70436_t
Valid prediction for GeneMark_model.70410_t
Valid prediction for snap_scaffold_17-snap.642-T1
Valid prediction for GeneMark_model.70426_t
Valid prediction for GeneMark_model.70404_t
Valid prediction for GlimmerHMM_glimmerT_40897-T1
Valid prediction for snap_scaffold_17-snap.669-T1
Valid prediction for GeneMark_model.70411_t
Valid prediction for snap_scaffold_17-snap.646-T1
Valid prediction for GeneMark_model.70437_t
Valid prediction for snap_scaffold_17-snap.666-T1
Valid prediction for GeneMark_model.70401_t
Valid prediction for Augustus_model.g27390.t1
Valid prediction for GeneMark_model.70418_t
Valid prediction for GeneMark_model.70439_t
Valid prediction for snap_scaffold_17-snap.636-T1
Valid prediction for snap_scaffold_17-snap.635-T1
Valid prediction for Augustus_model.g27393.t1
Valid prediction for snap_scaffold_17-snap.654-T1
Valid prediction for snap_scaffold_17-snap.639-T1
Valid prediction for GeneMark_model.70430_t
Valid prediction for Augustus_model.g27383.t1
Valid prediction for snap_scaffold_17-snap.663-T1
Valid prediction for snap_scaffold_17-snap.652-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 snap_scaffold_17-snap.640-T1
Valid prediction for GlimmerHMM_glimmerT_40906-T1
Valid prediction for GeneMark_model.70402_t
Valid prediction for snap_scaffold_17-snap.661-T1
Valid prediction for GlimmerHMM_glimmerT_40900-T1
Couldn't classify 157105, 157413
Sorry, prediction pasa_asmbl_18839.p1 fails validation.
(ATG)	 GG	153645-155552	GT	AGG
(GTG)	 AG	157105-157413	GA	GGG
-recovered pasa_asmbl_18839.p1, initial, 153645, 155552
Valid prediction for Augustus_model.g27389.t1
Valid prediction for snap_scaffold_17-snap.643-T1
Valid prediction for GlimmerHMM_glimmerT_40893-T1
Valid prediction for Augustus_model.g27384.t1
Valid prediction for GeneMark_model.70409_t
Valid prediction for GeneMark_model.70405_t
Valid prediction for GlimmerHMM_glimmerT_40904-T1
Valid prediction for snap_scaffold_17-snap.649-T1
Valid prediction for GlimmerHMM_glimmerT_40890-T1
Valid prediction for snap_scaffold_17-snap.657-T1
Valid prediction for GeneMark_model.70417_t
Valid prediction for snap_scaffold_17-snap.653-T1
Valid prediction for snap_scaffold_17-snap.662-T1
Valid prediction for GeneMark_model.70435_t
Valid prediction for snap_scaffold_17-snap.655-T1
Valid prediction for snap_scaffold_17-snap.658-T1
Valid prediction for Augustus_model.g27381.t1
Valid prediction for GeneMark_model.70438_t
Valid prediction for GeneMark_model.70428_t
Valid prediction for GeneMark_model.70412_t
Couldn't classify 64089, 64126
Sorry, prediction pasa_asmbl_18842.p1 fails validation.
(ACC)	 CC	64089-64126	GT	AAG
(GGA)	 AG	64374-64497	GT	AGG
(ATA)	 AG	65465-65604	GT	GCG
(GTC)	 AG	65839-65983	TA	AGT
-recovered pasa_asmbl_18842.p1, terminal, 65839, 65983
-recovered pasa_asmbl_18842.p1, internal, 64374, 64497
-recovered pasa_asmbl_18842.p1, internal, 65465, 65604
Valid prediction for GlimmerHMM_glimmerT_40894-T1
Valid prediction for GeneMark_model.70425_t
Valid prediction for HiQ_model.g27388.t1
Valid prediction for GlimmerHMM_glimmerT_40901-T1
Valid prediction for GeneMark_model.70407_t
Couldn't classify 153645, 155143
Couldn't classify 155180, 155552
Sorry, prediction CodingQuarry_transcript_21878-T1 fails validation.
(ATG)	 GG	153645-155143	AG	ACA
(CTA)	 AC	155180-155552	GT	AGG
(GTG)	 AG	157105-157695	GG	GAG
-recovered CodingQuarry_transcript_21878-T1, terminal, 157105, 157695
Valid prediction for snap_scaffold_17-snap.641-T1
Valid prediction for snap_scaffold_17-snap.665-T1
Valid prediction for GlimmerHMM_glimmerT_40896-T1
Valid prediction for snap_scaffold_17-snap.644-T1
Valid prediction for GeneMark_model.70414_t
Valid prediction for snap_scaffold_17-snap.648-T1
Valid prediction for GeneMark_model.70427_t
Valid prediction for GeneMark_model.70433_t
Valid prediction for GlimmerHMM_glimmerT_40895-T1
Valid prediction for HiQ_model.g27387.t1
Valid prediction for GlimmerHMM_glimmerT_40905-T1
Valid prediction for GlimmerHMM_glimmerT_40891-T1
Valid prediction for HiQ_model.g27380.t1
Valid prediction for GeneMark_model.70419_t
Valid prediction for pasa_asmbl_18846.p1
Valid prediction for GeneMark_model.70424_t
Valid prediction for GlimmerHMM_glimmerT_40892-T1
Valid prediction for GeneMark_model.70416_t
Valid prediction for snap_scaffold_17-snap.647-T1
Valid prediction for GeneMark_model.70431_t
Valid prediction for Augustus_model.g27386.t1
Valid prediction for CodingQuarry_transcript_21879-T1
Valid prediction for CodingQuarry_transcript_21880-T1
Valid prediction for GeneMark_model.70429_t
Valid prediction for GeneMark_model.70421_t
Valid prediction for snap_scaffold_17-snap.670-T1
Valid prediction for GeneMark_model.70403_t
Couldn't classify 50831, 50922
Couldn't classify 51509, 51621
Sorry, prediction pasa_asmbl_18848.p1 fails validation.
(GCA)	 TG	50831-50922	GT	CGG
(GGA)	 AG	51173-51285	GT	CAG
(CGG)	 AG	51509-51621	AA	AGA
-recovered pasa_asmbl_18848.p1, internal, 51173, 51285
Valid prediction for snap_scaffold_17-snap.637-T1
Valid prediction for snap_scaffold_17-snap.667-T1
Valid prediction for GlimmerHMM_glimmerT_40902-T1
Valid prediction for snap_scaffold_17-snap.656-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15083, rend_intergenic: 14489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18539, rend_intergenic: 15482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31531, rend_intergenic: 19157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38467, rend_intergenic: 32776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51317, rend_intergenic: 40760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59116, rend_intergenic: 52010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98239, rend_intergenic: 88919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135891, rend_intergenic: 131632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141178, rend_intergenic: 138357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145555, rend_intergenic: 141434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150371, rend_intergenic: 146557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156938, rend_intergenic: 154628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167939, rend_intergenic: 165073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172183
-exon list size: 511


building trellis

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98.1    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 15083, rend_intergenic: 14489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18539, rend_intergenic: 15482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31531, rend_intergenic: 19157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38467, rend_intergenic: 32776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51317, rend_intergenic: 40760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59116, rend_intergenic: 52010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98239, rend_intergenic: 88919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135891, rend_intergenic: 131632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141178, rend_intergenic: 138357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145555, rend_intergenic: 141434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150371, rend_intergenic: 146557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156938, rend_intergenic: 154628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167939, rend_intergenic: 165073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support