-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_1814547-1983830

-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_14-snap.320-T1
Valid prediction for snap_scaffold_14-snap.298-T1
Valid prediction for Augustus_model.g22929.t1
Valid prediction for GeneMark_model.58299_t
Valid prediction for snap_scaffold_14-snap.325-T1
Valid prediction for snap_scaffold_14-snap.307-T1
Valid prediction for GeneMark_model.58332_t
Valid prediction for snap_scaffold_14-snap.316-T1
Valid prediction for GlimmerHMM_glimmerT_34074-T1
Couldn't classify 141939, 141979
Couldn't classify 148898, 148978
Sorry, prediction pasa_asmbl_11814.p1 fails validation.
(CCC)	 CA	141939-141979	GT	AGG
(CTT)	 AG	144160-144244	GT	CGG
(AAC)	 AG	145387-145473	GT	CGG
(GAA)	 AG	147452-147628	GC	AGG
(GCC)	 AG	148898-148978	CA	GGC
-recovered pasa_asmbl_11814.p1, internal, 144160, 144244
-recovered pasa_asmbl_11814.p1, internal, 145387, 145473
-recovered pasa_asmbl_11814.p1, internal, 147452, 147628
Valid prediction for snap_scaffold_14-snap.304-T1
Valid prediction for GeneMark_model.58302_t
Valid prediction for GlimmerHMM_glimmerT_34077-T1
Valid prediction for GeneMark_model.58316_t
Valid prediction for GlimmerHMM_glimmerT_34091-T1
Valid prediction for GlimmerHMM_glimmerT_34087-T1
Valid prediction for GeneMark_model.58329_t
Valid prediction for GeneMark_model.58306_t
Valid prediction for Augustus_model.g22935.t1
Valid prediction for snap_scaffold_14-snap.312-T1
Valid prediction for HiQ_model.g22923.t1
Valid prediction for snap_scaffold_14-snap.303-T1
Valid prediction for GlimmerHMM_glimmerT_34083-T1
Valid prediction for GeneMark_model.58327_t
Valid prediction for snap_scaffold_14-snap.309-T1
Valid prediction for GeneMark_model.58314_t
Valid prediction for snap_scaffold_14-snap.323-T1
Valid prediction for GlimmerHMM_glimmerT_34095-T1
Valid prediction for Augustus_model.g22934.t1
Valid prediction for GlimmerHMM_glimmerT_34081-T1
Valid prediction for GeneMark_model.58334_t
Couldn't classify 154242, 154379
Sorry, prediction pasa_asmbl_11815.p1 fails validation.
(ATC)	 AG	154242-154379	GT	TGG
(CCG)	 AG	155673-155815	GT	GGG
(TTT)	 AG	156377-156575	GT	CGG
(ATC)	 AG	157837-158002	GT	CAG
(CTC)	 AG	158221-158366	GT	GGG
(CCT)	 AG	159103-159198	GC	GAG
-recovered pasa_asmbl_11815.p1, terminal, 159103, 159198
-recovered pasa_asmbl_11815.p1, internal, 154242, 154379
-recovered pasa_asmbl_11815.p1, internal, 155673, 155815
-recovered pasa_asmbl_11815.p1, internal, 156377, 156575
-recovered pasa_asmbl_11815.p1, internal, 157837, 158002
-recovered pasa_asmbl_11815.p1, internal, 158221, 158366
-recovered pasa_asmbl_11815.p1, internal, 159103, 159198
Valid prediction for snap_scaffold_14-snap.315-T1
Valid prediction for GeneMark_model.58333_t
Valid prediction for Augustus_model.g22937.t1
Valid prediction for GeneMark_model.58293_t
Valid prediction for GeneMark_model.58320_t
Valid prediction for GlimmerHMM_glimmerT_34076-T1
Valid prediction for GeneMark_model.58309_t
Valid prediction for snap_scaffold_14-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_34080-T1
Couldn't classify 50985, 51017
Couldn't classify 59449, 59505
Sorry, prediction pasa_asmbl_11810.p2 fails validation.
(CTG)	 AG	50985-51017	GT	AGG
(TTC)	 AG	52780-52869	GT	TGG
(GTG)	 AG	54011-54111	GT	ACG
(GAA)	 AG	54415-54543	GT	CAG
(GCT)	 AG	56716-56824	GT	AGG
(GGC)	 AG	59449-59505	CC	ATC
-recovered pasa_asmbl_11810.p2, internal, 50985, 51017
-recovered pasa_asmbl_11810.p2, internal, 52780, 52869
-recovered pasa_asmbl_11810.p2, internal, 54011, 54111
-recovered pasa_asmbl_11810.p2, internal, 54415, 54543
-recovered pasa_asmbl_11810.p2, internal, 56716, 56824
Valid prediction for Augustus_model.g22924.t1
Valid prediction for GeneMark_model.58325_t
Valid prediction for snap_scaffold_14-snap.314-T1
Valid prediction for snap_scaffold_14-snap.318-T1
Couldn't classify 127563, 127620
Couldn't classify 132072, 132120
Sorry, prediction pasa_asmbl_11811.p1 fails validation.
(TAC)	 GG	127563-127620	GT	AGG
(GTC)	 AG	128841-128989	GT	TGG
(TTT)	 AG	130177-130262	GT	ATG
(TCT)	 AG	130637-130793	GT	TGG
(AAC)	 AG	131727-131767	GT	AGG
(GTA)	 AG	132072-132120	GA	CAG
-recovered pasa_asmbl_11811.p1, internal, 128841, 128989
-recovered pasa_asmbl_11811.p1, internal, 130177, 130262
-recovered pasa_asmbl_11811.p1, internal, 130637, 130793
-recovered pasa_asmbl_11811.p1, internal, 131727, 131767
Valid prediction for GeneMark_model.58323_t
Valid prediction for GeneMark_model.58318_t
Couldn't classify 24865, 24922
Couldn't classify 32848, 32921
Sorry, prediction pasa_asmbl_11809.p1 fails validation.
(GAC)	 GT	24865-24922	GT	AGG
(GCT)	 AG	25278-25318	GT	AAG
(GGC)	 AG	25697-25752	GT	GGG
(GCA)	 AG	26411-26507	GT	TAG
(GGG)	 AG	27059-27207	GT	AAG
(GTA)	 AG	28597-28732	GT	GGG
(TCG)	 AG	30333-30490	GT	AGG
(TGA)	 AG	30673-30754	GT	CGG
(GAC)	 AG	31303-31438	GT	AGG
(TAA)	 AG	32848-32921	TG	CGT
-recovered pasa_asmbl_11809.p1, internal, 25278, 25318
-recovered pasa_asmbl_11809.p1, internal, 25697, 25752
-recovered pasa_asmbl_11809.p1, internal, 26411, 26507
-recovered pasa_asmbl_11809.p1, internal, 27059, 27207
-recovered pasa_asmbl_11809.p1, internal, 28597, 28732
-recovered pasa_asmbl_11809.p1, internal, 30333, 30490
-recovered pasa_asmbl_11809.p1, internal, 30673, 30754
-recovered pasa_asmbl_11809.p1, internal, 31303, 31438
Couldn't classify 36438, 36576
Couldn't classify 41187, 41258
Sorry, prediction pasa_asmbl_12700.p1 fails validation.
(CTA)	 GG	36438-36576	GT	AGG
(GTC)	 AG	38156-38281	GT	AGG
(GCG)	 AG	38417-38541	GT	AGG
(AAC)	 AG	40646-40744	GT	AGG
(GTC)	 AG	41187-41258	TG	ACT
-recovered pasa_asmbl_12700.p1, internal, 38156, 38281
-recovered pasa_asmbl_12700.p1, internal, 38417, 38541
-recovered pasa_asmbl_12700.p1, internal, 40646, 40744
Valid prediction for snap_scaffold_14-snap.301-T1
Valid prediction for GlimmerHMM_glimmerT_34078-T1
Valid prediction for GlimmerHMM_glimmerT_34092-T1
Valid prediction for GlimmerHMM_glimmerT_34085-T1
Valid prediction for GeneMark_model.58301_t
Valid prediction for snap_scaffold_14-snap.297-T1
Valid prediction for snap_scaffold_14-snap.317-T1
Valid prediction for Augustus_model.g22933.t1
Valid prediction for GeneMark_model.58311_t
Valid prediction for GeneMark_model.58297_t
Valid prediction for snap_scaffold_14-snap.319-T1
Valid prediction for snap_scaffold_14-snap.296-T1
Valid prediction for snap_scaffold_14-snap.305-T1
Valid prediction for Augustus_model.g22932.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_14-snap.300-T1
Valid prediction for snap_scaffold_14-snap.299-T1
Valid prediction for GeneMark_model.58315_t
Valid prediction for GeneMark_model.58319_t
Valid prediction for GeneMark_model.58313_t
Valid prediction for Augustus_model.g22931.t1
Valid prediction for snap_scaffold_14-snap.322-T1
Valid prediction for GeneMark_model.58310_t
Valid prediction for GeneMark_model.58303_t
Valid prediction for GeneMark_model.58304_t
Valid prediction for GeneMark_model.58317_t
Valid prediction for snap_scaffold_14-snap.311-T1
Valid prediction for GeneMark_model.58331_t
Valid prediction for snap_scaffold_14-snap.326-T1
Valid prediction for GeneMark_model.58312_t
Valid prediction for GlimmerHMM_glimmerT_34096-T1
Valid prediction for Augustus_model.g22925.t1
Valid prediction for GeneMark_model.58307_t
Valid prediction for GlimmerHMM_glimmerT_34088-T1
Valid prediction for snap_scaffold_14-snap.324-T1
Valid prediction for GeneMark_model.58300_t
Valid prediction for GeneMark_model.58292_t
Valid prediction for GeneMark_model.58326_t
Valid prediction for snap_scaffold_14-snap.295-T1
Valid prediction for snap_scaffold_14-snap.308-T1
Valid prediction for GeneMark_model.58294_t
Valid prediction for GlimmerHMM_glimmerT_34084-T1
Valid prediction for GeneMark_model.58324_t
Valid prediction for Augustus_model.g22927.t1
Valid prediction for GeneMark_model.58308_t
Valid prediction for GeneMark_model.58330_t
Valid prediction for GeneMark_model.58328_t
Valid prediction for snap_scaffold_14-snap.306-T1
Valid prediction for GlimmerHMM_glimmerT_34082-T1
Valid prediction for GlimmerHMM_glimmerT_34089-T1
Valid prediction for Augustus_model.g22928.t1
Valid prediction for snap_scaffold_14-snap.327-T1
Valid prediction for Augustus_model.g22926.t1
Valid prediction for GeneMark_model.58322_t
Valid prediction for snap_scaffold_14-snap.313-T1
Valid prediction for snap_scaffold_14-snap.302-T1
Valid prediction for GlimmerHMM_glimmerT_34094-T1
Valid prediction for GlimmerHMM_glimmerT_34086-T1
Valid prediction for Augustus_model.g22930.t1
Valid prediction for Augustus_model.g22922.t1
Valid prediction for GlimmerHMM_glimmerT_34079-T1
Valid prediction for GeneMark_model.58295_t
Valid prediction for GlimmerHMM_glimmerT_34073-T1
Valid prediction for GeneMark_model.58305_t
Valid prediction for GeneMark_model.58298_t
Valid prediction for GlimmerHMM_glimmerT_34090-T1
Valid prediction for Augustus_model.g22936.t1
Valid prediction for GlimmerHMM_glimmerT_34093-T1
Valid prediction for GlimmerHMM_glimmerT_34075-T1
Valid prediction for snap_scaffold_14-snap.321-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36599, rend_intergenic: 25643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49714, rend_intergenic: 43079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64088, rend_intergenic: 59863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87820, rend_intergenic: 84123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99374, rend_intergenic: 97674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154871, rend_intergenic: 144668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159787, rend_intergenic: 156836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169284
-exon list size: 540


building trellis

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99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 36599, rend_intergenic: 25643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49714, rend_intergenic: 43079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64088, rend_intergenic: 59863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87820, rend_intergenic: 84123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99374, rend_intergenic: 97674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154871, rend_intergenic: 144668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159787, rend_intergenic: 156836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 21296
-exon list size: 20


building trellis

4.5    
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18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-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 - 18735
-exon list size: 16


building trellis

5.6    
11.1    
16.7    
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27.8    
33.3    
38.9    
44.4    
50.0    
55.6    
61.1    
66.7    
72.2    
77.8    
83.3    
88.9    
94.4    
-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 - 12459
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-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 1669 - 12459
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-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