-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_10834681-11172824

-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 Augustus_model.g23153.t1
Valid prediction for Augustus_model.g23125.t1
Valid prediction for GlimmerHMM_glimmerT_34648-T1
Valid prediction for GlimmerHMM_glimmerT_34650-T1
Valid prediction for Augustus_model.g23140.t1
Valid prediction for snap_scaffold_14-snap.2278-T1
Valid prediction for GlimmerHMM_glimmerT_34642-T1
Valid prediction for GlimmerHMM_glimmerT_34645-T1
Valid prediction for snap_scaffold_14-snap.2221-T1
Valid prediction for GlimmerHMM_glimmerT_34652-T1
Valid prediction for snap_scaffold_14-snap.2234-T1
Valid prediction for snap_scaffold_14-snap.2241-T1
Valid prediction for snap_scaffold_14-snap.2229-T1
Valid prediction for Augustus_model.g23134.t1
Valid prediction for snap_scaffold_14-snap.2280-T1
Valid prediction for GlimmerHMM_glimmerT_34656-T1
Valid prediction for GlimmerHMM_glimmerT_34628-T1
Valid prediction for snap_scaffold_14-snap.2231-T1
Valid prediction for snap_scaffold_14-snap.2236-T1
Valid prediction for snap_scaffold_14-snap.2246-T1
Valid prediction for Augustus_model.g23124.t1
Couldn't classify 130270, 130428
Sorry, prediction pasa_asmbl_12356.p1 fails validation.
(GTG)	 CG	130270-130428	GT	CGG
(AGT)	 AG	130713-130889	GT	TGG
(ATT)	 AG	131043-131247	GT	AGG
(ACC)	 AG	131594-131752	GT	AGG
(GAG)	 AG	131889-132085	CA	AGC
-recovered pasa_asmbl_12356.p1, terminal, 131889, 132085
-recovered pasa_asmbl_12356.p1, internal, 130713, 130889
-recovered pasa_asmbl_12356.p1, internal, 131043, 131247
-recovered pasa_asmbl_12356.p1, internal, 131594, 131752
Valid prediction for GlimmerHMM_glimmerT_34655-T1
Valid prediction for snap_scaffold_14-snap.2247-T1
Valid prediction for Augustus_model.g23131.t1
Valid prediction for snap_scaffold_14-snap.2252-T1
Valid prediction for GlimmerHMM_glimmerT_34623-T1
Valid prediction for Augustus_model.g23138.t1
Valid prediction for snap_scaffold_14-snap.2254-T1
Valid prediction for snap_scaffold_14-snap.2267-T1
Valid prediction for Augustus_model.g23126.t1
Valid prediction for snap_scaffold_14-snap.2266-T1
Valid prediction for snap_scaffold_14-snap.2227-T1
Valid prediction for GlimmerHMM_glimmerT_34640-T1
Valid prediction for GlimmerHMM_glimmerT_34647-T1
Valid prediction for pasa_asmbl_12360.p1
Valid prediction for snap_scaffold_14-snap.2272-T1
Valid prediction for GlimmerHMM_glimmerT_34654-T1
Valid prediction for GlimmerHMM_glimmerT_34619-T1
Valid prediction for snap_scaffold_14-snap.2263-T1
Valid prediction for snap_scaffold_14-snap.2277-T1
Valid prediction for snap_scaffold_14-snap.2220-T1
Valid prediction for snap_scaffold_14-snap.2224-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_34630-T1
Valid prediction for GlimmerHMM_glimmerT_34641-T1
Couldn't classify 293209, 293416
Sorry, prediction pasa_asmbl_12364.p1 fails validation.
(GTT)	 AG	293209-293416	GT	AGG
(GTG)	 AG	295172-295342	GT	CGG
(GAT)	 AG	295674-295763	GT	TGG
(GTG)	 AG	295967-296205	GT	AGG
(GTA)	 AG	297917-298105	GA	GAG
-recovered pasa_asmbl_12364.p1, terminal, 297917, 298105
-recovered pasa_asmbl_12364.p1, internal, 293209, 293416
-recovered pasa_asmbl_12364.p1, internal, 295172, 295342
-recovered pasa_asmbl_12364.p1, internal, 295674, 295763
-recovered pasa_asmbl_12364.p1, internal, 295967, 296205
Valid prediction for Augustus_model.g23152.t1
Valid prediction for snap_scaffold_14-snap.2273-T1
Valid prediction for Augustus_model.g23148.t1
Valid prediction for Augustus_model.g23129.t1
Valid prediction for GlimmerHMM_glimmerT_34646-T1
Valid prediction for snap_scaffold_14-snap.2256-T1
Valid prediction for Augustus_model.g23130.t1
Valid prediction for GlimmerHMM_glimmerT_34634-T1
Valid prediction for snap_scaffold_14-snap.2251-T1
Valid prediction for GlimmerHMM_glimmerT_34631-T1
Valid prediction for GlimmerHMM_glimmerT_34636-T1
Valid prediction for snap_scaffold_14-snap.2276-T1
Valid prediction for Augustus_model.g23144.t1
Valid prediction for snap_scaffold_14-snap.2279-T1
Valid prediction for GlimmerHMM_glimmerT_34617-T1
Valid prediction for GlimmerHMM_glimmerT_34624-T1
Valid prediction for snap_scaffold_14-snap.2242-T1
Valid prediction for snap_scaffold_14-snap.2245-T1
Valid prediction for Augustus_model.g23128.t1
Valid prediction for Augustus_model.g23133.t1
Valid prediction for snap_scaffold_14-snap.2238-T1
Valid prediction for snap_scaffold_14-snap.2249-T1
Valid prediction for snap_scaffold_14-snap.2261-T1
Valid prediction for GlimmerHMM_glimmerT_34639-T1
Valid prediction for Augustus_model.g23151.t1
Valid prediction for Augustus_model.g23135.t1
Valid prediction for snap_scaffold_14-snap.2269-T1
Valid prediction for snap_scaffold_14-snap.2243-T1
Valid prediction for snap_scaffold_14-snap.2264-T1
Valid prediction for pasa_asmbl_12363.p1
Valid prediction for GlimmerHMM_glimmerT_34637-T1
Valid prediction for Augustus_model.g23145.t1
Valid prediction for Augustus_model.g23142.t1
Valid prediction for GlimmerHMM_glimmerT_34618-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_34651-T1
Valid prediction for GlimmerHMM_glimmerT_34620-T1
Valid prediction for GlimmerHMM_glimmerT_34653-T1
Valid prediction for Augustus_model.g23147.t1
Valid prediction for HiQ_model.g23149.t1
Valid prediction for GlimmerHMM_glimmerT_34622-T1
Valid prediction for GlimmerHMM_glimmerT_34638-T1
Valid prediction for GlimmerHMM_glimmerT_34627-T1
Valid prediction for snap_scaffold_14-snap.2244-T1
Valid prediction for snap_scaffold_14-snap.2235-T1
Valid prediction for Augustus_model.g23150.t1
Valid prediction for snap_scaffold_14-snap.2248-T1
Valid prediction for snap_scaffold_14-snap.2255-T1
Valid prediction for snap_scaffold_14-snap.2250-T1
Valid prediction for GlimmerHMM_glimmerT_34626-T1
Valid prediction for snap_scaffold_14-snap.2226-T1
Valid prediction for GlimmerHMM_glimmerT_34625-T1
Valid prediction for Augustus_model.g23132.t1
Valid prediction for Augustus_model.g23136.t1
Valid prediction for snap_scaffold_14-snap.2222-T1
Valid prediction for snap_scaffold_14-snap.2240-T1
Valid prediction for CodingQuarry_transcript_15826-T1
Valid prediction for CodingQuarry_transcript_15825-T1
Valid prediction for Augustus_model.g23139.t1
Valid prediction for pasa_asmbl_13449.p1
Valid prediction for Augustus_model.g23141.t1
Valid prediction for Augustus_model.g23146.t1
Valid prediction for snap_scaffold_14-snap.2268-T1
Valid prediction for Augustus_model.g23127.t1
Valid prediction for snap_scaffold_14-snap.2274-T1
Valid prediction for snap_scaffold_14-snap.2239-T1
Valid prediction for GlimmerHMM_glimmerT_34629-T1
Valid prediction for snap_scaffold_14-snap.2265-T1
Valid prediction for GlimmerHMM_glimmerT_34643-T1
Valid prediction for snap_scaffold_14-snap.2223-T1
Valid prediction for snap_scaffold_14-snap.2225-T1
Valid prediction for GlimmerHMM_glimmerT_34633-T1
Valid prediction for snap_scaffold_14-snap.2232-T1
Valid prediction for HiQ_model.g23143.t1
Valid prediction for GlimmerHMM_glimmerT_34649-T1
Valid prediction for snap_scaffold_14-snap.2260-T1
Valid prediction for snap_scaffold_14-snap.2257-T1
Valid prediction for snap_scaffold_14-snap.2253-T1
Valid prediction for snap_scaffold_14-snap.2270-T1
Valid prediction for snap_scaffold_14-snap.2230-T1
Valid prediction for GlimmerHMM_glimmerT_34621-T1
Valid prediction for snap_scaffold_14-snap.2237-T1
Valid prediction for snap_scaffold_14-snap.2228-T1
Valid prediction for Augustus_model.g23123.t1
Couldn't classify 95420, 95453
Sorry, prediction pasa_asmbl_13444.p1 fails validation.
(ACA)	 AA	95420-95453	GT	TGG
(CAA)	 AG	96057-96185	GT	TGG
(CTC)	 AG	96296-96360	GT	AGG
(GAG)	 AG	96567-96625	GT	AGG
(AAT)	 AG	96756-96846	GT	AGG
(GTG)	 AG	96969-97105	GT	AAG
(GAA)	 AG	97251-97445	GT	CAG
(GCA)	 AG	97712-97858	GT	TGG
(GCA)	 AG	98036-98185	GT	AGG
(GTA)	 AG	98301-98361	GT	AGG
(GAG)	 AG	98474-98616	GT	AGG
(GAT)	 AG	99061-99229	GA	AAG
add_exon() Sorry, pasa_asmbl_13444.p1 96969-97105-terminal-2 is invalid.
-recovered pasa_asmbl_13444.p1, terminal, 96969, 97105
add_exon() Sorry, pasa_asmbl_13444.p1 98474-98616-terminal-2 is invalid.
-recovered pasa_asmbl_13444.p1, terminal, 98474, 98616
-recovered pasa_asmbl_13444.p1, terminal, 99061, 99229
-recovered pasa_asmbl_13444.p1, internal, 96057, 96185
-recovered pasa_asmbl_13444.p1, internal, 96296, 96360
-recovered pasa_asmbl_13444.p1, internal, 96567, 96625
-recovered pasa_asmbl_13444.p1, internal, 96756, 96846
-recovered pasa_asmbl_13444.p1, internal, 96969, 97105
-recovered pasa_asmbl_13444.p1, internal, 97251, 97445
-recovered pasa_asmbl_13444.p1, internal, 97712, 97858
-recovered pasa_asmbl_13444.p1, internal, 98036, 98185
-recovered pasa_asmbl_13444.p1, internal, 98301, 98361
-recovered pasa_asmbl_13444.p1, internal, 98474, 98616
Valid prediction for snap_scaffold_14-snap.2271-T1
Valid prediction for snap_scaffold_14-snap.2258-T1
Valid prediction for GlimmerHMM_glimmerT_34635-T1
Valid prediction for snap_scaffold_14-snap.2233-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g23137.t1
Valid prediction for CodingQuarry_transcript_15824-T1
Valid prediction for snap_scaffold_14-snap.2259-T1
Valid prediction for GlimmerHMM_glimmerT_34644-T1
Valid prediction for snap_scaffold_14-snap.2275-T1
Valid prediction for snap_scaffold_14-snap.2262-T1
Valid prediction for GlimmerHMM_glimmerT_34632-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40373, rend_intergenic: 39046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65217, rend_intergenic: 40508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70583, rend_intergenic: 65459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76020, rend_intergenic: 70982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78278, rend_intergenic: 77025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96468, rend_intergenic: 82362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106900, rend_intergenic: 103927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113207, rend_intergenic: 107001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115728, rend_intergenic: 113643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119680, rend_intergenic: 116093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132479, rend_intergenic: 120599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180541, rend_intergenic: 171259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195760, rend_intergenic: 195010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202239, rend_intergenic: 197983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205624, rend_intergenic: 202809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220392, rend_intergenic: 206506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234989, rend_intergenic: 229797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 338144
-exon list size: 582


building trellis

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92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 48 predictions from path traversal
Error with prediction: snap lend_intergenic: 40373, rend_intergenic: 39046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65217, rend_intergenic: 40508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70583, rend_intergenic: 65459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76020, rend_intergenic: 70982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78278, rend_intergenic: 77025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96468, rend_intergenic: 82362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106900, rend_intergenic: 103927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113207, rend_intergenic: 107001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115728, rend_intergenic: 113643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119680, rend_intergenic: 116093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132479, rend_intergenic: 120599  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180541, rend_intergenic: 171259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195760, rend_intergenic: 195010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202239, rend_intergenic: 197983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205624, rend_intergenic: 202809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220392, rend_intergenic: 206506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234989, rend_intergenic: 229797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20590
-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 - 20125
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1 - 18611