-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_12373374-12598552

-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_12-snap.2273-T1
Valid prediction for Augustus_model.g19988.t1
Valid prediction for snap_scaffold_12-snap.2302-T1
Valid prediction for GlimmerHMM_glimmerT_30205-T1
Valid prediction for snap_scaffold_12-snap.2282-T1
Valid prediction for GlimmerHMM_glimmerT_30190-T1
Couldn't classify 128849, 129270
Couldn't classify 129338, 129362
Sorry, prediction CodingQuarry_transcript_10429-T1 fails validation.
(ATG)	 TC	128849-129270	CT	CCC
(CCC)	 AC	129338-129362	CC	GAC
Valid prediction for snap_scaffold_12-snap.2292-T1
Valid prediction for Augustus_model.g19989.t1
Valid prediction for HiQ_model.g19984.t1
Valid prediction for Augustus_model.g19996.t1
Valid prediction for snap_scaffold_12-snap.2283-T1
Valid prediction for GlimmerHMM_glimmerT_30192-T1
Couldn't classify 62290, 62548
Sorry, prediction pasa_asmbl_8001.p1 fails validation.
(TAC)	 AT	62290-62548	GT	AGG
(TGT)	 AG	62741-62836	GT	AGG
(TTC)	 AG	62980-63038	GT	AGG
(GGC)	 AG	63190-63312	GT	AGG
(GGT)	 AG	63880-63939	TG	GAT
-recovered pasa_asmbl_8001.p1, terminal, 62741, 62836
-recovered pasa_asmbl_8001.p1, terminal, 63880, 63939
-recovered pasa_asmbl_8001.p1, internal, 62741, 62836
-recovered pasa_asmbl_8001.p1, internal, 62980, 63038
-recovered pasa_asmbl_8001.p1, internal, 63190, 63312
Valid prediction for CodingQuarry_transcript_10426-T1
Valid prediction for snap_scaffold_12-snap.2297-T1
Couldn't classify 189986, 190138
Couldn't classify 193298, 193447
Sorry, prediction pasa_asmbl_8014.p1 fails validation.
(CAG)	 AG	189986-190138	GT	TGG
(GTG)	 AG	192081-192200	GT	AGG
(GAA)	 AG	193298-193447	CA	AGC
-recovered pasa_asmbl_8014.p1, internal, 189986, 190138
-recovered pasa_asmbl_8014.p1, internal, 192081, 192200
Valid prediction for snap_scaffold_12-snap.2311-T1
Valid prediction for GlimmerHMM_glimmerT_30199-T1
Valid prediction for Augustus_model.g19979.t1
Valid prediction for Augustus_model.g19992.t1
Valid prediction for GlimmerHMM_glimmerT_30188-T1
Valid prediction for pasa_asmbl_8007.p1
Valid prediction for snap_scaffold_12-snap.2312-T1
Valid prediction for Augustus_model.g19980.t1
Valid prediction for snap_scaffold_12-snap.2290-T1
Valid prediction for CodingQuarry_transcript_10424-T1
Valid prediction for GlimmerHMM_glimmerT_30184-T1
Valid prediction for Augustus_model.g19998.t1
Valid prediction for snap_scaffold_12-snap.2309-T1
Valid prediction for GlimmerHMM_glimmerT_30179-T1
Valid prediction for snap_scaffold_12-snap.2286-T1
Valid prediction for Augustus_model.g19997.t1
Valid prediction for snap_scaffold_12-snap.2310-T1
Valid prediction for snap_scaffold_12-snap.2285-T1
Valid prediction for Augustus_model.g19993.t1
Valid prediction for GlimmerHMM_glimmerT_30203-T1
Valid prediction for GlimmerHMM_glimmerT_30189-T1
Valid prediction for HiQ_model.g19987.t1
Valid prediction for HiQ_model.g19976.t1
Valid prediction for snap_scaffold_12-snap.2296-T1
Valid prediction for snap_scaffold_12-snap.2301-T1
Valid prediction for CodingQuarry_transcript_10421-T1
Valid prediction for HiQ_model.g19985.t1
Valid prediction for snap_scaffold_12-snap.2299-T1
Valid prediction for GlimmerHMM_glimmerT_30201-T1
Valid prediction for CodingQuarry_transcript_10425-T1
Valid prediction for snap_scaffold_12-snap.2277-T1
Valid prediction for snap_scaffold_12-snap.2271-T1
Valid prediction for snap_scaffold_12-snap.2308-T1
Valid prediction for GlimmerHMM_glimmerT_30195-T1
Valid prediction for CodingQuarry_transcript_10430-T1
Valid prediction for snap_scaffold_12-snap.2305-T1
Valid prediction for pasa_asmbl_8008.p1
Valid prediction for snap_scaffold_12-snap.2275-T1
Valid prediction for snap_scaffold_12-snap.2284-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_12-snap.2287-T1
Valid prediction for CodingQuarry_transcript_10423-T1
Valid prediction for GlimmerHMM_glimmerT_30194-T1
Valid prediction for Augustus_model.g19978.t1
Couldn't classify 178913, 178952
Sorry, prediction pasa_asmbl_8883.p1 fails validation.
(TCC)	 CG	178913-178952	GT	CAG
(CTG)	 AG	179072-179238	GT	TGG
(GTG)	 AG	179645-179753	GT	GGG
(GTT)	 AG	179922-180052	TG	AAT
-recovered pasa_asmbl_8883.p1, terminal, 179922, 180052
-recovered pasa_asmbl_8883.p1, internal, 179072, 179238
-recovered pasa_asmbl_8883.p1, internal, 179645, 179753
Valid prediction for GlimmerHMM_glimmerT_30181-T1
Valid prediction for Augustus_model.g19975.t1
Valid prediction for snap_scaffold_12-snap.2293-T1
Valid prediction for snap_scaffold_12-snap.2281-T1
Valid prediction for Augustus_model.g19994.t1
Couldn't classify 62127, 62253
Sorry, prediction pasa_asmbl_8889.p1 fails validation.
(ATG)	 AG	59915-60327	GT	AGG
(GTA)	 AG	62127-62253	CG	TCC
-recovered pasa_asmbl_8889.p1, initial, 59915, 60327
-recovered pasa_asmbl_8889.p1, internal, 59915, 60327
Valid prediction for snap_scaffold_12-snap.2291-T1
Couldn't classify 200939, 201091
Couldn't classify 201450, 201542
Sorry, prediction pasa_asmbl_8880.p1 fails validation.
(CGC)	 AC	200939-201091	GT	AGG
(GTG)	 AG	201252-201344	GT	AGG
(GTG)	 AG	201450-201542	CA	CCC
-recovered pasa_asmbl_8880.p1, internal, 201252, 201344
Valid prediction for Augustus_model.g19999.t1
Valid prediction for HiQ_model.g19995.t1
Valid prediction for snap_scaffold_12-snap.2307-T1
Valid prediction for GlimmerHMM_glimmerT_30197-T1
Valid prediction for snap_scaffold_12-snap.2304-T1
Couldn't classify 215239, 222243
Sorry, prediction pasa_asmbl_8877.p1 fails validation.
(ATG)	 CG	215239-222243	AA	ACA
Valid prediction for Augustus_model.g19982.t1
Valid prediction for snap_scaffold_12-snap.2274-T1
Valid prediction for GlimmerHMM_glimmerT_30187-T1
Valid prediction for snap_scaffold_12-snap.2270-T1
Valid prediction for snap_scaffold_12-snap.2276-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_30206-T1
Valid prediction for GlimmerHMM_glimmerT_30193-T1
Valid prediction for snap_scaffold_12-snap.2288-T1
Valid prediction for GlimmerHMM_glimmerT_30178-T1
Valid prediction for GlimmerHMM_glimmerT_30185-T1
Valid prediction for GlimmerHMM_glimmerT_30183-T1
Valid prediction for snap_scaffold_12-snap.2300-T1
Valid prediction for snap_scaffold_12-snap.2306-T1
Valid prediction for GlimmerHMM_glimmerT_30200-T1
Valid prediction for GlimmerHMM_glimmerT_30182-T1
Valid prediction for GlimmerHMM_glimmerT_30204-T1
Valid prediction for Augustus_model.g19991.t1
Valid prediction for Augustus_model.g19983.t1
Valid prediction for Augustus_model.g19986.t1
Valid prediction for snap_scaffold_12-snap.2278-T1
Valid prediction for Augustus_model.g19981.t1
Valid prediction for snap_scaffold_12-snap.2279-T1
Valid prediction for snap_scaffold_12-snap.2272-T1
Valid prediction for snap_scaffold_12-snap.2303-T1
Valid prediction for GlimmerHMM_glimmerT_30198-T1
Valid prediction for snap_scaffold_12-snap.2298-T1
Valid prediction for CodingQuarry_transcript_10427-T1
Valid prediction for snap_scaffold_12-snap.2294-T1
Valid prediction for snap_scaffold_12-snap.2269-T1
Valid prediction for Augustus_model.g19977.t1
Valid prediction for snap_scaffold_12-snap.2295-T1
Valid prediction for snap_scaffold_12-snap.2289-T1
Valid prediction for GlimmerHMM_glimmerT_30196-T1
Couldn't classify 198752, 198777
Couldn't classify 200136, 200270
Sorry, prediction pasa_asmbl_8882.p1 fails validation.
(CTG)	 AG	198752-198777	GT	AGG
(GAA)	 AG	199063-199243	GT	AGG
(CCT)	 AG	200136-200270	AC	ACA
-recovered pasa_asmbl_8882.p1, internal, 198752, 198777
-recovered pasa_asmbl_8882.p1, internal, 199063, 199243
Valid prediction for Augustus_model.g19990.t1
Valid prediction for GlimmerHMM_glimmerT_30186-T1
Valid prediction for snap_scaffold_12-snap.2280-T1
Valid prediction for snap_scaffold_12-snap.2313-T1
Valid prediction for GlimmerHMM_glimmerT_30180-T1
Valid prediction for GlimmerHMM_glimmerT_30191-T1
Valid prediction for GlimmerHMM_glimmerT_30202-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9941, rend_intergenic: 8796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12908, rend_intergenic: 9968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27906, rend_intergenic: 22236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41063, rend_intergenic: 37051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77097, rend_intergenic: 72743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92945, rend_intergenic: 89663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94102, rend_intergenic: 92949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106077, rend_intergenic: 102032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111125, rend_intergenic: 111009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123921, rend_intergenic: 112190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225179
-exon list size: 411


building trellis

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36.3    
36.6    
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37.3    
37.5    
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38.5    
38.7    
39.0    
39.2    
39.5    
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40.9    
41.2    
41.4    
41.6    
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42.1    
42.4    
42.6    
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43.1    
43.3    
43.6    
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44.1    
44.3    
44.6    
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45.3    
45.5    
45.8    
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91.8    
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97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 9941, rend_intergenic: 8796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12908, rend_intergenic: 9968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27906, rend_intergenic: 22236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41063, rend_intergenic: 37051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77097, rend_intergenic: 72743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92945, rend_intergenic: 89663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94102, rend_intergenic: 92949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106077, rend_intergenic: 102032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111125, rend_intergenic: 111009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123921, rend_intergenic: 112190  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