-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_10139686-10490482

-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 pasa_asmbl_5928.p1
Valid prediction for GlimmerHMM_glimmerT_27806-T1
Valid prediction for snap_scaffold_11-snap.2303-T1
Valid prediction for snap_scaffold_11-snap.2325-T1
Valid prediction for pasa_asmbl_5936.p1
Valid prediction for pasa_asmbl_5934.p1
Valid prediction for snap_scaffold_11-snap.2320-T1
Couldn't classify 249596, 249726
Couldn't classify 250597, 250687
Sorry, prediction pasa_asmbl_5937.p1 fails validation.
(GAG)	 AG	249596-249726	GT	AAG
(GAA)	 AG	249984-250107	GT	GGG
(GCG)	 AG	250197-250309	GT	AGG
(TTC)	 AG	250597-250687	GT	CGG
-recovered pasa_asmbl_5937.p1, internal, 249596, 249726
-recovered pasa_asmbl_5937.p1, internal, 249984, 250107
-recovered pasa_asmbl_5937.p1, internal, 250197, 250309
-recovered pasa_asmbl_5937.p1, internal, 250597, 250687
Valid prediction for GlimmerHMM_glimmerT_27789-T1
Valid prediction for Augustus_model.g18426.t1
Valid prediction for GlimmerHMM_glimmerT_27790-T1
Valid prediction for HiQ_model.g18412.t1
Valid prediction for GlimmerHMM_glimmerT_27810-T1
Valid prediction for GlimmerHMM_glimmerT_27808-T1
Valid prediction for snap_scaffold_11-snap.2311-T1
Valid prediction for snap_scaffold_11-snap.2304-T1
Valid prediction for Augustus_model.g18405.t1
Valid prediction for GlimmerHMM_glimmerT_27795-T1
Valid prediction for GlimmerHMM_glimmerT_27813-T1
Couldn't classify 133192, 133326
Sorry, prediction pasa_asmbl_5932.p1 fails validation.
(GTG)	 GT	133192-133326	GT	AGG
(ATG)	 AG	133570-133748	GT	AAG
(ATT)	 AG	133970-134075	TG	GAT
-recovered pasa_asmbl_5932.p1, initial, 133570, 133748
-recovered pasa_asmbl_5932.p1, terminal, 133970, 134075
-recovered pasa_asmbl_5932.p1, internal, 133570, 133748
Valid prediction for pasa_asmbl_5944.p1
Valid prediction for snap_scaffold_11-snap.2310-T1
Valid prediction for snap_scaffold_11-snap.2300-T1
Valid prediction for pasa_asmbl_6293.p1
Valid prediction for snap_scaffold_11-snap.2302-T1
Valid prediction for HiQ_model.g18417.t1
Valid prediction for Augustus_model.g18404.t1
Valid prediction for HiQ_model.g18415.t1
Valid prediction for snap_scaffold_11-snap.2305-T1
Valid prediction for GlimmerHMM_glimmerT_27800-T1
Valid prediction for GlimmerHMM_glimmerT_27802-T1
Couldn't classify 255595, 255793
Sorry, prediction pasa_asmbl_5943.p1 fails validation.
(CAG)	 TC	255595-255793	GT	GGG
(GAG)	 AG	256079-256282	GT	GGG
(GCT)	 AG	256753-256929	GT	TGG
(CGG)	 AG	257101-257238	GT	AGG
(CTT)	 AG	257722-257958	GT	AGG
(ACT)	 AG	258158-258311	GT	AAG
(TTG)	 AG	258563-258720	GT	CTG
(CTC)	 AG	258966-259197	GT	AGG
(TGA)	 AG	259379-259596	GT	ATG
(ACA)	 AG	259798-260049	GT	TGG
(GCT)	 AG	260353-260556	GT	AGG
(AGC)	 AG	260873-261067	GT	GGG
(ATT)	 AG	261320-261454	GT	AGG
(CAC)	 AG	261753-261918	GT	AGG
(GCT)	 AG	262442-262658	AT	GAA
-recovered pasa_asmbl_5943.p1, terminal, 262442, 262658
-recovered pasa_asmbl_5943.p1, internal, 256079, 256282
-recovered pasa_asmbl_5943.p1, internal, 256753, 256929
-recovered pasa_asmbl_5943.p1, internal, 257101, 257238
-recovered pasa_asmbl_5943.p1, internal, 257722, 257958
-recovered pasa_asmbl_5943.p1, internal, 258158, 258311
-recovered pasa_asmbl_5943.p1, internal, 258563, 258720
-recovered pasa_asmbl_5943.p1, internal, 258966, 259197
-recovered pasa_asmbl_5943.p1, internal, 259379, 259596
-recovered pasa_asmbl_5943.p1, internal, 259798, 260049
-recovered pasa_asmbl_5943.p1, internal, 260353, 260556
-recovered pasa_asmbl_5943.p1, internal, 260873, 261067
-recovered pasa_asmbl_5943.p1, internal, 261320, 261454
-recovered pasa_asmbl_5943.p1, internal, 261753, 261918
Valid prediction for GlimmerHMM_glimmerT_27793-T1
Valid prediction for GlimmerHMM_glimmerT_27785-T1
Valid prediction for HiQ_model.g18400.t1
Valid prediction for snap_scaffold_11-snap.2309-T1
Valid prediction for CodingQuarry_transcript_8236-T1
Valid prediction for GlimmerHMM_glimmerT_27819-T1
Valid prediction for snap_scaffold_11-snap.2275-T1
Valid prediction for GlimmerHMM_glimmerT_27805-T1
Valid prediction for snap_scaffold_11-snap.2286-T1
Couldn't classify 28524, 28631
Sorry, prediction pasa_asmbl_5925.p1 fails validation.
(ATG)	 AC	26824-28194	GT	AGG
(GGT)	 AG	28524-28631	CA	AGC
-recovered pasa_asmbl_5925.p1, initial, 26824, 28194
Valid prediction for CodingQuarry_transcript_8235-T1
Valid prediction for snap_scaffold_11-snap.2327-T1
Valid prediction for Augustus_model.g18397.t1
Valid prediction for snap_scaffold_11-snap.2278-T1
Valid prediction for snap_scaffold_11-snap.2281-T1
Valid prediction for snap_scaffold_11-snap.2291-T1
Valid prediction for CodingQuarry_transcript_8237-T1
Valid prediction for CodingQuarry_transcript_8229-T1
Valid prediction for Augustus_model.g18416.t1
Valid prediction for Augustus_model.g18407.t1
Valid prediction for snap_scaffold_11-snap.2306-T1
Valid prediction for snap_scaffold_11-snap.2283-T1
Valid prediction for Augustus_model.g18399.t1
Valid prediction for snap_scaffold_11-snap.2280-T1
Valid prediction for GlimmerHMM_glimmerT_27807-T1
Valid prediction for GlimmerHMM_glimmerT_27809-T1
Valid prediction for Augustus_model.g18418.t1
Valid prediction for snap_scaffold_11-snap.2313-T1
Valid prediction for Augustus_model.g18396.t1
Valid prediction for GlimmerHMM_glimmerT_27814-T1
Valid prediction for snap_scaffold_11-snap.2312-T1
Valid prediction for snap_scaffold_11-snap.2322-T1
Valid prediction for GlimmerHMM_glimmerT_27818-T1
Valid prediction for GlimmerHMM_glimmerT_27794-T1
Couldn't classify 253848, 253987
Couldn't classify 254939, 255015
Sorry, prediction pasa_asmbl_5938.p1 fails validation.
(ACC)	 CC	253848-253987	GT	AGG
(GAG)	 AG	254254-254434	GT	AGG
(CTC)	 AG	254588-254768	GT	AGG
(CCA)	 AG	254939-255015	AT	AGA
-recovered pasa_asmbl_5938.p1, internal, 254254, 254434
-recovered pasa_asmbl_5938.p1, internal, 254588, 254768
Couldn't classify 245802, 245919
Couldn't classify 247491, 247514
Sorry, prediction pasa_asmbl_6357.p1 fails validation.
(CGT)	 CT	245802-245919	GT	AGG
(CCG)	 AG	246121-246332	GT	AGG
(GCC)	 AG	247491-247514	AC	ACA
-recovered pasa_asmbl_6357.p1, internal, 246121, 246332
Valid prediction for GlimmerHMM_glimmerT_27816-T1
Valid prediction for snap_scaffold_11-snap.2308-T1
Valid prediction for snap_scaffold_11-snap.2299-T1
Valid prediction for Augustus_model.g18419.t1
Valid prediction for HiQ_model.g18424.t1
Valid prediction for snap_scaffold_11-snap.2307-T1
Valid prediction for snap_scaffold_11-snap.2293-T1
Valid prediction for pasa_asmbl_5927.p1
Valid prediction for GlimmerHMM_glimmerT_27804-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_27797-T1
Valid prediction for snap_scaffold_11-snap.2314-T1
Valid prediction for snap_scaffold_11-snap.2292-T1
Valid prediction for snap_scaffold_11-snap.2295-T1
Valid prediction for snap_scaffold_11-snap.2294-T1
Valid prediction for Augustus_model.g18409.t1
Valid prediction for Augustus_model.g18398.t1
Valid prediction for snap_scaffold_11-snap.2296-T1
Valid prediction for CodingQuarry_transcript_8232-T1
Valid prediction for HiQ_model.g18413.t1
Valid prediction for snap_scaffold_11-snap.2298-T1
Valid prediction for Augustus_model.g18393.t1
Valid prediction for snap_scaffold_11-snap.2276-T1
Valid prediction for Augustus_model.g18421.t1
Valid prediction for snap_scaffold_11-snap.2297-T1
Valid prediction for GlimmerHMM_glimmerT_27787-T1
Valid prediction for CodingQuarry_transcript_8233-T1
Valid prediction for GlimmerHMM_glimmerT_27791-T1
Valid prediction for snap_scaffold_11-snap.2290-T1
Valid prediction for HiQ_model.g18414.t1
Valid prediction for GlimmerHMM_glimmerT_27792-T1
Valid prediction for Augustus_model.g18420.t1
Valid prediction for pasa_asmbl_6994.p1
Valid prediction for GlimmerHMM_glimmerT_27796-T1
Valid prediction for snap_scaffold_11-snap.2287-T1
Valid prediction for snap_scaffold_11-snap.2317-T1
Valid prediction for pasa_asmbl_6993.p1
Valid prediction for snap_scaffold_11-snap.2282-T1
Valid prediction for Augustus_model.g18403.t1
Valid prediction for Augustus_model.g18410.t1
Valid prediction for Augustus_model.g18422.t1
Valid prediction for Augustus_model.g18411.t1
Valid prediction for CodingQuarry_transcript_8230-T1
Valid prediction for GlimmerHMM_glimmerT_27788-T1
Valid prediction for snap_scaffold_11-snap.2279-T1
Valid prediction for Augustus_model.g18408.t1
Valid prediction for snap_scaffold_11-snap.2326-T1
Valid prediction for HiQ_model.g18406.t1
Valid prediction for Augustus_model.g18425.t1
Valid prediction for snap_scaffold_11-snap.2328-T1
Valid prediction for Augustus_model.g18423.t1
Valid prediction for GlimmerHMM_glimmerT_27817-T1
Valid prediction for snap_scaffold_11-snap.2285-T1
Valid prediction for snap_scaffold_11-snap.2315-T1
Couldn't classify 22669, 22823
Sorry, prediction pasa_asmbl_6997.p1 fails validation.
(TTC)	 TC	22669-22823	GT	CAG
(GAA)	 AG	23211-23301	GT	AGG
(ACG)	 AG	23431-23624	GT	AGG
(TTT)	 AG	23825-24287	CT	GAC
-recovered pasa_asmbl_6997.p1, terminal, 23825, 24287
-recovered pasa_asmbl_6997.p1, internal, 23211, 23301
-recovered pasa_asmbl_6997.p1, internal, 23431, 23624
Valid prediction for Augustus_model.g18395.t1
Couldn't classify 341893, 342062
Couldn't classify 344775, 344913
Sorry, prediction pasa_asmbl_6985.p1 fails validation.
(AGT)	 TC	341893-342062	GT	TGG
(GGT)	 AG	343250-343417	GT	AAG
(GAG)	 AG	344775-344913	GT	GGG
-recovered pasa_asmbl_6985.p1, internal, 343250, 343417
-recovered pasa_asmbl_6985.p1, internal, 344775, 344913
Valid prediction for snap_scaffold_11-snap.2316-T1
Valid prediction for GlimmerHMM_glimmerT_27798-T1
Valid prediction for CodingQuarry_transcript_8231-T1
Valid prediction for Augustus_model.g18402.t1
Valid prediction for snap_scaffold_11-snap.2288-T1
Valid prediction for GlimmerHMM_glimmerT_27815-T1
Couldn't classify 328470, 328599
Couldn't classify 330166, 330187
Sorry, prediction pasa_asmbl_6987.p1 fails validation.
(CAC)	 TC	328470-328599	GT	AAG
(CCA)	 AG	329739-329895	GT	TGG
(GAC)	 AG	330166-330187	CT	GGC
-recovered pasa_asmbl_6987.p1, internal, 329739, 329895
Valid prediction for snap_scaffold_11-snap.2284-T1
Valid prediction for snap_scaffold_11-snap.2324-T1
Valid prediction for Augustus_model.g18394.t1
Valid prediction for pasa_asmbl_6992.p1
Valid prediction for snap_scaffold_11-snap.2321-T1
Valid prediction for snap_scaffold_11-snap.2301-T1
Valid prediction for snap_scaffold_11-snap.2289-T1
Valid prediction for pasa_asmbl_6991.p1
Valid prediction for GlimmerHMM_glimmerT_27801-T1
Valid prediction for GlimmerHMM_glimmerT_27799-T1
Valid prediction for snap_scaffold_11-snap.2323-T1
Valid prediction for snap_scaffold_11-snap.2319-T1
Valid prediction for Augustus_model.g18401.t1
Valid prediction for snap_scaffold_11-snap.2277-T1
Valid prediction for GlimmerHMM_glimmerT_27812-T1
Valid prediction for GlimmerHMM_glimmerT_27786-T1
Valid prediction for CodingQuarry_transcript_8228-T1
Valid prediction for GlimmerHMM_glimmerT_27811-T1
Valid prediction for snap_scaffold_11-snap.2318-T1
Valid prediction for CodingQuarry_transcript_8234-T1
Valid prediction for GlimmerHMM_glimmerT_27803-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12781, rend_intergenic: 5849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15432, rend_intergenic: 12791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22008, rend_intergenic: 15611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26082, rend_intergenic: 23573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36392, rend_intergenic: 27876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38496, rend_intergenic: 36546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 348985, rend_intergenic: 344394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 350797
-exon list size: 517


building trellis

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95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 12781, rend_intergenic: 5849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15432, rend_intergenic: 12791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22008, rend_intergenic: 15611  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26082, rend_intergenic: 23573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36392, rend_intergenic: 27876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38496, rend_intergenic: 36546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 348985, rend_intergenic: 344394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 39 predictions persist after filtering for low support