-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_13909680-14166019

-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 GlimmerHMM_glimmerT_30417-T1
Valid prediction for snap_scaffold_12-snap.2618-T1
Valid prediction for snap_scaffold_12-snap.2642-T1
Valid prediction for GlimmerHMM_glimmerT_30413-T1
Valid prediction for GlimmerHMM_glimmerT_30428-T1
Valid prediction for Augustus_model.g20146.t1
Valid prediction for GlimmerHMM_glimmerT_30438-T1
Valid prediction for pasa_asmbl_8049.p1
Valid prediction for snap_scaffold_12-snap.2606-T1
Couldn't classify 158223, 158292
Sorry, prediction pasa_asmbl_8051.p1 fails validation.
(CAA)	 TA	158223-158292	GT	AGG
(GTG)	 AG	158468-159018	GC	GAG
-recovered pasa_asmbl_8051.p1, terminal, 158468, 159018
-recovered pasa_asmbl_8051.p1, internal, 158468, 159018
Valid prediction for snap_scaffold_12-snap.2623-T1
Valid prediction for Augustus_model.g20137.t1
Valid prediction for GlimmerHMM_glimmerT_30414-T1
Valid prediction for Augustus_model.g20122.t1
Valid prediction for GlimmerHMM_glimmerT_30420-T1
Valid prediction for Augustus_model.g20136.t1
Valid prediction for Augustus_model.g20126.t1
Valid prediction for GlimmerHMM_glimmerT_30427-T1
Valid prediction for GlimmerHMM_glimmerT_30409-T1
Valid prediction for snap_scaffold_12-snap.2638-T1
Valid prediction for Augustus_model.g20138.t1
Valid prediction for GlimmerHMM_glimmerT_30441-T1
Valid prediction for snap_scaffold_12-snap.2643-T1
Valid prediction for GlimmerHMM_glimmerT_30442-T1
Valid prediction for Augustus_model.g20147.t1
Valid prediction for snap_scaffold_12-snap.2639-T1
Valid prediction for snap_scaffold_12-snap.2644-T1
Valid prediction for HiQ_model.g20132.t1
Valid prediction for snap_scaffold_12-snap.2617-T1
Valid prediction for Augustus_model.g20148.t1
Valid prediction for snap_scaffold_12-snap.2612-T1
Valid prediction for Augustus_model.g20149.t1
Valid prediction for snap_scaffold_12-snap.2630-T1
Valid prediction for GlimmerHMM_glimmerT_30429-T1
Valid prediction for snap_scaffold_12-snap.2636-T1
Valid prediction for snap_scaffold_12-snap.2620-T1
Couldn't classify 173106, 173139
Sorry, prediction pasa_asmbl_8052.p1 fails validation.
(CAG)	 TC	173106-173139	GT	AGG
(AGC)	 AG	173253-173387	GT	CTG
(GTG)	 AG	173552-173661	GT	AGG
(TTT)	 AG	173882-174029	GT	AGG
(AAT)	 AG	174218-174243	CG	GAC
-recovered pasa_asmbl_8052.p1, terminal, 174218, 174243
-recovered pasa_asmbl_8052.p1, internal, 173253, 173387
-recovered pasa_asmbl_8052.p1, internal, 173552, 173661
-recovered pasa_asmbl_8052.p1, internal, 173882, 174029
Valid prediction for GlimmerHMM_glimmerT_30410-T1
Valid prediction for snap_scaffold_12-snap.2598-T1
Valid prediction for GlimmerHMM_glimmerT_30423-T1
Valid prediction for HiQ_model.g20150.t1
Valid prediction for pasa_asmbl_8048.p1
Valid prediction for snap_scaffold_12-snap.2645-T1
Couldn't classify 251596, 251787
Sorry, prediction pasa_asmbl_8060.p1 fails validation.
(CTG)	 AC	251596-251787	GT	AGG
(GTG)	 AG	251912-252019	GT	GGG
(GTG)	 AG	252227-252346	GT	GGG
(GTG)	 AG	252627-252764	GT	AGG
(CTG)	 AG	253300-253995	AG	AGA
-recovered pasa_asmbl_8060.p1, terminal, 253300, 253995
-recovered pasa_asmbl_8060.p1, internal, 251912, 252019
-recovered pasa_asmbl_8060.p1, internal, 252227, 252346
-recovered pasa_asmbl_8060.p1, internal, 252627, 252764
Valid prediction for Augustus_model.g20127.t1
Valid prediction for snap_scaffold_12-snap.2604-T1
Valid prediction for snap_scaffold_12-snap.2608-T1
Valid prediction for GlimmerHMM_glimmerT_30424-T1
Valid prediction for HiQ_model.g20133.t1
Valid prediction for CodingQuarry_transcript_10457-T1
Valid prediction for snap_scaffold_12-snap.2607-T1
Valid prediction for snap_scaffold_12-snap.2626-T1
Couldn't classify 225834, 225878
Sorry, prediction pasa_asmbl_8057.p1 fails validation.
(AAT)	 AC	225834-225878	GT	AAG
(TTG)	 AG	226093-226232	GT	GGG
(GAT)	 AG	226403-226524	GT	TGG
(AGC)	 AG	226840-226983	GT	CGG
(TGA)	 AG	227391-227498	GT	AGG
(GGG)	 AG	227655-227841	GT	GCG
(TTT)	 AG	227957-228080	GT	ACG
(GTG)	 AG	228134-228247	AC	AGA
-recovered pasa_asmbl_8057.p1, terminal, 228134, 228247
-recovered pasa_asmbl_8057.p1, internal, 226093, 226232
-recovered pasa_asmbl_8057.p1, internal, 226403, 226524
-recovered pasa_asmbl_8057.p1, internal, 226840, 226983
-recovered pasa_asmbl_8057.p1, internal, 227391, 227498
-recovered pasa_asmbl_8057.p1, internal, 227655, 227841
-recovered pasa_asmbl_8057.p1, internal, 227957, 228080
Valid prediction for GlimmerHMM_glimmerT_30412-T1
Valid prediction for snap_scaffold_12-snap.2609-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_30440-T1
Valid prediction for GlimmerHMM_glimmerT_30430-T1
Couldn't classify 157106, 157195
Sorry, prediction pasa_asmbl_8050.p1 fails validation.
(ATG)	 GA	154402-154908	GT	AGG
(GAA)	 AG	155659-155754	GT	AGG
(GAG)	 AG	157106-157195	NN	NNN
-recovered pasa_asmbl_8050.p1, initial, 154402, 154908
-recovered pasa_asmbl_8050.p1, internal, 155659, 155754
Valid prediction for Augustus_model.g20125.t1
Valid prediction for snap_scaffold_12-snap.2600-T1
Valid prediction for GlimmerHMM_glimmerT_30419-T1
Valid prediction for Augustus_model.g20121.t1
Valid prediction for GlimmerHMM_glimmerT_30432-T1
Valid prediction for Augustus_model.g20135.t1
Valid prediction for GlimmerHMM_glimmerT_30416-T1
Valid prediction for snap_scaffold_12-snap.2640-T1
Valid prediction for Augustus_model.g20129.t1
Valid prediction for snap_scaffold_12-snap.2631-T1
Valid prediction for Augustus_model.g20124.t1
Couldn't classify 225469, 225539
Sorry, prediction pasa_asmbl_8053.p1 fails validation.
(ATG)	 GC	222428-222611	GT	AGG
(ACT)	 AG	222771-222900	GT	ATG
(ATC)	 AG	225073-225119	GT	AGG
(AGC)	 AG	225469-225539	AT	ACA
-recovered pasa_asmbl_8053.p1, initial, 222428, 222611
-recovered pasa_asmbl_8053.p1, internal, 222771, 222900
-recovered pasa_asmbl_8053.p1, internal, 225073, 225119
Valid prediction for snap_scaffold_12-snap.2634-T1
Valid prediction for Augustus_model.g20140.t1
Valid prediction for snap_scaffold_12-snap.2622-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 CodingQuarry_transcript_10456-T1
Valid prediction for GlimmerHMM_glimmerT_30415-T1
Valid prediction for snap_scaffold_12-snap.2641-T1
Valid prediction for snap_scaffold_12-snap.2610-T1
Valid prediction for pasa_asmbl_8975.p1
Valid prediction for snap_scaffold_12-snap.2614-T1
Valid prediction for pasa_asmbl_8955.p1
Valid prediction for GlimmerHMM_glimmerT_30408-T1
Valid prediction for GlimmerHMM_glimmerT_30434-T1
Valid prediction for GlimmerHMM_glimmerT_30437-T1
Valid prediction for snap_scaffold_12-snap.2627-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.2625-T1
Valid prediction for snap_scaffold_12-snap.2616-T1
Valid prediction for pasa_asmbl_8990.p1
Valid prediction for snap_scaffold_12-snap.2602-T1
Couldn't classify 110474, 110683
Sorry, prediction pasa_asmbl_8968.p1 fails validation.
(CGA)	 CC	110474-110683	GT	AGG
(TAT)	 AG	110901-111073	GT	AGG
(GAT)	 AG	111260-111326	GC	GAG
-recovered pasa_asmbl_8968.p1, terminal, 111260, 111326
-recovered pasa_asmbl_8968.p1, internal, 110901, 111073
-recovered pasa_asmbl_8968.p1, internal, 111260, 111326
Valid prediction for Augustus_model.g20144.t1
Valid prediction for HiQ_model.g20131.t1
Valid prediction for Augustus_model.g20143.t1
Valid prediction for GlimmerHMM_glimmerT_30431-T1
Valid prediction for snap_scaffold_12-snap.2629-T1
Valid prediction for GlimmerHMM_glimmerT_30436-T1
Valid prediction for GlimmerHMM_glimmerT_30418-T1
Valid prediction for Augustus_model.g20139.t1
Valid prediction for snap_scaffold_12-snap.2633-T1
Valid prediction for snap_scaffold_12-snap.2597-T1
Valid prediction for snap_scaffold_12-snap.2635-T1
Couldn't classify 45331, 45690
Sorry, prediction pasa_asmbl_8986.p1 fails validation.
(GCC)	 CA	45331-45690	AA	GGA
Valid prediction for HiQ_model.g20145.t1
Valid prediction for snap_scaffold_12-snap.2615-T1
Valid prediction for Augustus_model.g20141.t1
Valid prediction for HiQ_model.g20128.t1
Couldn't classify 69249, 69848
Sorry, prediction pasa_asmbl_9164.p1 fails validation.
(CCC)	 TT	69249-69848	CT	CTC
Valid prediction for CodingQuarry_transcript_10455-T1
Valid prediction for CodingQuarry_transcript_10454-T1
Valid prediction for GlimmerHMM_glimmerT_30422-T1
Valid prediction for Augustus_model.g20130.t1
Valid prediction for snap_scaffold_12-snap.2594-T1
Valid prediction for GlimmerHMM_glimmerT_30435-T1
Valid prediction for Augustus_model.g20134.t1
Valid prediction for snap_scaffold_12-snap.2599-T1
Valid prediction for snap_scaffold_12-snap.2637-T1
Valid prediction for Augustus_model.g20142.t1
Valid prediction for GlimmerHMM_glimmerT_30421-T1
Valid prediction for GlimmerHMM_glimmerT_30426-T1
Valid prediction for snap_scaffold_12-snap.2613-T1
Valid prediction for snap_scaffold_12-snap.2628-T1
Valid prediction for snap_scaffold_12-snap.2603-T1
Valid prediction for snap_scaffold_12-snap.2619-T1
Valid prediction for snap_scaffold_12-snap.2601-T1
Valid prediction for snap_scaffold_12-snap.2595-T1
Valid prediction for snap_scaffold_12-snap.2624-T1
Valid prediction for GlimmerHMM_glimmerT_30439-T1
Valid prediction for GlimmerHMM_glimmerT_30411-T1
Valid prediction for snap_scaffold_12-snap.2632-T1
Couldn't classify 69909, 71465
Sorry, prediction pasa_asmbl_8971.p1 fails validation.
(CCC)	 AA	69909-71465	TA	GAT
Valid prediction for snap_scaffold_12-snap.2611-T1
Valid prediction for snap_scaffold_12-snap.2593-T1
Valid prediction for snap_scaffold_12-snap.2605-T1
Couldn't classify 67366, 67940
Sorry, prediction pasa_asmbl_8972.p2 fails validation.
(ATG)	 GG	67128-67230	GT	GGG
(GCG)	 AG	67366-67940	AT	AGA
-recovered pasa_asmbl_8972.p2, initial, 67128, 67230
Valid prediction for GlimmerHMM_glimmerT_30433-T1
Valid prediction for GlimmerHMM_glimmerT_30425-T1
Valid prediction for snap_scaffold_12-snap.2596-T1
Valid prediction for snap_scaffold_12-snap.2621-T1
Valid prediction for Augustus_model.g20123.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31119, rend_intergenic: 30558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32913, rend_intergenic: 31966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36410, rend_intergenic: 32962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55432, rend_intergenic: 37429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58988, rend_intergenic: 55497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61811, rend_intergenic: 59317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103728, rend_intergenic: 62503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115833, rend_intergenic: 104746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159018, rend_intergenic: 155450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168001, rend_intergenic: 160573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174243, rend_intergenic: 169941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183868, rend_intergenic: 182021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208119, rend_intergenic: 193319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215660, rend_intergenic: 214298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226090, rend_intergenic: 224672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226236, rend_intergenic: 226132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228283, rend_intergenic: 226404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244358, rend_intergenic: 238552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245958, rend_intergenic: 245302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256340
-exon list size: 516


building trellis

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91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
95.9    
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    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 31119, rend_intergenic: 30558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32913, rend_intergenic: 31966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36410, rend_intergenic: 32962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55432, rend_intergenic: 37429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58988, rend_intergenic: 55497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61811, rend_intergenic: 59317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103728, rend_intergenic: 62503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115833, rend_intergenic: 104746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159018, rend_intergenic: 155450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168001, rend_intergenic: 160573  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174243, rend_intergenic: 169941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183868, rend_intergenic: 182021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208119, rend_intergenic: 193319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215660, rend_intergenic: 214298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226090, rend_intergenic: 224672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226236, rend_intergenic: 226132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 228283, rend_intergenic: 226404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244358, rend_intergenic: 238552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245958, rend_intergenic: 245302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support