-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_9093243-9256727

-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_4256-T1
Valid prediction for snap_scaffold_2-snap.1805-T1
Valid prediction for snap_scaffold_2-snap.1785-T1
Valid prediction for snap_scaffold_2-snap.1787-T1
Valid prediction for snap_scaffold_2-snap.1793-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_4250-T1
Valid prediction for snap_scaffold_2-snap.1811-T1
Valid prediction for GlimmerHMM_glimmerT_4247-T1
Valid prediction for GlimmerHMM_glimmerT_4253-T1
Valid prediction for CodingQuarry_transcript_28642-T1
Valid prediction for Augustus_model.g2869.t1
Valid prediction for snap_scaffold_2-snap.1796-T1
Couldn't classify 39270, 39965
Sorry, prediction pasa_asmbl_24669.p1 fails validation.
(AGA)	 AA	39270-39965	CG	GGC
Valid prediction for CodingQuarry_transcript_28635-T1
Valid prediction for GlimmerHMM_glimmerT_4251-T1
Couldn't classify 62205, 62233
Sorry, prediction pasa_asmbl_24672.p1 fails validation.
(AAC)	 TC	62205-62233	GT	AGG
(GCT)	 AG	62340-62526	GT	CCG
(TCT)	 AG	62618-62782	GT	CGG
(GAA)	 AG	63508-63648	GT	AGG
(ATT)	 AG	63760-63823	GT	AGG
(GTT)	 AG	64483-64544	GT	AGG
(ATG)	 AG	64992-65090	GT	AGG
(AGT)	 AG	65179-65268	GT	AGG
(GTT)	 AG	65444-65525	GT	GGG
(GAA)	 AG	65636-65725	GT	AGG
(GTG)	 AG	66403-66441	GT	AGG
(ACA)	 AG	66772-66843	GT	AAG
(TCT)	 AG	68072-68265	GT	AGG
(GAG)	 AG	68390-68536	GT	AGG
(GCT)	 AG	68761-68886	GA	GAG
-recovered pasa_asmbl_24672.p1, initial, 64992, 65090
-recovered pasa_asmbl_24672.p1, terminal, 68761, 68886
-recovered pasa_asmbl_24672.p1, internal, 62340, 62526
-recovered pasa_asmbl_24672.p1, internal, 62618, 62782
-recovered pasa_asmbl_24672.p1, internal, 63508, 63648
-recovered pasa_asmbl_24672.p1, internal, 63760, 63823
-recovered pasa_asmbl_24672.p1, internal, 64483, 64544
-recovered pasa_asmbl_24672.p1, internal, 64992, 65090
-recovered pasa_asmbl_24672.p1, internal, 65179, 65268
-recovered pasa_asmbl_24672.p1, internal, 65444, 65525
-recovered pasa_asmbl_24672.p1, internal, 65636, 65725
-recovered pasa_asmbl_24672.p1, internal, 66403, 66441
-recovered pasa_asmbl_24672.p1, internal, 66772, 66843
-recovered pasa_asmbl_24672.p1, internal, 68072, 68265
-recovered pasa_asmbl_24672.p1, internal, 68390, 68536
Valid prediction for Augustus_model.g2870.t1
Valid prediction for snap_scaffold_2-snap.1783-T1
Valid prediction for snap_scaffold_2-snap.1789-T1
Valid prediction for Augustus_model.g2868.t1
Valid prediction for snap_scaffold_2-snap.1808-T1
Couldn't classify 74944, 75249
Sorry, prediction pasa_asmbl_24674.p1 fails validation.
(CTG)	 GA	74944-75249	GA	GAG
Valid prediction for HiQ_model.g2863.t1
Valid prediction for HiQ_model.g2865.t1
Couldn't classify 15828, 15865
Sorry, prediction pasa_asmbl_24662.p1 fails validation.
(ATG)	 GA	12683-12690	GT	AGG
(GAT)	 AG	13159-13299	GT	AGG
(GGT)	 AG	13624-13735	GT	AGG
(GTG)	 AG	13985-14131	GT	AGG
(GAG)	 AG	14958-15094	GT	CTG
(CTA)	 AG	15178-15313	GT	AGG
(ACG)	 AG	15458-15659	GT	GGG
(TTT)	 AG	15828-15865	CC	CCC
-recovered pasa_asmbl_24662.p1, initial, 12683, 12690
-recovered pasa_asmbl_24662.p1, internal, 13159, 13299
-recovered pasa_asmbl_24662.p1, internal, 13624, 13735
-recovered pasa_asmbl_24662.p1, internal, 13985, 14131
-recovered pasa_asmbl_24662.p1, internal, 14958, 15094
-recovered pasa_asmbl_24662.p1, internal, 15178, 15313
-recovered pasa_asmbl_24662.p1, internal, 15458, 15659
Valid prediction for GlimmerHMM_glimmerT_4261-T1
Valid prediction for GlimmerHMM_glimmerT_4258-T1
Valid prediction for CodingQuarry_transcript_28634-T1
Valid prediction for snap_scaffold_2-snap.1810-T1
Valid prediction for pasa_asmbl_24664.p1
Valid prediction for GlimmerHMM_glimmerT_4257-T1
Valid prediction for GlimmerHMM_glimmerT_4246-T1
Valid prediction for Augustus_model.g2866.t1
Valid prediction for snap_scaffold_2-snap.1806-T1
Valid prediction for snap_scaffold_2-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_4254-T1
Valid prediction for snap_scaffold_2-snap.1801-T1
Valid prediction for GlimmerHMM_glimmerT_4266-T1
Valid prediction for HiQ_model.g2874.t1
Valid prediction for snap_scaffold_2-snap.1802-T1
Valid prediction for pasa_asmbl_24675.p1
Valid prediction for CodingQuarry_transcript_28636-T1
Valid prediction for snap_scaffold_2-snap.1799-T1
Couldn't classify 35927, 35941
Couldn't classify 38857, 39068
Sorry, prediction pasa_asmbl_24668.p1 fails validation.
(CCG)	 AC	35927-35941	GT	ATG
(TCA)	 AG	36018-36108	GT	TGG
(GAG)	 AG	36269-36369	GT	AGG
(ACC)	 AG	36474-36541	GT	TGG
(GCT)	 AG	37220-37298	GT	CAG
(TGG)	 AG	37400-37466	GT	CGG
(ACG)	 AG	37692-37829	GT	GAG
(TCC)	 AG	38042-38151	GT	TTG
(GTG)	 AG	38244-38344	GT	AGG
(GTT)	 AG	38608-38666	GT	AGG
(ACT)	 AG	38857-39068	GA	AGG
-recovered pasa_asmbl_24668.p1, internal, 36018, 36108
-recovered pasa_asmbl_24668.p1, internal, 36269, 36369
-recovered pasa_asmbl_24668.p1, internal, 36474, 36541
-recovered pasa_asmbl_24668.p1, internal, 37220, 37298
-recovered pasa_asmbl_24668.p1, internal, 37400, 37466
-recovered pasa_asmbl_24668.p1, internal, 37692, 37829
-recovered pasa_asmbl_24668.p1, internal, 38042, 38151
-recovered pasa_asmbl_24668.p1, internal, 38244, 38344
-recovered pasa_asmbl_24668.p1, internal, 38608, 38666
Couldn't classify 40047, 40231
Sorry, prediction pasa_asmbl_24670.p1 fails validation.
(CCG)	 CG	40047-40231	GT	AAG
(CCG)	 AG	40369-40622	GT	CGG
(TTA)	 AG	40726-40879	GT	AGG
(GTA)	 AG	40990-41062	GT	CTG
(GAC)	 AG	41254-41407	GT	AGG
(GCT)	 AG	41632-41758	GT	AGG
(GCT)	 AG	41857-41968	CC	AGC
-recovered pasa_asmbl_24670.p1, terminal, 41857, 41968
-recovered pasa_asmbl_24670.p1, internal, 40369, 40622
-recovered pasa_asmbl_24670.p1, internal, 40726, 40879
-recovered pasa_asmbl_24670.p1, internal, 40990, 41062
-recovered pasa_asmbl_24670.p1, internal, 41254, 41407
-recovered pasa_asmbl_24670.p1, internal, 41632, 41758

-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_2-snap.1786-T1
Valid prediction for GlimmerHMM_glimmerT_4275-T1
Valid prediction for snap_scaffold_2-snap.1813-T1
Valid prediction for snap_scaffold_2-snap.1803-T1
Valid prediction for Augustus_model.g2876.t1
Valid prediction for GlimmerHMM_glimmerT_4272-T1
Valid prediction for GlimmerHMM_glimmerT_4248-T1
Valid prediction for snap_scaffold_2-snap.1812-T1
Valid prediction for snap_scaffold_2-snap.1794-T1
Valid prediction for GlimmerHMM_glimmerT_4268-T1
Valid prediction for GlimmerHMM_glimmerT_4270-T1
Valid prediction for HiQ_model.g2867.t1
Valid prediction for GlimmerHMM_glimmerT_4259-T1
Valid prediction for GlimmerHMM_glimmerT_4265-T1
Valid prediction for HiQ_model.g2872.t1
Valid prediction for snap_scaffold_2-snap.1814-T1
Couldn't classify 43068, 43082
Couldn't classify 44668, 44690
Sorry, prediction pasa_asmbl_23368.p1 fails validation.
(ACA)	 CC	43068-43082	GT	AGG
(GCA)	 AG	43212-43305	GT	AGG
(GGT)	 AG	43404-43577	GT	GGG
(ACT)	 AG	43751-43833	GT	AGG
(GTG)	 AG	44405-44525	GT	CCG
(AGC)	 AG	44668-44690	AC	CCA
-recovered pasa_asmbl_23368.p1, internal, 43212, 43305
-recovered pasa_asmbl_23368.p1, internal, 43404, 43577
-recovered pasa_asmbl_23368.p1, internal, 43751, 43833
-recovered pasa_asmbl_23368.p1, internal, 44405, 44525
Valid prediction for snap_scaffold_2-snap.1790-T1
Valid prediction for Augustus_model.g2864.t1
Valid prediction for pasa_asmbl_23352.p1
Couldn't classify 46370, 46440
Couldn't classify 47533, 47832
Sorry, prediction pasa_asmbl_23367.p1 fails validation.
(GGG)	 AT	46370-46440	GT	AGG
(TAT)	 AG	46564-46675	GT	AGG
(GTT)	 AG	46800-46901	GT	AGG
(GTG)	 AG	47247-47411	GT	AGG
(GTG)	 AG	47533-47832	GG	GTG
-recovered pasa_asmbl_23367.p1, internal, 46564, 46675
-recovered pasa_asmbl_23367.p1, internal, 46800, 46901
-recovered pasa_asmbl_23367.p1, internal, 47247, 47411
Valid prediction for GlimmerHMM_glimmerT_4273-T1
Valid prediction for snap_scaffold_2-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_4249-T1
Valid prediction for Augustus_model.g2875.t1
Valid prediction for snap_scaffold_2-snap.1816-T1
Valid prediction for pasa_asmbl_23363.p1
Valid prediction for pasa_asmbl_23369.p1
Valid prediction for CodingQuarry_transcript_28639-T1
Valid prediction for snap_scaffold_2-snap.1797-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1815-T1
Valid prediction for snap_scaffold_2-snap.1798-T1
Valid prediction for GlimmerHMM_glimmerT_4255-T1
Valid prediction for GlimmerHMM_glimmerT_4252-T1
Valid prediction for HiQ_model.g2873.t1
Valid prediction for CodingQuarry_transcript_28637-T1
Valid prediction for snap_scaffold_2-snap.1809-T1
Valid prediction for CodingQuarry_transcript_28640-T1
Valid prediction for snap_scaffold_2-snap.1782-T1
Valid prediction for CodingQuarry_transcript_28641-T1
Valid prediction for snap_scaffold_2-snap.1807-T1
Valid prediction for Augustus_model.g2877.t1
Valid prediction for GlimmerHMM_glimmerT_4271-T1
Valid prediction for GlimmerHMM_glimmerT_4264-T1
Valid prediction for pasa_asmbl_23365.p1
Valid prediction for GlimmerHMM_glimmerT_4267-T1
Valid prediction for pasa_asmbl_23356.p1
Valid prediction for GlimmerHMM_glimmerT_4274-T1
Valid prediction for Augustus_model.g2871.t1
Valid prediction for snap_scaffold_2-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_4262-T1
Valid prediction for Augustus_model.g2878.t1
Valid prediction for GlimmerHMM_glimmerT_4263-T1
Valid prediction for GlimmerHMM_glimmerT_4260-T1
Valid prediction for snap_scaffold_2-snap.1784-T1
Valid prediction for snap_scaffold_2-snap.1804-T1
Valid prediction for snap_scaffold_2-snap.1791-T1
Valid prediction for snap_scaffold_2-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_4269-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11663, rend_intergenic: 4199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17333, rend_intergenic: 13160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24959, rend_intergenic: 20641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41968, rend_intergenic: 36240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68886, rend_intergenic: 51161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75249, rend_intergenic: 72184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80435, rend_intergenic: 76905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87588, rend_intergenic: 80658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94466, rend_intergenic: 89348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103267, rend_intergenic: 95179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112864, rend_intergenic: 109520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114754, rend_intergenic: 112871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129567, rend_intergenic: 115297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138369, rend_intergenic: 129844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139639, rend_intergenic: 139168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163485
-exon list size: 573


building trellis

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85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.6    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.7    
96.9    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 11663, rend_intergenic: 4199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17333, rend_intergenic: 13160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24959, rend_intergenic: 20641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41968, rend_intergenic: 36240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68886, rend_intergenic: 51161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75249, rend_intergenic: 72184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80435, rend_intergenic: 76905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87588, rend_intergenic: 80658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94466, rend_intergenic: 89348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103267, rend_intergenic: 95179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112864, rend_intergenic: 109520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114754, rend_intergenic: 112871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129567, rend_intergenic: 115297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138369, rend_intergenic: 129844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139639, rend_intergenic: 139168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support