-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_7616805-7834131

-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_15013-T1
Valid prediction for GlimmerHMM_glimmerT_15008-T1
Valid prediction for GlimmerHMM_glimmerT_14998-T1
Valid prediction for Augustus_model.g9929.t1
Valid prediction for snap_scaffold_6-snap.1723-T1
Valid prediction for GlimmerHMM_glimmerT_15009-T1
Valid prediction for Augustus_model.g9925.t1
Valid prediction for GlimmerHMM_glimmerT_15006-T1
Valid prediction for snap_scaffold_6-snap.1709-T1
Valid prediction for GlimmerHMM_glimmerT_15010-T1
Valid prediction for Augustus_model.g9940.t1
Valid prediction for snap_scaffold_6-snap.1696-T1
Couldn't classify 189485, 189541
Sorry, prediction Augustus_model.g9941.t1 fails validation.
(ATG)	 AC	167140-167149	GT	AGG
(TTT)	 AG	167721-167796	GT	CGG
(AGT)	 AG	168982-169200	GT	AGG
(GTG)	 AG	169865-170043	GT	AGG
(TGG)	 AG	172333-172495	GT	AGG
(GTA)	 AG	174030-174136	GT	CTG
(ATA)	 AG	174688-174835	GT	ATG
(AGC)	 AG	176312-176445	GT	GGG
(ATG)	 AG	177601-177712	GT	AGG
(GCC)	 AG	178196-178386	GT	CGG
(AGC)	 AG	178505-178588	GT	AGG
(GAG)	 AG	178705-178899	GT	CAG
(GTA)	 AG	179323-179439	GT	AGG
(GTG)	 AG	179587-179754	GT	GGG
(CCA)	 AG	179935-180037	GT	AGG
(GCA)	 AG	180635-180811	GT	AGG
(GCA)	 AG	181197-181333	GT	CAG
(ATG)	 AG	181693-181840	GT	CGG
(ACT)	 AG	183061-183201	GT	AGG
(GTA)	 AG	183959-184140	GT	AGG
(TGC)	 AG	184411-184526	GT	AGG
(CTG)	 AG	184675-184870	GT	CAG
(AAC)	 AG	185007-185105	GT	AGG
(GCT)	 AG	185221-185412	GT	AGG
(AGA)	 AG	185676-185797	GT	AGG
(GTT)	 AG	185886-185995	GT	AGG
(GTT)	 AG	186115-186265	GT	TGG
(CCT)	 AG	186501-186738	GT	TGG
(TGC)	 AG	186873-186988	GT	AGG
(GTG)	 AG	187165-187354	GT	CGG
(TGC)	 AG	187559-187657	GT	GGG
(CCT)	 AG	187795-187989	GT	AGG
(CGA)	 AG	188115-188316	GT	AGG
(GCT)	 AG	188418-188521	GT	CGG
(CCC)	 AG	188819-188889	GT	AGG
(CCT)	 AG	189065-189200	GT	CGG
(CCC)	 AG	189485-189541	GT	CAG
-recovered Augustus_model.g9941.t1, initial, 167140, 167149
add_exon() Sorry, Augustus_model.g9941.t1 177601-177712-initial-1 is invalid.
-recovered Augustus_model.g9941.t1, initial, 177601, 177712
add_exon() Sorry, Augustus_model.g9941.t1 181693-181840-initial-1 is invalid.
-recovered Augustus_model.g9941.t1, initial, 181693, 181840
-recovered Augustus_model.g9941.t1, internal, 167721, 167796
-recovered Augustus_model.g9941.t1, internal, 168982, 169200
-recovered Augustus_model.g9941.t1, internal, 169865, 170043
-recovered Augustus_model.g9941.t1, internal, 172333, 172495
-recovered Augustus_model.g9941.t1, internal, 174030, 174136
-recovered Augustus_model.g9941.t1, internal, 174688, 174835
-recovered Augustus_model.g9941.t1, internal, 176312, 176445
-recovered Augustus_model.g9941.t1, internal, 177601, 177712
-recovered Augustus_model.g9941.t1, internal, 178196, 178386
-recovered Augustus_model.g9941.t1, internal, 178505, 178588
-recovered Augustus_model.g9941.t1, internal, 178705, 178899
-recovered Augustus_model.g9941.t1, internal, 179323, 179439
-recovered Augustus_model.g9941.t1, internal, 179587, 179754
-recovered Augustus_model.g9941.t1, internal, 179935, 180037
-recovered Augustus_model.g9941.t1, internal, 180635, 180811
-recovered Augustus_model.g9941.t1, internal, 181197, 181333
-recovered Augustus_model.g9941.t1, internal, 181693, 181840
-recovered Augustus_model.g9941.t1, internal, 183061, 183201
-recovered Augustus_model.g9941.t1, internal, 183959, 184140
-recovered Augustus_model.g9941.t1, internal, 184411, 184526
-recovered Augustus_model.g9941.t1, internal, 184675, 184870
-recovered Augustus_model.g9941.t1, internal, 185007, 185105
-recovered Augustus_model.g9941.t1, internal, 185221, 185412
-recovered Augustus_model.g9941.t1, internal, 185676, 185797
-recovered Augustus_model.g9941.t1, internal, 185886, 185995
-recovered Augustus_model.g9941.t1, internal, 186115, 186265
-recovered Augustus_model.g9941.t1, internal, 186501, 186738
-recovered Augustus_model.g9941.t1, internal, 186873, 186988
-recovered Augustus_model.g9941.t1, internal, 187165, 187354
-recovered Augustus_model.g9941.t1, internal, 187559, 187657
-recovered Augustus_model.g9941.t1, internal, 187795, 187989
-recovered Augustus_model.g9941.t1, internal, 188115, 188316
-recovered Augustus_model.g9941.t1, internal, 188418, 188521
-recovered Augustus_model.g9941.t1, internal, 188819, 188889
-recovered Augustus_model.g9941.t1, internal, 189065, 189200
-recovered Augustus_model.g9941.t1, internal, 189485, 189541
Valid prediction for snap_scaffold_6-snap.1702-T1
Valid prediction for pasa_asmbl_47084.p1
Valid prediction for GlimmerHMM_glimmerT_15002-T1
Valid prediction for Augustus_model.g9927.t1
Valid prediction for Augustus_model.g9918.t1
Valid prediction for GlimmerHMM_glimmerT_15012-T1
Valid prediction for snap_scaffold_6-snap.1703-T1
Valid prediction for snap_scaffold_6-snap.1693-T1
Valid prediction for snap_scaffold_6-snap.1705-T1
Valid prediction for snap_scaffold_6-snap.1697-T1
Valid prediction for GlimmerHMM_glimmerT_14990-T1
Valid prediction for GlimmerHMM_glimmerT_14976-T1
Valid prediction for GlimmerHMM_glimmerT_14977-T1
Valid prediction for GlimmerHMM_glimmerT_14982-T1
Couldn't classify 30443, 30525
Sorry, prediction pasa_asmbl_47086.p1 fails validation.
(CCC)	 CC	30443-30525	GT	AGG
(TGA)	 AG	31115-31199	GT	AGG
(GAG)	 AG	31306-31427	GT	TGG
(GAC)	 AG	32136-32285	GT	TGG
(GTA)	 AG	32988-36411	GT	AGG
(GAG)	 AG	36545-36716	GT	GAG
(GTG)	 AG	36880-37086	GT	AGG
(GAA)	 AG	37214-37239	CT	GAC
-recovered pasa_asmbl_47086.p1, terminal, 37214, 37239
-recovered pasa_asmbl_47086.p1, internal, 31115, 31199
-recovered pasa_asmbl_47086.p1, internal, 31306, 31427
-recovered pasa_asmbl_47086.p1, internal, 32136, 32285
-recovered pasa_asmbl_47086.p1, internal, 32988, 36411
-recovered pasa_asmbl_47086.p1, internal, 36545, 36716
-recovered pasa_asmbl_47086.p1, internal, 36880, 37086
Valid prediction for snap_scaffold_6-snap.1719-T1
Valid prediction for snap_scaffold_6-snap.1732-T1
Valid prediction for Augustus_model.g9942.t1
Valid prediction for snap_scaffold_6-snap.1733-T1
Valid prediction for GlimmerHMM_glimmerT_15011-T1
Valid prediction for snap_scaffold_6-snap.1699-T1
Valid prediction for GlimmerHMM_glimmerT_14997-T1
Valid prediction for Augustus_model.g9943.t1
Valid prediction for snap_scaffold_6-snap.1731-T1
Valid prediction for CodingQuarry_transcript_55109-T1
Valid prediction for GlimmerHMM_glimmerT_14984-T1
Valid prediction for Augustus_model.g9921.t1
Valid prediction for GlimmerHMM_glimmerT_14981-T1
Valid prediction for snap_scaffold_6-snap.1692-T1
Valid prediction for snap_scaffold_6-snap.1700-T1
Valid prediction for snap_scaffold_6-snap.1725-T1
Valid prediction for GlimmerHMM_glimmerT_15003-T1
Valid prediction for GlimmerHMM_glimmerT_14986-T1
Valid prediction for Augustus_model.g9922.t1
Valid prediction for snap_scaffold_6-snap.1716-T1
Valid prediction for Augustus_model.g9930.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_14993-T1
Valid prediction for Augustus_model.g9937.t1
Valid prediction for GlimmerHMM_glimmerT_14988-T1
Couldn't classify 135867, 135880
Sorry, prediction CodingQuarry_transcript_55110-T1 fails validation.
(ATG)	 AG	135867-135880	TA	AGT
(GAA)	 AG	136074-136161	GT	TGG
(GTT)	 AG	136308-136394	GT	AGG
(GTC)	 AG	136863-136928	GT	GGG
(CAA)	 AG	137024-137104	GT	AGG
(GGA)	 AG	137231-137300	GT	AGG
(AGA)	 AG	137512-137561	AG	AGA
-recovered CodingQuarry_transcript_55110-T1, terminal, 137512, 137561
-recovered CodingQuarry_transcript_55110-T1, internal, 136074, 136161
-recovered CodingQuarry_transcript_55110-T1, internal, 136308, 136394
-recovered CodingQuarry_transcript_55110-T1, internal, 136863, 136928
-recovered CodingQuarry_transcript_55110-T1, internal, 137024, 137104
-recovered CodingQuarry_transcript_55110-T1, internal, 137231, 137300
Valid prediction for GlimmerHMM_glimmerT_14983-T1
Valid prediction for Augustus_model.g9935.t1
Valid prediction for Augustus_model.g9934.t1
Valid prediction for GlimmerHMM_glimmerT_14985-T1
Valid prediction for GlimmerHMM_glimmerT_15001-T1
Valid prediction for Augustus_model.g9931.t1
Valid prediction for GlimmerHMM_glimmerT_14979-T1
Valid prediction for snap_scaffold_6-snap.1714-T1
Valid prediction for Augustus_model.g9926.t1
Valid prediction for snap_scaffold_6-snap.1724-T1
Valid prediction for snap_scaffold_6-snap.1722-T1
Valid prediction for GlimmerHMM_glimmerT_14991-T1
Valid prediction for Augustus_model.g9933.t1
Valid prediction for snap_scaffold_6-snap.1698-T1
Valid prediction for snap_scaffold_6-snap.1727-T1
Valid prediction for GlimmerHMM_glimmerT_14999-T1
Valid prediction for Augustus_model.g9939.t1
Valid prediction for snap_scaffold_6-snap.1708-T1
Valid prediction for snap_scaffold_6-snap.1711-T1
Valid prediction for GlimmerHMM_glimmerT_14996-T1
Couldn't classify 125884, 125921
Couldn't classify 130721, 130802
Sorry, prediction pasa_asmbl_49441.p1 fails validation.
(CTG)	 GT	125884-125921	GT	ACG
(GAT)	 AG	126955-127027	GT	TGG
(GGC)	 AG	128991-129060	GT	AGG
(ATG)	 AG	129223-129278	GT	AGG
(TCG)	 AG	130017-130109	GT	AGG
(AGA)	 AG	130233-130325	GT	AGG
(GAC)	 AG	130429-130571	GT	AGG
(GGA)	 AG	130721-130802	CA	CTC
add_exon() Sorry, pasa_asmbl_49441.p1 129223-129278-initial-1 is invalid.
-recovered pasa_asmbl_49441.p1, initial, 129223, 129278
-recovered pasa_asmbl_49441.p1, internal, 126955, 127027
-recovered pasa_asmbl_49441.p1, internal, 128991, 129060
-recovered pasa_asmbl_49441.p1, internal, 129223, 129278
-recovered pasa_asmbl_49441.p1, internal, 130017, 130109
-recovered pasa_asmbl_49441.p1, internal, 130233, 130325
-recovered pasa_asmbl_49441.p1, internal, 130429, 130571
Valid prediction for GlimmerHMM_glimmerT_14994-T1
Valid prediction for snap_scaffold_6-snap.1720-T1
Valid prediction for GlimmerHMM_glimmerT_14995-T1
Valid prediction for snap_scaffold_6-snap.1704-T1
Valid prediction for snap_scaffold_6-snap.1729-T1
Valid prediction for Augustus_model.g9923.t1
Valid prediction for snap_scaffold_6-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_14978-T1
Valid prediction for pasa_asmbl_48508.p1
Valid prediction for snap_scaffold_6-snap.1728-T1
Valid prediction for snap_scaffold_6-snap.1717-T1
Valid prediction for GlimmerHMM_glimmerT_15007-T1
Valid prediction for snap_scaffold_6-snap.1712-T1
Valid prediction for snap_scaffold_6-snap.1726-T1
Valid prediction for snap_scaffold_6-snap.1721-T1
Valid prediction for GlimmerHMM_glimmerT_15005-T1
Valid prediction for Augustus_model.g9928.t1
Valid prediction for GlimmerHMM_glimmerT_15000-T1
Valid prediction for Augustus_model.g9919.t1
Valid prediction for snap_scaffold_6-snap.1710-T1
Valid prediction for GlimmerHMM_glimmerT_14989-T1
Valid prediction for snap_scaffold_6-snap.1701-T1
Valid prediction for snap_scaffold_6-snap.1706-T1
Valid prediction for HiQ_model.g9932.t1
Valid prediction for snap_scaffold_6-snap.1694-T1
Valid prediction for snap_scaffold_6-snap.1715-T1
Valid prediction for GlimmerHMM_glimmerT_14980-T1
Valid prediction for GlimmerHMM_glimmerT_15004-T1
Valid prediction for Augustus_model.g9936.t1
Valid prediction for snap_scaffold_6-snap.1718-T1
Valid prediction for snap_scaffold_6-snap.1707-T1
Valid prediction for CodingQuarry_transcript_55111-T1
Valid prediction for snap_scaffold_6-snap.1730-T1
Valid prediction for Augustus_model.g9924.t1
Valid prediction for Augustus_model.g9920.t1
Valid prediction for GlimmerHMM_glimmerT_14992-T1
Valid prediction for snap_scaffold_6-snap.1713-T1
Valid prediction for Augustus_model.g9938.t1
Valid prediction for GlimmerHMM_glimmerT_14987-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25864, rend_intergenic: 10856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28389, rend_intergenic: 25976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28876, rend_intergenic: 28615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61123, rend_intergenic: 49875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72928, rend_intergenic: 62248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98271, rend_intergenic: 96965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100573, rend_intergenic: 98677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161150, rend_intergenic: 144154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166763, rend_intergenic: 166667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169668, rend_intergenic: 167276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200150, rend_intergenic: 170002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217327
-exon list size: 461


building trellis

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87.0    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 25864, rend_intergenic: 10856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28389, rend_intergenic: 25976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28876, rend_intergenic: 28615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61123, rend_intergenic: 49875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72928, rend_intergenic: 62248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98271, rend_intergenic: 96965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100573, rend_intergenic: 98677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161150, rend_intergenic: 144154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166763, rend_intergenic: 166667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169668, rend_intergenic: 167276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200150, rend_intergenic: 170002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support