-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_10765982-11048593

-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_7-snap.2102-T1
Valid prediction for GlimmerHMM_glimmerT_18079-T1
Valid prediction for Augustus_model.g12157.t1
Valid prediction for Augustus_model.g12155.t1
Valid prediction for GlimmerHMM_glimmerT_18078-T1
Valid prediction for GlimmerHMM_glimmerT_18048-T1
Valid prediction for snap_scaffold_7-snap.2058-T1
Valid prediction for snap_scaffold_7-snap.2094-T1
Valid prediction for Augustus_model.g12137.t1
Couldn't classify 71922, 72064
Couldn't classify 74602, 74656
Sorry, prediction pasa_asmbl_50145.p1 fails validation.
(AGG)	 CT	71922-72064	GT	AAG
(ACA)	 AG	72164-72189	GT	AGG
(CCA)	 AG	72584-72619	GT	AGG
(AGG)	 AG	74265-74388	GT	GTG
(ATA)	 AG	74602-74656	GA	GGG
-recovered pasa_asmbl_50145.p1, internal, 72164, 72189
-recovered pasa_asmbl_50145.p1, internal, 72584, 72619
-recovered pasa_asmbl_50145.p1, internal, 74265, 74388
Valid prediction for snap_scaffold_7-snap.2086-T1
Valid prediction for GlimmerHMM_glimmerT_18091-T1
Valid prediction for GlimmerHMM_glimmerT_18052-T1
Valid prediction for snap_scaffold_7-snap.2067-T1
Valid prediction for GlimmerHMM_glimmerT_18055-T1
Valid prediction for GlimmerHMM_glimmerT_18083-T1
Valid prediction for GlimmerHMM_glimmerT_18075-T1
Valid prediction for snap_scaffold_7-snap.2082-T1
Valid prediction for GlimmerHMM_glimmerT_18065-T1
Valid prediction for snap_scaffold_7-snap.2070-T1
Valid prediction for Augustus_model.g12149.t1
Valid prediction for GlimmerHMM_glimmerT_18087-T1
Valid prediction for Augustus_model.g12154.t1
Valid prediction for snap_scaffold_7-snap.2056-T1
Valid prediction for snap_scaffold_7-snap.2060-T1
Valid prediction for snap_scaffold_7-snap.2101-T1
Valid prediction for snap_scaffold_7-snap.2097-T1
Valid prediction for GlimmerHMM_glimmerT_18071-T1
Valid prediction for GlimmerHMM_glimmerT_18086-T1
Valid prediction for GlimmerHMM_glimmerT_18050-T1
Valid prediction for Augustus_model.g12150.t1
Valid prediction for GlimmerHMM_glimmerT_18067-T1
Valid prediction for GlimmerHMM_glimmerT_18080-T1
Valid prediction for snap_scaffold_7-snap.2099-T1
Valid prediction for GlimmerHMM_glimmerT_18051-T1
Valid prediction for snap_scaffold_7-snap.2090-T1
Valid prediction for snap_scaffold_7-snap.2068-T1
Valid prediction for Augustus_model.g12158.t1
Valid prediction for snap_scaffold_7-snap.2079-T1
Valid prediction for snap_scaffold_7-snap.2052-T1
Valid prediction for GlimmerHMM_glimmerT_18085-T1
Valid prediction for snap_scaffold_7-snap.2091-T1
Valid prediction for snap_scaffold_7-snap.2055-T1
Valid prediction for snap_scaffold_7-snap.2062-T1
Valid prediction for GlimmerHMM_glimmerT_18054-T1
Valid prediction for GlimmerHMM_glimmerT_18064-T1
Valid prediction for snap_scaffold_7-snap.2077-T1
Valid prediction for Augustus_model.g12156.t1
Valid prediction for GlimmerHMM_glimmerT_18061-T1
Valid prediction for GlimmerHMM_glimmerT_18090-T1
Valid prediction for GlimmerHMM_glimmerT_18070-T1
Valid prediction for GlimmerHMM_glimmerT_18074-T1
Valid prediction for Augustus_model.g12144.t1
Valid prediction for Augustus_model.g12136.t1
Couldn't classify 75198, 75266
Couldn't classify 84634, 84945
Sorry, prediction pasa_asmbl_50146.p1 fails validation.
(CTT)	 GC	75198-75266	GT	GGG
(CCG)	 AG	75904-76014	GT	CAG
(GAT)	 AG	76988-77083	GT	AGG
(TCA)	 AG	77195-77329	GT	GGG
(AAA)	 AG	77589-77724	GT	AGG
(GAG)	 AG	79187-79338	GT	AGG
(GTC)	 AG	79511-79636	GT	AGG
(GGT)	 AG	79765-79896	GT	ATG
(GAG)	 AG	80263-80330	GT	AAG
(ATG)	 AG	80440-80528	GT	AGG
(ATG)	 AG	80659-80756	GT	CTG
(GGA)	 AG	82937-83024	GT	CTG
(GGG)	 AG	83127-83225	GT	TGG
(GGG)	 AG	84331-84461	GT	AGG
(GCC)	 AG	84634-84945	GA	CCG
-recovered pasa_asmbl_50146.p1, initial, 80440, 80528
-recovered pasa_asmbl_50146.p1, initial, 80659, 80756
add_exon() Sorry, pasa_asmbl_50146.p1 80440-80528-terminal-2 is invalid.
-recovered pasa_asmbl_50146.p1, terminal, 80440, 80528
-recovered pasa_asmbl_50146.p1, internal, 75904, 76014
-recovered pasa_asmbl_50146.p1, internal, 76988, 77083
-recovered pasa_asmbl_50146.p1, internal, 77195, 77329
-recovered pasa_asmbl_50146.p1, internal, 77589, 77724
-recovered pasa_asmbl_50146.p1, internal, 79187, 79338
-recovered pasa_asmbl_50146.p1, internal, 79511, 79636
-recovered pasa_asmbl_50146.p1, internal, 79765, 79896
-recovered pasa_asmbl_50146.p1, internal, 80263, 80330
-recovered pasa_asmbl_50146.p1, internal, 80440, 80528
-recovered pasa_asmbl_50146.p1, internal, 80659, 80756
-recovered pasa_asmbl_50146.p1, internal, 82937, 83024
-recovered pasa_asmbl_50146.p1, internal, 83127, 83225
-recovered pasa_asmbl_50146.p1, internal, 84331, 84461
Valid prediction for snap_scaffold_7-snap.2075-T1
Valid prediction for GlimmerHMM_glimmerT_18060-T1
Valid prediction for snap_scaffold_7-snap.2074-T1
Valid prediction for GlimmerHMM_glimmerT_18084-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_7-snap.2092-T1
Valid prediction for GlimmerHMM_glimmerT_18058-T1
Valid prediction for snap_scaffold_7-snap.2078-T1
Valid prediction for snap_scaffold_7-snap.2054-T1
Valid prediction for pasa_asmbl_51144.p1
Valid prediction for snap_scaffold_7-snap.2087-T1
Couldn't classify 192951, 193170
Sorry, prediction pasa_asmbl_51141.p1 fails validation.
(GTT)	 TT	192951-193170	GT	GAG
(AGT)	 AG	193324-193409	AA	AGA
-recovered pasa_asmbl_51141.p1, terminal, 193324, 193409
Valid prediction for snap_scaffold_7-snap.2073-T1
Valid prediction for CodingQuarry_transcript_57624-T1
Valid prediction for CodingQuarry_transcript_57625-T1
Valid prediction for GlimmerHMM_glimmerT_18088-T1
Valid prediction for GlimmerHMM_glimmerT_18072-T1
Valid prediction for GlimmerHMM_glimmerT_18069-T1
Valid prediction for Augustus_model.g12142.t1
Valid prediction for Augustus_model.g12146.t1
Valid prediction for snap_scaffold_7-snap.2096-T1
Valid prediction for GlimmerHMM_glimmerT_18056-T1
Couldn't classify 131962, 131995
Sorry, prediction pasa_asmbl_51146.p1 fails validation.
(TCT)	 CC	131962-131995	GT	AGG
(CCG)	 AG	132172-132317	GT	AGG
(ACT)	 AG	132505-132573	GT	TGG
(GAA)	 AG	132807-132889	GT	CAG
(GTA)	 AG	133121-133193	CC	GAC
-recovered pasa_asmbl_51146.p1, terminal, 133121, 133193
-recovered pasa_asmbl_51146.p1, internal, 132172, 132317
-recovered pasa_asmbl_51146.p1, internal, 132505, 132573
-recovered pasa_asmbl_51146.p1, internal, 132807, 132889
Valid prediction for GlimmerHMM_glimmerT_18057-T1
Valid prediction for snap_scaffold_7-snap.2059-T1
Valid prediction for snap_scaffold_7-snap.2095-T1
Valid prediction for snap_scaffold_7-snap.2064-T1
Valid prediction for snap_scaffold_7-snap.2088-T1
Valid prediction for Augustus_model.g12145.t1
Valid prediction for HiQ_model.g12141.t1
Valid prediction for snap_scaffold_7-snap.2057-T1
Valid prediction for Augustus_model.g12151.t1
Valid prediction for Augustus_model.g12148.t1
Valid prediction for GlimmerHMM_glimmerT_18053-T1
Valid prediction for snap_scaffold_7-snap.2083-T1
Valid prediction for snap_scaffold_7-snap.2098-T1
Valid prediction for GlimmerHMM_glimmerT_18047-T1
Valid prediction for Augustus_model.g12140.t1
Valid prediction for snap_scaffold_7-snap.2072-T1
Valid prediction for Augustus_model.g12143.t1
Valid prediction for snap_scaffold_7-snap.2089-T1
Couldn't classify 160349, 160501
Sorry, prediction pasa_asmbl_51142.p1 fails validation.
(GCT)	 AA	160349-160501	GT	AGG
(GGG)	 AG	160981-161115	GT	AGG
(AGG)	 AG	161233-161373	AC	GAA
-recovered pasa_asmbl_51142.p1, terminal, 161233, 161373
-recovered pasa_asmbl_51142.p1, internal, 160981, 161115
Valid prediction for snap_scaffold_7-snap.2081-T1
Valid prediction for snap_scaffold_7-snap.2069-T1
Valid prediction for GlimmerHMM_glimmerT_18077-T1
Valid prediction for Augustus_model.g12147.t1
Valid prediction for HiQ_model.g12138.t1
Valid prediction for snap_scaffold_7-snap.2066-T1
Valid prediction for GlimmerHMM_glimmerT_18046-T1
Valid prediction for snap_scaffold_7-snap.2053-T1
Valid prediction for snap_scaffold_7-snap.2085-T1
Valid prediction for snap_scaffold_7-snap.2063-T1
Couldn't classify 131754, 131799
Sorry, prediction pasa_asmbl_51147.p1 fails validation.
(ATG)	 TC	130174-130262	GT	ATG
(GCA)	 AG	130475-130553	GT	AGG
(CTC)	 AG	131090-131173	GT	AGG
(ATG)	 AG	131390-131496	GT	AGG
(GTA)	 AG	131754-131799	TA	TCT
-recovered pasa_asmbl_51147.p1, initial, 130174, 130262
-recovered pasa_asmbl_51147.p1, initial, 131390, 131496
-recovered pasa_asmbl_51147.p1, internal, 130475, 130553
-recovered pasa_asmbl_51147.p1, internal, 131090, 131173
-recovered pasa_asmbl_51147.p1, internal, 131390, 131496
Valid prediction for GlimmerHMM_glimmerT_18089-T1
Valid prediction for GlimmerHMM_glimmerT_18066-T1
Valid prediction for snap_scaffold_7-snap.2071-T1
Valid prediction for GlimmerHMM_glimmerT_18068-T1
Valid prediction for GlimmerHMM_glimmerT_18059-T1
Valid prediction for snap_scaffold_7-snap.2061-T1
Valid prediction for GlimmerHMM_glimmerT_18082-T1
Valid prediction for GlimmerHMM_glimmerT_18076-T1
Valid prediction for snap_scaffold_7-snap.2084-T1
Valid prediction for Augustus_model.g12152.t1
Valid prediction for GlimmerHMM_glimmerT_18063-T1
Valid prediction for CodingQuarry_transcript_57626-T1
Valid prediction for snap_scaffold_7-snap.2076-T1
Valid prediction for Augustus_model.g12153.t1
Valid prediction for Augustus_model.g12139.t1
Valid prediction for GlimmerHMM_glimmerT_18062-T1
Valid prediction for snap_scaffold_7-snap.2100-T1
Valid prediction for snap_scaffold_7-snap.2080-T1
Valid prediction for GlimmerHMM_glimmerT_18073-T1
Valid prediction for GlimmerHMM_glimmerT_18081-T1
Valid prediction for snap_scaffold_7-snap.2065-T1
Valid prediction for snap_scaffold_7-snap.2093-T1
Valid prediction for GlimmerHMM_glimmerT_18049-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11161, rend_intergenic: 5275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17626, rend_intergenic: 12492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37206, rend_intergenic: 31627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52841, rend_intergenic: 41364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72826, rend_intergenic: 53799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85143, rend_intergenic: 73246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96346, rend_intergenic: 95984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118718, rend_intergenic: 116716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158159, rend_intergenic: 154687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160064, rend_intergenic: 159459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175965, rend_intergenic: 160248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180096, rend_intergenic: 176257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188854, rend_intergenic: 181103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206799, rend_intergenic: 191294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218239, rend_intergenic: 206848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218699, rend_intergenic: 218517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224902, rend_intergenic: 219501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232556, rend_intergenic: 225187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236147, rend_intergenic: 232872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240944, rend_intergenic: 236340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 275675, rend_intergenic: 242179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 282612
-exon list size: 494


building trellis

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92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 11161, rend_intergenic: 5275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17626, rend_intergenic: 12492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37206, rend_intergenic: 31627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52841, rend_intergenic: 41364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72826, rend_intergenic: 53799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85143, rend_intergenic: 73246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96346, rend_intergenic: 95984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118718, rend_intergenic: 116716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158159, rend_intergenic: 154687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160064, rend_intergenic: 159459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175965, rend_intergenic: 160248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180096, rend_intergenic: 176257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188854, rend_intergenic: 181103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206799, rend_intergenic: 191294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218239, rend_intergenic: 206848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218699, rend_intergenic: 218517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224902, rend_intergenic: 219501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232556, rend_intergenic: 225187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236147, rend_intergenic: 232872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240944, rend_intergenic: 236340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 275675, rend_intergenic: 242179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support