-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_5989509-6158689

-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 GeneMark_model.59444_t
Valid prediction for snap_scaffold_14-snap.1249-T1
Valid prediction for GeneMark_model.59498_t
Valid prediction for snap_scaffold_14-snap.1219-T1
Valid prediction for GlimmerHMM_glimmerT_34709-T1
Valid prediction for GlimmerHMM_glimmerT_34713-T1
Valid prediction for GeneMark_model.59478_t
Valid prediction for snap_scaffold_14-snap.1230-T1
Valid prediction for GeneMark_model.59468_t
Valid prediction for CodingQuarry_transcript_15611-T1
Valid prediction for snap_scaffold_14-snap.1225-T1
Valid prediction for GeneMark_model.59461_t
Valid prediction for GeneMark_model.59484_t
Valid prediction for GeneMark_model.59471_t
Valid prediction for snap_scaffold_14-snap.1240-T1
Valid prediction for GlimmerHMM_glimmerT_34722-T1
Valid prediction for Augustus_model.g23333.t1
Valid prediction for GeneMark_model.59455_t
Valid prediction for GeneMark_model.59496_t
Valid prediction for GeneMark_model.59445_t
Valid prediction for GeneMark_model.59450_t
Valid prediction for snap_scaffold_14-snap.1222-T1
Valid prediction for snap_scaffold_14-snap.1243-T1
Couldn't classify 59524, 59624
Sorry, prediction pasa_asmbl_12024.p1 fails validation.
(AGA)	 AT	59524-59624	GT	TGG
(GTA)	 AG	59980-60138	GT	AGG
(TGG)	 AG	60650-60728	CA	AAC
-recovered pasa_asmbl_12024.p1, terminal, 60650, 60728
-recovered pasa_asmbl_12024.p1, internal, 59980, 60138
Valid prediction for GeneMark_model.59437_t
Valid prediction for GeneMark_model.59480_t
Valid prediction for GeneMark_model.59448_t
Valid prediction for snap_scaffold_14-snap.1232-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_34715-T1
Valid prediction for GeneMark_model.59473_t
Valid prediction for snap_scaffold_14-snap.1223-T1
Valid prediction for GeneMark_model.59443_t
Valid prediction for snap_scaffold_14-snap.1235-T1
Valid prediction for GeneMark_model.59494_t
Valid prediction for snap_scaffold_14-snap.1255-T1
Valid prediction for GeneMark_model.59470_t
Valid prediction for GlimmerHMM_glimmerT_34730-T1
Valid prediction for snap_scaffold_14-snap.1253-T1
Valid prediction for snap_scaffold_14-snap.1241-T1
Valid prediction for snap_scaffold_14-snap.1247-T1
Valid prediction for snap_scaffold_14-snap.1246-T1
Valid prediction for GlimmerHMM_glimmerT_34726-T1
Valid prediction for Augustus_model.g23339.t1
Valid prediction for Augustus_model.g23335.t1
Valid prediction for Augustus_model.g23332.t1
Valid prediction for Augustus_model.g23342.t1
Valid prediction for GeneMark_model.59459_t
Valid prediction for GeneMark_model.59475_t
Valid prediction for snap_scaffold_14-snap.1238-T1
Valid prediction for GlimmerHMM_glimmerT_34707-T1
Valid prediction for GeneMark_model.59440_t
Valid prediction for snap_scaffold_14-snap.1261-T1
Valid prediction for GeneMark_model.59442_t
Valid prediction for Augustus_model.g23331.t1
Valid prediction for GeneMark_model.59462_t
Valid prediction for GeneMark_model.59453_t
Valid prediction for GeneMark_model.59466_t
Valid prediction for Augustus_model.g23343.t1
Valid prediction for GeneMark_model.59464_t
Valid prediction for GeneMark_model.59482_t
Valid prediction for Augustus_model.g23337.t1
Valid prediction for GlimmerHMM_glimmerT_34717-T1
Valid prediction for GlimmerHMM_glimmerT_34711-T1
Valid prediction for GeneMark_model.59490_t
Valid prediction for snap_scaffold_14-snap.1228-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: -)Couldn't classify 44813, 44942
Sorry, prediction pasa_asmbl_13093.p1 fails validation.
(ATG)	 GT	44143-44579	GT	AGG
(ACT)	 AG	44813-44942	GA	GCG
-recovered pasa_asmbl_13093.p1, initial, 44143, 44579
Valid prediction for GeneMark_model.59451_t
Valid prediction for GeneMark_model.59500_t
Valid prediction for GlimmerHMM_glimmerT_34719-T1
Valid prediction for GeneMark_model.59481_t
Valid prediction for GlimmerHMM_glimmerT_34725-T1
Valid prediction for GeneMark_model.59454_t
Valid prediction for GlimmerHMM_glimmerT_34723-T1
Valid prediction for GeneMark_model.59491_t
Valid prediction for GeneMark_model.59474_t
Valid prediction for snap_scaffold_14-snap.1244-T1
Valid prediction for GeneMark_model.59493_t
Valid prediction for snap_scaffold_14-snap.1237-T1
Valid prediction for GeneMark_model.59465_t
Valid prediction for GeneMark_model.59486_t
Valid prediction for GeneMark_model.59502_t
Valid prediction for snap_scaffold_14-snap.1233-T1
Valid prediction for GlimmerHMM_glimmerT_34710-T1
Valid prediction for GeneMark_model.59439_t
Valid prediction for GeneMark_model.59458_t
Valid prediction for Augustus_model.g23341.t1
Valid prediction for Augustus_model.g23340.t1
Valid prediction for GeneMark_model.59452_t
Valid prediction for GeneMark_model.59497_t
Valid prediction for Augustus_model.g23334.t1
Valid prediction for GlimmerHMM_glimmerT_34727-T1
Valid prediction for GeneMark_model.59495_t
Valid prediction for snap_scaffold_14-snap.1260-T1
Valid prediction for snap_scaffold_14-snap.1227-T1
Valid prediction for snap_scaffold_14-snap.1239-T1
Valid prediction for GeneMark_model.59467_t
Valid prediction for snap_scaffold_14-snap.1217-T1
Valid prediction for GlimmerHMM_glimmerT_34720-T1
Valid prediction for snap_scaffold_14-snap.1245-T1
Valid prediction for GlimmerHMM_glimmerT_34721-T1
Valid prediction for GlimmerHMM_glimmerT_34706-T1
Valid prediction for GeneMark_model.59449_t
Valid prediction for GeneMark_model.59487_t
Valid prediction for GlimmerHMM_glimmerT_34729-T1
Valid prediction for GlimmerHMM_glimmerT_34714-T1
Valid prediction for GeneMark_model.59492_t
Valid prediction for GeneMark_model.59456_t
Valid prediction for GeneMark_model.59476_t
Valid prediction for snap_scaffold_14-snap.1236-T1
Valid prediction for GeneMark_model.59460_t
Valid prediction for snap_scaffold_14-snap.1220-T1
Valid prediction for GeneMark_model.59499_t
Valid prediction for snap_scaffold_14-snap.1256-T1
Valid prediction for GlimmerHMM_glimmerT_34716-T1
Valid prediction for GlimmerHMM_glimmerT_34731-T1
Valid prediction for snap_scaffold_14-snap.1259-T1
Couldn't classify 45771, 46181
Sorry, prediction pasa_asmbl_13092.p1 fails validation.
(AGT)	 GC	45771-46181	GG	GAG
Valid prediction for snap_scaffold_14-snap.1254-T1
Valid prediction for GeneMark_model.59472_t
Valid prediction for snap_scaffold_14-snap.1258-T1
Valid prediction for GeneMark_model.59441_t
Valid prediction for snap_scaffold_14-snap.1218-T1
Valid prediction for GeneMark_model.59479_t
Valid prediction for GeneMark_model.59457_t
Valid prediction for GeneMark_model.59438_t
Valid prediction for GeneMark_model.59477_t
Valid prediction for snap_scaffold_14-snap.1224-T1
Valid prediction for snap_scaffold_14-snap.1257-T1
Valid prediction for GeneMark_model.59501_t
Valid prediction for snap_scaffold_14-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_34705-T1
Valid prediction for Augustus_model.g23336.t1
Valid prediction for Augustus_model.g23330.t1
Valid prediction for GlimmerHMM_glimmerT_34712-T1
Valid prediction for snap_scaffold_14-snap.1234-T1
Valid prediction for GeneMark_model.59483_t
Valid prediction for GeneMark_model.59447_t
Valid prediction for snap_scaffold_14-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_34724-T1
Valid prediction for GeneMark_model.59446_t
Valid prediction for GlimmerHMM_glimmerT_34728-T1
Valid prediction for Augustus_model.g23338.t1
Valid prediction for snap_scaffold_14-snap.1250-T1
Valid prediction for GeneMark_model.59489_t
Valid prediction for snap_scaffold_14-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_34708-T1
Valid prediction for snap_scaffold_14-snap.1248-T1
Valid prediction for GeneMark_model.59488_t
Valid prediction for GeneMark_model.59463_t
Valid prediction for snap_scaffold_14-snap.1242-T1
Valid prediction for snap_scaffold_14-snap.1231-T1
Valid prediction for GeneMark_model.59469_t
Valid prediction for GlimmerHMM_glimmerT_34718-T1
Valid prediction for snap_scaffold_14-snap.1252-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8944, rend_intergenic: 8391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15580, rend_intergenic: 9556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17088, rend_intergenic: 16033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23746, rend_intergenic: 22510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29639, rend_intergenic: 25602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37954, rend_intergenic: 29755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40547, rend_intergenic: 40281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44904, rend_intergenic: 40614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51121, rend_intergenic: 45628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62692, rend_intergenic: 52979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73617, rend_intergenic: 64820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74907, rend_intergenic: 74015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78769, rend_intergenic: 77976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87589, rend_intergenic: 78783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89919, rend_intergenic: 89234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103031, rend_intergenic: 91989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107129, rend_intergenic: 103254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110359, rend_intergenic: 107290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118497, rend_intergenic: 112207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128093, rend_intergenic: 127054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133906, rend_intergenic: 128164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138749, rend_intergenic: 136214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142869, rend_intergenic: 138930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156989, rend_intergenic: 145327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169181
-exon list size: 716


building trellis

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88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 8944, rend_intergenic: 8391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15580, rend_intergenic: 9556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17088, rend_intergenic: 16033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23746, rend_intergenic: 22510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29639, rend_intergenic: 25602  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37954, rend_intergenic: 29755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40547, rend_intergenic: 40281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44904, rend_intergenic: 40614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51121, rend_intergenic: 45628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62692, rend_intergenic: 52979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73617, rend_intergenic: 64820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74907, rend_intergenic: 74015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78769, rend_intergenic: 77976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87589, rend_intergenic: 78783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89919, rend_intergenic: 89234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103031, rend_intergenic: 91989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107129, rend_intergenic: 103254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110359, rend_intergenic: 107290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118497, rend_intergenic: 112207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128093, rend_intergenic: 127054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133906, rend_intergenic: 128164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138749, rend_intergenic: 136214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142869, rend_intergenic: 138930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156989, rend_intergenic: 145327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support