-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_4232782-4427105

-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.101780_t
Valid prediction for GeneMark_model.101786_t
Valid prediction for snap_scaffold_27-snap.1025-T1
Valid prediction for snap_scaffold_27-snap.1021-T1
Valid prediction for snap_scaffold_27-snap.1048-T1
Valid prediction for Augustus_model.g39029.t1
Valid prediction for snap_scaffold_27-snap.1031-T1
Valid prediction for Augustus_model.g39033.t1
Valid prediction for GlimmerHMM_glimmerT_58548-T1
Valid prediction for GeneMark_model.101790_t
Valid prediction for pasa_asmbl_36241.p2
Valid prediction for GeneMark_model.101796_t
Valid prediction for GlimmerHMM_glimmerT_58552-T1
Valid prediction for GeneMark_model.101776_t
Valid prediction for pasa_asmbl_36230.p1
Valid prediction for GlimmerHMM_glimmerT_58553-T1
Valid prediction for GlimmerHMM_glimmerT_58567-T1
Valid prediction for GeneMark_model.101789_t
Valid prediction for snap_scaffold_27-snap.1053-T1
Valid prediction for Augustus_model.g39027.t1
Valid prediction for GlimmerHMM_glimmerT_58564-T1
Valid prediction for GlimmerHMM_glimmerT_58550-T1
Valid prediction for snap_scaffold_27-snap.1028-T1
Valid prediction for GeneMark_model.101803_t
Valid prediction for GlimmerHMM_glimmerT_58568-T1
Valid prediction for GlimmerHMM_glimmerT_58566-T1
Valid prediction for GeneMark_model.101802_t
Valid prediction for CodingQuarry_transcript_41785-T1
Couldn't classify 10522, 10555
Sorry, prediction pasa_asmbl_36226.p1 fails validation.
(GGA)	 AA	10522-10555	GT	AGG
(ATT)	 AG	10873-10938	GT	AGG
(GTA)	 AG	11101-11227	GT	GAG
(GTC)	 AG	11460-11586	GT	TGG
(AGG)	 AG	11809-11889	AA	GAA
-recovered pasa_asmbl_36226.p1, terminal, 10873, 10938
-recovered pasa_asmbl_36226.p1, terminal, 11809, 11889
-recovered pasa_asmbl_36226.p1, internal, 10873, 10938
-recovered pasa_asmbl_36226.p1, internal, 11101, 11227
-recovered pasa_asmbl_36226.p1, internal, 11460, 11586
Valid prediction for Augustus_model.g39032.t1
Valid prediction for Augustus_model.g39017.t1
Valid prediction for snap_scaffold_27-snap.1045-T1
Valid prediction for Augustus_model.g39023.t1
Valid prediction for GlimmerHMM_glimmerT_58546-T1
Valid prediction for HiQ_model.g39024.t1
Valid prediction for GeneMark_model.101813_t
Valid prediction for HiQ_model.g39014.t1
Valid prediction for Augustus_model.g39028.t1
Valid prediction for snap_scaffold_27-snap.1035-T1
Valid prediction for GeneMark_model.101794_t
Valid prediction for GlimmerHMM_glimmerT_58545-T1
Valid prediction for GeneMark_model.101778_t
Valid prediction for GlimmerHMM_glimmerT_58543-T1
Valid prediction for GeneMark_model.101810_t
Valid prediction for snap_scaffold_27-snap.1020-T1
Valid prediction for snap_scaffold_27-snap.1055-T1
Valid prediction for snap_scaffold_27-snap.1037-T1
Valid prediction for pasa_asmbl_36233.p1
Valid prediction for snap_scaffold_27-snap.1023-T1
Valid prediction for GlimmerHMM_glimmerT_58561-T1
Valid prediction for GeneMark_model.101809_t
Valid prediction for GlimmerHMM_glimmerT_58554-T1
Valid prediction for GlimmerHMM_glimmerT_58549-T1
Valid prediction for snap_scaffold_27-snap.1038-T1
Valid prediction for CodingQuarry_transcript_41787-T1
Couldn't classify 168378, 168539
Couldn't classify 169679, 169838
Sorry, prediction pasa_asmbl_36243.p1 fails validation.
(TTT)	 AG	168378-168539	GT	GAG
(GTC)	 AG	169228-169324	GT	CAG
(GTA)	 AG	169405-169510	GT	TGG
(CGC)	 AG	169679-169838	CT	GCC
-recovered pasa_asmbl_36243.p1, internal, 168378, 168539
-recovered pasa_asmbl_36243.p1, internal, 169228, 169324
-recovered pasa_asmbl_36243.p1, internal, 169405, 169510
Valid prediction for GlimmerHMM_glimmerT_58557-T1
Valid prediction for snap_scaffold_27-snap.1017-T1
Valid prediction for Augustus_model.g39031.t1
Valid prediction for HiQ_model.g39030.t1
Valid prediction for GlimmerHMM_glimmerT_58558-T1
Valid prediction for HiQ_model.g39026.t1
Valid prediction for GeneMark_model.101787_t
Valid prediction for CodingQuarry_transcript_41786-T1
Valid prediction for GeneMark_model.101800_t
Valid prediction for snap_scaffold_27-snap.1036-T1
Valid prediction for snap_scaffold_27-snap.1050-T1
Valid prediction for GeneMark_model.101807_t
Valid prediction for snap_scaffold_27-snap.1047-T1
Valid prediction for snap_scaffold_27-snap.1041-T1
Valid prediction for snap_scaffold_27-snap.1049-T1
Valid prediction for GlimmerHMM_glimmerT_58562-T1
Valid prediction for pasa_asmbl_36244.p1
Valid prediction for snap_scaffold_27-snap.1042-T1
Valid prediction for snap_scaffold_27-snap.1018-T1
Valid prediction for GeneMark_model.101784_t
Valid prediction for GlimmerHMM_glimmerT_58556-T1
Valid prediction for snap_scaffold_27-snap.1027-T1
Valid prediction for HiQ_model.g39019.t1
Valid prediction for Augustus_model.g39021.t1
Valid prediction for snap_scaffold_27-snap.1051-T1
Valid prediction for HiQ_model.g39015.t1
Valid prediction for GlimmerHMM_glimmerT_58569-T1
Valid prediction for GeneMark_model.101792_t
Couldn't classify 5672, 5761
Sorry, prediction pasa_asmbl_36224.p1 fails validation.
(TTC)	 CC	5672-5761	GT	AGG
(ATT)	 AG	6442-6479	GT	AGG
(GGT)	 AG	6593-6734	GT	ACG
(CTG)	 AG	6847-7001	GT	AGG
(GCT)	 AG	7268-7375	GT	AGG
(AAT)	 AG	7481-7601	GT	GCG
(TAC)	 AG	7724-7857	GT	GTG
(ATT)	 AG	8447-8548	GT	CCG
(TTG)	 AG	9254-9374	CC	GAC
add_exon() Sorry, pasa_asmbl_36224.p1 7268-7375-terminal-1 is invalid.
-recovered pasa_asmbl_36224.p1, terminal, 7268, 7375
-recovered pasa_asmbl_36224.p1, terminal, 9254, 9374
-recovered pasa_asmbl_36224.p1, internal, 6442, 6479
-recovered pasa_asmbl_36224.p1, internal, 6593, 6734
-recovered pasa_asmbl_36224.p1, internal, 6847, 7001
-recovered pasa_asmbl_36224.p1, internal, 7268, 7375
-recovered pasa_asmbl_36224.p1, internal, 7481, 7601
-recovered pasa_asmbl_36224.p1, internal, 7724, 7857
-recovered pasa_asmbl_36224.p1, internal, 8447, 8548
Valid prediction for CodingQuarry_transcript_41784-T1
Valid prediction for GeneMark_model.101798_t
Valid prediction for snap_scaffold_27-snap.1030-T1
Valid prediction for GeneMark_model.101797_t
Valid prediction for GlimmerHMM_glimmerT_58565-T1
Valid prediction for GeneMark_model.101782_t
Valid prediction for snap_scaffold_27-snap.1057-T1
Valid prediction for pasa_asmbl_36231.p2

-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 GeneMark_model.101777_t
Valid prediction for GeneMark_model.101774_t
Valid prediction for GlimmerHMM_glimmerT_58563-T1
Valid prediction for snap_scaffold_27-snap.1032-T1
Valid prediction for GeneMark_model.101815_t
Valid prediction for GlimmerHMM_glimmerT_58555-T1
Valid prediction for Augustus_model.g39022.t1
Valid prediction for snap_scaffold_27-snap.1046-T1
Valid prediction for snap_scaffold_27-snap.1019-T1
Valid prediction for snap_scaffold_27-snap.1016-T1
Valid prediction for snap_scaffold_27-snap.1039-T1
Valid prediction for GeneMark_model.101806_t
Valid prediction for GeneMark_model.101788_t
Valid prediction for Augustus_model.g39018.t1
Valid prediction for snap_scaffold_27-snap.1029-T1
Valid prediction for snap_scaffold_27-snap.1040-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.101775_t
Valid prediction for snap_scaffold_27-snap.1056-T1
Valid prediction for snap_scaffold_27-snap.1043-T1
Valid prediction for GeneMark_model.101791_t
Valid prediction for GeneMark_model.101781_t
Valid prediction for snap_scaffold_27-snap.1024-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1044-T1
Valid prediction for GeneMark_model.101779_t
Valid prediction for GeneMark_model.101801_t
Valid prediction for snap_scaffold_27-snap.1022-T1
Valid prediction for GeneMark_model.101783_t
Valid prediction for GlimmerHMM_glimmerT_58544-T1
Valid prediction for snap_scaffold_27-snap.1054-T1
Valid prediction for GeneMark_model.101804_t
Valid prediction for Augustus_model.g39016.t1
Couldn't classify 179983, 180713
Sorry, prediction pasa_asmbl_37151.p1 fails validation.
(ATG)	 AG	177806-178005	GT	CGG
(GCA)	 AG	178544-178651	GT	AAG
(GGT)	 AG	178861-178938	GT	AAG
(GGA)	 AG	179098-179209	GT	AGG
(GCC)	 AG	179470-179710	GT	AAG
(ATG)	 AG	179983-180713	GA	AGG
-recovered pasa_asmbl_37151.p1, initial, 177806, 178005
-recovered pasa_asmbl_37151.p1, internal, 177806, 178005
-recovered pasa_asmbl_37151.p1, internal, 178544, 178651
-recovered pasa_asmbl_37151.p1, internal, 178861, 178938
-recovered pasa_asmbl_37151.p1, internal, 179098, 179209
-recovered pasa_asmbl_37151.p1, internal, 179470, 179710
Valid prediction for Augustus_model.g39013.t1
Valid prediction for GeneMark_model.101812_t
Valid prediction for GeneMark_model.101785_t
Couldn't classify 122102, 122110
Sorry, prediction pasa_asmbl_36906.p3 fails validation.
(TAC)	 TC	122102-122110	GT	AGG
(GGT)	 AG	122276-122450	GT	CGG
(GCA)	 AG	122648-122763	AG	AGA
-recovered pasa_asmbl_36906.p3, terminal, 122648, 122763
-recovered pasa_asmbl_36906.p3, internal, 122276, 122450
Valid prediction for snap_scaffold_27-snap.1052-T1
Valid prediction for Augustus_model.g39025.t1
Valid prediction for GlimmerHMM_glimmerT_58551-T1
Valid prediction for snap_scaffold_27-snap.1033-T1
Valid prediction for Augustus_model.g39020.t1
Valid prediction for GlimmerHMM_glimmerT_58560-T1
Valid prediction for GeneMark_model.101811_t
Valid prediction for GlimmerHMM_glimmerT_58547-T1
Valid prediction for GeneMark_model.101808_t
Valid prediction for snap_scaffold_27-snap.1026-T1
Valid prediction for GeneMark_model.101814_t
Valid prediction for GeneMark_model.101795_t
Valid prediction for GeneMark_model.101793_t
Valid prediction for snap_scaffold_27-snap.1034-T1
Valid prediction for GeneMark_model.101799_t
Valid prediction for GlimmerHMM_glimmerT_58559-T1
Valid prediction for GlimmerHMM_glimmerT_58542-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16519, rend_intergenic: 15066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22641, rend_intergenic: 21474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26348, rend_intergenic: 23010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32570, rend_intergenic: 27369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79035, rend_intergenic: 72539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81008, rend_intergenic: 79120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86515, rend_intergenic: 83901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106057, rend_intergenic: 103387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120161, rend_intergenic: 118067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130841, rend_intergenic: 122736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133055, rend_intergenic: 131167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137114, rend_intergenic: 135059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174581, rend_intergenic: 171220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174868, rend_intergenic: 174659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179096, rend_intergenic: 175457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185794, rend_intergenic: 180671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194324
-exon list size: 662


building trellis

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81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 16519, rend_intergenic: 15066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22641, rend_intergenic: 21474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26348, rend_intergenic: 23010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32570, rend_intergenic: 27369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79035, rend_intergenic: 72539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81008, rend_intergenic: 79120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86515, rend_intergenic: 83901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106057, rend_intergenic: 103387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120161, rend_intergenic: 118067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130841, rend_intergenic: 122736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133055, rend_intergenic: 131167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137114, rend_intergenic: 135059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174581, rend_intergenic: 171220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174868, rend_intergenic: 174659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179096, rend_intergenic: 175457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185794, rend_intergenic: 180671  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