-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_4584973-4743507

-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_60125-T1
Valid prediction for CodingQuarry_transcript_43544-T1
Valid prediction for snap_scaffold_28-snap.1087-T1
Valid prediction for GeneMark_model.104768_t
Valid prediction for snap_scaffold_28-snap.1107-T1
Valid prediction for Augustus_model.g40018.t1
Valid prediction for snap_scaffold_28-snap.1110-T1
Valid prediction for HiQ_model.g40024.t1
Valid prediction for snap_scaffold_28-snap.1104-T1
Valid prediction for Augustus_model.g40014.t1
Valid prediction for GlimmerHMM_glimmerT_60114-T1
Valid prediction for snap_scaffold_28-snap.1073-T1
Valid prediction for snap_scaffold_28-snap.1085-T1
Valid prediction for snap_scaffold_28-snap.1077-T1
Valid prediction for GeneMark_model.104781_t
Valid prediction for pasa_asmbl_38236.p1
Valid prediction for GeneMark_model.104760_t
Valid prediction for GeneMark_model.104785_t
Valid prediction for GlimmerHMM_glimmerT_60111-T1
Valid prediction for GeneMark_model.104751_t
Valid prediction for GlimmerHMM_glimmerT_60118-T1
Valid prediction for GeneMark_model.104773_t
Valid prediction for HiQ_model.g40021.t1
Valid prediction for GeneMark_model.104763_t
Valid prediction for GeneMark_model.104765_t
Valid prediction for GeneMark_model.104759_t
Valid prediction for GeneMark_model.104767_t
Valid prediction for GeneMark_model.104779_t
Valid prediction for snap_scaffold_28-snap.1106-T1
Couldn't classify 125151, 125378
Sorry, prediction pasa_asmbl_38239.p1 fails validation.
(GCG)	 TA	125151-125378	GT	AGG
(GTG)	 AG	126046-126155	GT	AGG
(AGA)	 AG	126800-126900	GT	AGG
(GGC)	 AG	126992-127209	GA	GAG
-recovered pasa_asmbl_38239.p1, terminal, 126992, 127209
-recovered pasa_asmbl_38239.p1, internal, 126046, 126155
-recovered pasa_asmbl_38239.p1, internal, 126800, 126900
Valid prediction for GeneMark_model.104749_t
Valid prediction for GeneMark_model.104772_t
Valid prediction for CodingQuarry_transcript_43547-T1
Valid prediction for GlimmerHMM_glimmerT_60113-T1
Valid prediction for GlimmerHMM_glimmerT_60121-T1
Valid prediction for GlimmerHMM_glimmerT_60120-T1
Valid prediction for snap_scaffold_28-snap.1099-T1
Valid prediction for GeneMark_model.104745_t
Valid prediction for GeneMark_model.104756_t
Valid prediction for snap_scaffold_28-snap.1078-T1
Valid prediction for snap_scaffold_28-snap.1079-T1
Valid prediction for GlimmerHMM_glimmerT_60106-T1
Valid prediction for snap_scaffold_28-snap.1095-T1
Valid prediction for snap_scaffold_28-snap.1100-T1
Valid prediction for snap_scaffold_28-snap.1101-T1
Valid prediction for GeneMark_model.104783_t
Valid prediction for GlimmerHMM_glimmerT_60122-T1
Valid prediction for GeneMark_model.104754_t
Valid prediction for snap_scaffold_28-snap.1082-T1
Valid prediction for GeneMark_model.104775_t
Valid prediction for GeneMark_model.104771_t
Valid prediction for snap_scaffold_28-snap.1093-T1
Valid prediction for snap_scaffold_28-snap.1097-T1
Valid prediction for GeneMark_model.104747_t
Valid prediction for GeneMark_model.104777_t

-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_60112-T1
Valid prediction for pasa_asmbl_37544.p1
Valid prediction for GlimmerHMM_glimmerT_60129-T1
Valid prediction for GlimmerHMM_glimmerT_60110-T1
Valid prediction for Augustus_model.g40009.t1
Valid prediction for HiQ_model.g40022.t1
Valid prediction for GeneMark_model.104752_t
Valid prediction for GlimmerHMM_glimmerT_60117-T1
Valid prediction for GlimmerHMM_glimmerT_60127-T1
Valid prediction for snap_scaffold_28-snap.1090-T1
Valid prediction for GlimmerHMM_glimmerT_60103-T1
Valid prediction for snap_scaffold_28-snap.1094-T1
Valid prediction for snap_scaffold_28-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_60130-T1
Valid prediction for GeneMark_model.104776_t
Valid prediction for Augustus_model.g40023.t1
Valid prediction for snap_scaffold_28-snap.1075-T1
Valid prediction for GlimmerHMM_glimmerT_60119-T1
Valid prediction for Augustus_model.g40020.t1
Valid prediction for GeneMark_model.104778_t
Valid prediction for snap_scaffold_28-snap.1096-T1
Valid prediction for CodingQuarry_transcript_43546-T1
Valid prediction for Augustus_model.g40015.t1
Valid prediction for GeneMark_model.104761_t
Valid prediction for GeneMark_model.104766_t
Valid prediction for CodingQuarry_transcript_43545-T1
Valid prediction for GeneMark_model.104758_t
Valid prediction for GlimmerHMM_glimmerT_60123-T1
Valid prediction for GlimmerHMM_glimmerT_60116-T1
Valid prediction for snap_scaffold_28-snap.1098-T1
Valid prediction for snap_scaffold_28-snap.1102-T1
Couldn't classify 19008, 19175
Couldn't classify 20791, 20898
Sorry, prediction pasa_asmbl_37547.p1 fails validation.
(CAT)	 AG	19008-19175	GT	AGG
(GAC)	 AG	19620-19808	GT	CGG
(GAG)	 AG	20791-20898	CG	GAC
-recovered pasa_asmbl_37547.p1, internal, 19008, 19175
-recovered pasa_asmbl_37547.p1, internal, 19620, 19808
Valid prediction for snap_scaffold_28-snap.1083-T1
Valid prediction for Augustus_model.g40010.t1
Couldn't classify 9845, 9973
Couldn't classify 15467, 15593
Sorry, prediction pasa_asmbl_37548.p1 fails validation.
(TCA)	 CC	9845-9973	GT	TTG
(GCA)	 AG	10677-10748	GT	AGG
(AAG)	 AG	11260-11361	GT	GGG
(CTT)	 AG	11591-11636	GT	GGG
(TTC)	 AG	12127-12223	GT	AGG
(AGA)	 AG	13018-13131	GT	TGG
(GAT)	 AG	13702-13793	GT	AGG
(CGG)	 AG	14001-14094	GT	TGG
(GTC)	 AG	15467-15593	AC	TCA
add_exon() Sorry, pasa_asmbl_37548.p1 13702-13793-terminal-2 is invalid.
-recovered pasa_asmbl_37548.p1, terminal, 13702, 13793
-recovered pasa_asmbl_37548.p1, internal, 10677, 10748
-recovered pasa_asmbl_37548.p1, internal, 11260, 11361
-recovered pasa_asmbl_37548.p1, internal, 11591, 11636
-recovered pasa_asmbl_37548.p1, internal, 12127, 12223
-recovered pasa_asmbl_37548.p1, internal, 13018, 13131
-recovered pasa_asmbl_37548.p1, internal, 13702, 13793
-recovered pasa_asmbl_37548.p1, internal, 14001, 14094
Valid prediction for GlimmerHMM_glimmerT_60115-T1
Valid prediction for GlimmerHMM_glimmerT_60105-T1
Valid prediction for Augustus_model.g40019.t1
Valid prediction for GeneMark_model.104746_t
Valid prediction for snap_scaffold_28-snap.1089-T1
Valid prediction for GeneMark_model.104784_t
Valid prediction for GlimmerHMM_glimmerT_60109-T1
Valid prediction for GeneMark_model.104753_t
Valid prediction for snap_scaffold_28-snap.1109-T1
Valid prediction for GeneMark_model.104780_t
Valid prediction for Augustus_model.g40012.t1
Valid prediction for snap_scaffold_28-snap.1076-T1
Valid prediction for Augustus_model.g40013.t1
Valid prediction for snap_scaffold_28-snap.1105-T1
Valid prediction for GeneMark_model.104755_t
Valid prediction for Augustus_model.g40025.t1
Valid prediction for snap_scaffold_28-snap.1092-T1
Valid prediction for Augustus_model.g40017.t1
Valid prediction for GeneMark_model.104762_t
Valid prediction for GlimmerHMM_glimmerT_60104-T1
Valid prediction for snap_scaffold_28-snap.1103-T1
Valid prediction for snap_scaffold_28-snap.1081-T1
Valid prediction for GeneMark_model.104769_t
Valid prediction for Augustus_model.g40011.t1
Valid prediction for GlimmerHMM_glimmerT_60107-T1
Valid prediction for Augustus_model.g40016.t1
Valid prediction for GeneMark_model.104770_t
Valid prediction for GeneMark_model.104774_t
Couldn't classify 24470, 24682
Sorry, prediction pasa_asmbl_37546.p1 fails validation.
(GAG)	 AT	24470-24682	GT	AGG
(ATG)	 AG	24927-25055	GT	AGG
(GAG)	 AG	26093-26296	GT	AGG
(GAG)	 AG	26863-27102	GT	AGG
(GCC)	 AG	27362-27574	GT	CGG
(CTG)	 AG	28332-28514	GT	AGG
(ATC)	 AG	29689-29850	GG	GAG
-recovered pasa_asmbl_37546.p1, initial, 24927, 25055
-recovered pasa_asmbl_37546.p1, terminal, 29689, 29850
-recovered pasa_asmbl_37546.p1, internal, 24927, 25055
-recovered pasa_asmbl_37546.p1, internal, 26093, 26296
-recovered pasa_asmbl_37546.p1, internal, 26863, 27102
-recovered pasa_asmbl_37546.p1, internal, 27362, 27574
-recovered pasa_asmbl_37546.p1, internal, 28332, 28514
Valid prediction for snap_scaffold_28-snap.1091-T1
Valid prediction for snap_scaffold_28-snap.1074-T1
Valid prediction for snap_scaffold_28-snap.1084-T1
Valid prediction for GlimmerHMM_glimmerT_60124-T1
Valid prediction for GeneMark_model.104757_t
Valid prediction for Augustus_model.g40026.t1
Valid prediction for GlimmerHMM_glimmerT_60128-T1
Valid prediction for GeneMark_model.104744_t
Valid prediction for GeneMark_model.104748_t
Valid prediction for GlimmerHMM_glimmerT_60108-T1
Valid prediction for GeneMark_model.104782_t
Valid prediction for snap_scaffold_28-snap.1080-T1
Valid prediction for GeneMark_model.104764_t
Valid prediction for GeneMark_model.104750_t
Valid prediction for snap_scaffold_28-snap.1086-T1
Valid prediction for snap_scaffold_28-snap.1108-T1
Valid prediction for GlimmerHMM_glimmerT_60126-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 30515, rend_intergenic: 30512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5334, rend_intergenic: 3167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17270, rend_intergenic: 10306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22350, rend_intergenic: 20133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29843, rend_intergenic: 25812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44391, rend_intergenic: 40200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83138, rend_intergenic: 79822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91618, rend_intergenic: 84400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140654, rend_intergenic: 129986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145690, rend_intergenic: 140879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158535
-exon list size: 583


building trellis

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99.8    
-found 26 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 30515, rend_intergenic: 30512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 5334, rend_intergenic: 3167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17270, rend_intergenic: 10306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22350, rend_intergenic: 20133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29843, rend_intergenic: 25812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44391, rend_intergenic: 40200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83138, rend_intergenic: 79822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91618, rend_intergenic: 84400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140654, rend_intergenic: 129986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145690, rend_intergenic: 140879  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