-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_452908-771072

-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_41668-T1
Valid prediction for HiQ_model.g27730.t1
Valid prediction for snap_scaffold_18-snap.96-T1
Valid prediction for snap_scaffold_18-snap.105-T1
Valid prediction for snap_scaffold_18-snap.88-T1
Valid prediction for Augustus_model.g27718.t1
Valid prediction for snap_scaffold_18-snap.104-T1
Valid prediction for snap_scaffold_18-snap.75-T1
Valid prediction for snap_scaffold_18-snap.124-T1
Valid prediction for snap_scaffold_18-snap.93-T1
Valid prediction for CodingQuarry_transcript_23645-T1
Valid prediction for Augustus_model.g27734.t1
Valid prediction for CodingQuarry_transcript_23641-T1
Valid prediction for snap_scaffold_18-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_41654-T1
Valid prediction for snap_scaffold_18-snap.122-T1
Valid prediction for snap_scaffold_18-snap.111-T1
Valid prediction for Augustus_model.g27733.t1
Valid prediction for GlimmerHMM_glimmerT_41659-T1
Valid prediction for GlimmerHMM_glimmerT_41673-T1
Valid prediction for HiQ_model.g27727.t1
Valid prediction for snap_scaffold_18-snap.109-T1
Valid prediction for GlimmerHMM_glimmerT_41657-T1
Valid prediction for Augustus_model.g27750.t1
Valid prediction for Augustus_model.g27748.t1
Valid prediction for snap_scaffold_18-snap.97-T1
Valid prediction for snap_scaffold_18-snap.127-T1
Valid prediction for GlimmerHMM_glimmerT_41676-T1
Valid prediction for Augustus_model.g27747.t1
Valid prediction for GlimmerHMM_glimmerT_41653-T1
Valid prediction for pasa_asmbl_20314.p1
Valid prediction for Augustus_model.g27743.t1
Valid prediction for snap_scaffold_18-snap.94-T1
Couldn't classify 179593, 179658
Sorry, prediction pasa_asmbl_20312.p1 fails validation.
(TTC)	 TC	179593-179658	GT	GGG
(GAC)	 AG	179946-180053	GT	AGG
(GTG)	 AG	180194-180257	GT	AGG
(GAA)	 AG	180704-180758	GT	GGG
(GTA)	 AG	180838-180926	GT	AAG
(GGA)	 AG	181088-181227	CC	AAC
add_exon() Sorry, pasa_asmbl_20312.p1 180194-180257-terminal-3 is invalid.
-recovered pasa_asmbl_20312.p1, terminal, 180194, 180257
-recovered pasa_asmbl_20312.p1, terminal, 181088, 181227
-recovered pasa_asmbl_20312.p1, internal, 179946, 180053
-recovered pasa_asmbl_20312.p1, internal, 180194, 180257
-recovered pasa_asmbl_20312.p1, internal, 180704, 180758
-recovered pasa_asmbl_20312.p1, internal, 180838, 180926
Valid prediction for Augustus_model.g27719.t1
Valid prediction for Augustus_model.g27723.t1
Valid prediction for snap_scaffold_18-snap.132-T1
Valid prediction for snap_scaffold_18-snap.87-T1
Valid prediction for Augustus_model.g27746.t1
Valid prediction for snap_scaffold_18-snap.74-T1
Valid prediction for Augustus_model.g27737.t1
Valid prediction for Augustus_model.g27740.t1
Valid prediction for CodingQuarry_transcript_23642-T1
Valid prediction for Augustus_model.g27725.t1
Valid prediction for snap_scaffold_18-snap.110-T1
Valid prediction for snap_scaffold_18-snap.114-T1
Valid prediction for HiQ_model.g27738.t1
Valid prediction for snap_scaffold_18-snap.99-T1
Valid prediction for GlimmerHMM_glimmerT_41664-T1
Valid prediction for GlimmerHMM_glimmerT_41666-T1
Valid prediction for CodingQuarry_transcript_23647-T1
Valid prediction for GlimmerHMM_glimmerT_41671-T1
Valid prediction for snap_scaffold_18-snap.73-T1
Valid prediction for snap_scaffold_18-snap.102-T1
Valid prediction for snap_scaffold_18-snap.121-T1
Valid prediction for snap_scaffold_18-snap.107-T1
Valid prediction for snap_scaffold_18-snap.131-T1
Valid prediction for Augustus_model.g27742.t1
Valid prediction for HiQ_model.g27729.t1
Valid prediction for snap_scaffold_18-snap.106-T1
Valid prediction for HiQ_model.g27732.t1
Valid prediction for GlimmerHMM_glimmerT_41678-T1
Valid prediction for pasa_asmbl_20302.p1
Valid prediction for snap_scaffold_18-snap.101-T1
Valid prediction for pasa_asmbl_20301.p1
Valid prediction for snap_scaffold_18-snap.137-T1
Valid prediction for Augustus_model.g27749.t1
Valid prediction for snap_scaffold_18-snap.117-T1
Valid prediction for Augustus_model.g27741.t1
Valid prediction for GlimmerHMM_glimmerT_41667-T1
Valid prediction for Augustus_model.g27735.t1
Valid prediction for snap_scaffold_18-snap.103-T1
Valid prediction for GlimmerHMM_glimmerT_41669-T1
Valid prediction for snap_scaffold_18-snap.76-T1
Valid prediction for Augustus_model.g27726.t1
Valid prediction for Augustus_model.g27745.t1
Valid prediction for GlimmerHMM_glimmerT_41670-T1
Valid prediction for GlimmerHMM_glimmerT_41661-T1
Valid prediction for snap_scaffold_18-snap.85-T1
Valid prediction for snap_scaffold_18-snap.113-T1
Valid prediction for pasa_asmbl_20306.p1
Valid prediction for GlimmerHMM_glimmerT_41674-T1
Couldn't classify 194119, 194290
Sorry, prediction pasa_asmbl_20318.p1 fails validation.
(AAA)	 TC	194119-194290	GT	GGG
(GGT)	 AG	194465-194565	GT	TGG
(CAC)	 AG	194899-194998	GT	GGG
(AGG)	 AG	196196-196293	GT	AGG
(ATT)	 AG	196802-196918	GT	AGG
(CAC)	 AG	197276-197362	GT	AGG
(GAC)	 AG	197503-197757	TA	AAT
-recovered pasa_asmbl_20318.p1, terminal, 197503, 197757
-recovered pasa_asmbl_20318.p1, internal, 194465, 194565
-recovered pasa_asmbl_20318.p1, internal, 194899, 194998
-recovered pasa_asmbl_20318.p1, internal, 196196, 196293
-recovered pasa_asmbl_20318.p1, internal, 196802, 196918
-recovered pasa_asmbl_20318.p1, internal, 197276, 197362
Valid prediction for snap_scaffold_18-snap.95-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_18-snap.136-T1
Valid prediction for snap_scaffold_18-snap.92-T1
Valid prediction for Augustus_model.g27728.t1
Valid prediction for GlimmerHMM_glimmerT_41656-T1
Valid prediction for snap_scaffold_18-snap.120-T1
Valid prediction for snap_scaffold_18-snap.118-T1
Valid prediction for GlimmerHMM_glimmerT_41665-T1
Valid prediction for snap_scaffold_18-snap.80-T1
Valid prediction for HiQ_model.g27731.t1
Valid prediction for snap_scaffold_18-snap.81-T1
Valid prediction for snap_scaffold_18-snap.133-T1
Valid prediction for Augustus_model.g27720.t1
Valid prediction for snap_scaffold_18-snap.115-T1
Valid prediction for snap_scaffold_18-snap.82-T1
Valid prediction for GlimmerHMM_glimmerT_41655-T1
Valid prediction for GlimmerHMM_glimmerT_41672-T1
Valid prediction for snap_scaffold_18-snap.77-T1
Valid prediction for snap_scaffold_18-snap.126-T1
Valid prediction for Augustus_model.g27744.t1
Valid prediction for snap_scaffold_18-snap.119-T1
Valid prediction for snap_scaffold_18-snap.129-T1
Valid prediction for Augustus_model.g27739.t1
Valid prediction for GlimmerHMM_glimmerT_41663-T1
Valid prediction for GlimmerHMM_glimmerT_41677-T1
Valid prediction for snap_scaffold_18-snap.134-T1
Valid prediction for snap_scaffold_18-snap.100-T1
Valid prediction for snap_scaffold_18-snap.71-T1
Valid prediction for snap_scaffold_18-snap.86-T1
Valid prediction for snap_scaffold_18-snap.78-T1
Valid prediction for Augustus_model.g27736.t1
Valid prediction for GlimmerHMM_glimmerT_41662-T1
Valid prediction for Augustus_model.g27717.t1
Valid prediction for snap_scaffold_18-snap.108-T1
Valid prediction for GlimmerHMM_glimmerT_41675-T1
Valid prediction for snap_scaffold_18-snap.79-T1
Valid prediction for snap_scaffold_18-snap.90-T1
Valid prediction for snap_scaffold_18-snap.112-T1
Valid prediction for Augustus_model.g27721.t1
Valid prediction for GlimmerHMM_glimmerT_41660-T1
Couldn't classify 261712, 261748
Couldn't classify 262908, 262948
Sorry, prediction pasa_asmbl_19590.p1 fails validation.
(GAG)	 AC	261712-261748	GT	AGG
(TTC)	 AG	261823-261984	GT	AAG
(ACC)	 AG	262363-262560	GT	TGG
(CTC)	 AG	262908-262948	TA	CGT
-recovered pasa_asmbl_19590.p1, internal, 261823, 261984
-recovered pasa_asmbl_19590.p1, internal, 262363, 262560
Valid prediction for Augustus_model.g27724.t1
Valid prediction for snap_scaffold_18-snap.72-T1
Valid prediction for pasa_asmbl_19591.p1
Valid prediction for snap_scaffold_18-snap.98-T1
Valid prediction for snap_scaffold_18-snap.123-T1
Valid prediction for snap_scaffold_18-snap.135-T1
Valid prediction for snap_scaffold_18-snap.116-T1
Valid prediction for snap_scaffold_18-snap.84-T1
Valid prediction for GlimmerHMM_glimmerT_41658-T1
Valid prediction for CodingQuarry_transcript_23644-T1
Valid prediction for snap_scaffold_18-snap.91-T1
Valid prediction for snap_scaffold_18-snap.125-T1
Valid prediction for CodingQuarry_transcript_23643-T1
Valid prediction for snap_scaffold_18-snap.83-T1
Valid prediction for snap_scaffold_18-snap.130-T1
Valid prediction for snap_scaffold_18-snap.89-T1
Valid prediction for Augustus_model.g27722.t1
Valid prediction for GlimmerHMM_glimmerT_41679-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42204, rend_intergenic: 37215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188336, rend_intergenic: 185351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197839, rend_intergenic: 189309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207961, rend_intergenic: 203658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213016, rend_intergenic: 208196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223246, rend_intergenic: 216191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235872, rend_intergenic: 226703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245214, rend_intergenic: 238958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252099, rend_intergenic: 249963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256996, rend_intergenic: 252298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264495, rend_intergenic: 258456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266089, rend_intergenic: 264967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 276337, rend_intergenic: 269978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 279510, rend_intergenic: 277443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 305746, rend_intergenic: 281086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 317850, rend_intergenic: 308269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 235678, rend_intergenic: 235675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 318165
-exon list size: 509


building trellis

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-found 49 predictions from path traversal
Error with prediction: snap lend_intergenic: 42204, rend_intergenic: 37215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188336, rend_intergenic: 185351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197839, rend_intergenic: 189309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207961, rend_intergenic: 203658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213016, rend_intergenic: 208196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223246, rend_intergenic: 216191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235872, rend_intergenic: 226703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245214, rend_intergenic: 238958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 252099, rend_intergenic: 249963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 256996, rend_intergenic: 252298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264495, rend_intergenic: 258456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266089, rend_intergenic: 264967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 276337, rend_intergenic: 269978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 279510, rend_intergenic: 277443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 305746, rend_intergenic: 281086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 317850, rend_intergenic: 308269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 235678, rend_intergenic: 235675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support
	-no exons in range 1 - 18303