-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_15065895-15279028

-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 CodingQuarry_transcript_55356-T1
Valid prediction for snap_scaffold_6-snap.3213-T1
Valid prediction for snap_scaffold_6-snap.3184-T1
Valid prediction for GlimmerHMM_glimmerT_16073-T1
Valid prediction for GlimmerHMM_glimmerT_16069-T1
Valid prediction for GlimmerHMM_glimmerT_16049-T1
Valid prediction for snap_scaffold_6-snap.3195-T1
Valid prediction for snap_scaffold_6-snap.3188-T1
Valid prediction for GlimmerHMM_glimmerT_16046-T1
Valid prediction for snap_scaffold_6-snap.3204-T1
Valid prediction for CodingQuarry_transcript_55358-T1
Valid prediction for GlimmerHMM_glimmerT_16047-T1
Valid prediction for GlimmerHMM_glimmerT_16058-T1
Valid prediction for GlimmerHMM_glimmerT_16054-T1
Valid prediction for GlimmerHMM_glimmerT_16039-T1
Valid prediction for HiQ_model.g10780.t1
Couldn't classify 27767, 27799
Sorry, prediction pasa_asmbl_47653.p2 fails validation.
(TTT)	 TC	27767-27799	GT	AGG
(GCA)	 AG	28296-28370	GT	AGG
(ATG)	 AG	28737-28806	GT	CTG
(CGT)	 AG	28979-29116	GT	AGG
(TCA)	 AG	29239-29327	GC	GAG
-recovered pasa_asmbl_47653.p2, initial, 28737, 28806
-recovered pasa_asmbl_47653.p2, terminal, 29239, 29327
-recovered pasa_asmbl_47653.p2, internal, 28296, 28370
-recovered pasa_asmbl_47653.p2, internal, 28737, 28806
-recovered pasa_asmbl_47653.p2, internal, 28979, 29116
-recovered pasa_asmbl_47653.p2, internal, 29239, 29327
Valid prediction for pasa_asmbl_47650.p2
Valid prediction for snap_scaffold_6-snap.3172-T1
Valid prediction for GlimmerHMM_glimmerT_16052-T1
Valid prediction for Augustus_model.g10787.t1
Valid prediction for GlimmerHMM_glimmerT_16051-T1
Valid prediction for snap_scaffold_6-snap.3185-T1
Valid prediction for snap_scaffold_6-snap.3191-T1
Valid prediction for GlimmerHMM_glimmerT_16042-T1
Valid prediction for snap_scaffold_6-snap.3198-T1
Valid prediction for snap_scaffold_6-snap.3197-T1
Valid prediction for snap_scaffold_6-snap.3173-T1
Valid prediction for Augustus_model.g10783.t1
Valid prediction for GlimmerHMM_glimmerT_16065-T1
Valid prediction for Augustus_model.g10786.t1
Valid prediction for snap_scaffold_6-snap.3177-T1
Valid prediction for snap_scaffold_6-snap.3180-T1
Valid prediction for GlimmerHMM_glimmerT_16056-T1
Valid prediction for snap_scaffold_6-snap.3192-T1
Valid prediction for Augustus_model.g10789.t1
Valid prediction for snap_scaffold_6-snap.3187-T1
Valid prediction for Augustus_model.g10781.t1
Valid prediction for snap_scaffold_6-snap.3211-T1
Valid prediction for snap_scaffold_6-snap.3209-T1
Valid prediction for snap_scaffold_6-snap.3190-T1
Valid prediction for Augustus_model.g10792.t1
Valid prediction for snap_scaffold_6-snap.3212-T1
Valid prediction for GlimmerHMM_glimmerT_16038-T1
Valid prediction for snap_scaffold_6-snap.3200-T1
Valid prediction for GlimmerHMM_glimmerT_16061-T1
Valid prediction for Augustus_model.g10797.t1
Valid prediction for snap_scaffold_6-snap.3174-T1
Valid prediction for snap_scaffold_6-snap.3202-T1
Valid prediction for snap_scaffold_6-snap.3215-T1
Valid prediction for GlimmerHMM_glimmerT_16075-T1
Valid prediction for snap_scaffold_6-snap.3207-T1
Valid prediction for CodingQuarry_transcript_55357-T1
Valid prediction for snap_scaffold_6-snap.3189-T1
Valid prediction for GlimmerHMM_glimmerT_16066-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 Augustus_model.g10799.t1
Valid prediction for snap_scaffold_6-snap.3179-T1
Valid prediction for Augustus_model.g10798.t1
Valid prediction for snap_scaffold_6-snap.3178-T1
Couldn't classify 181543, 181606
Sorry, prediction pasa_asmbl_49052.p1 fails validation.
(AAG)	 CA	181543-181606	GT	TGG
(TAC)	 AG	181919-182061	GT	AGG
(CCA)	 AG	182275-182400	GC	AGG
(GGG)	 AG	182589-182712	GT	GAG
(AAT)	 AG	182823-182920	GT	AGG
(GAG)	 AG	183003-183210	GT	ACG
(ACA)	 AG	183341-183426	TC	GAT
-recovered pasa_asmbl_49052.p1, terminal, 183341, 183426
-recovered pasa_asmbl_49052.p1, internal, 181919, 182061
-recovered pasa_asmbl_49052.p1, internal, 182275, 182400
-recovered pasa_asmbl_49052.p1, internal, 182589, 182712
-recovered pasa_asmbl_49052.p1, internal, 182823, 182920
-recovered pasa_asmbl_49052.p1, internal, 183003, 183210
Valid prediction for snap_scaffold_6-snap.3208-T1
Valid prediction for GlimmerHMM_glimmerT_16050-T1
Valid prediction for GlimmerHMM_glimmerT_16044-T1
Valid prediction for snap_scaffold_6-snap.3201-T1
Valid prediction for snap_scaffold_6-snap.3199-T1
Valid prediction for snap_scaffold_6-snap.3214-T1
Valid prediction for Augustus_model.g10790.t1
Valid prediction for Augustus_model.g10794.t1
Valid prediction for snap_scaffold_6-snap.3193-T1
Valid prediction for snap_scaffold_6-snap.3176-T1
Valid prediction for GlimmerHMM_glimmerT_16041-T1
Valid prediction for snap_scaffold_6-snap.3203-T1
Valid prediction for GlimmerHMM_glimmerT_16072-T1
Valid prediction for snap_scaffold_6-snap.3182-T1
Valid prediction for snap_scaffold_6-snap.3183-T1
Valid prediction for GlimmerHMM_glimmerT_16055-T1
Valid prediction for GlimmerHMM_glimmerT_16071-T1
Valid prediction for GlimmerHMM_glimmerT_16057-T1
Couldn't classify 178398, 178481
Sorry, prediction pasa_asmbl_49053.p1 fails validation.
(ATG)	 AG	175808-175878	GT	AGG
(GAC)	 AG	176493-176599	GT	AGG
(GGT)	 AG	177156-177577	GT	AGG
(CAA)	 AG	177867-177926	GT	AGG
(TCT)	 AG	178028-178105	GT	GGG
(CCC)	 AG	178398-178481	CC	CCC
-recovered pasa_asmbl_49053.p1, initial, 175808, 175878
-recovered pasa_asmbl_49053.p1, internal, 175808, 175878
-recovered pasa_asmbl_49053.p1, internal, 176493, 176599
-recovered pasa_asmbl_49053.p1, internal, 177156, 177577
-recovered pasa_asmbl_49053.p1, internal, 177867, 177926
-recovered pasa_asmbl_49053.p1, internal, 178028, 178105
Valid prediction for GlimmerHMM_glimmerT_16053-T1
Valid prediction for Augustus_model.g10791.t1
Couldn't classify 164687, 164825
Sorry, prediction pasa_asmbl_49055.p1 fails validation.
(GTC)	 CA	164687-164825	GT	AGG
(TGT)	 AG	165476-165591	GT	AGG
(GGG)	 AG	165735-165866	AC	GAA
-recovered pasa_asmbl_49055.p1, terminal, 165735, 165866
-recovered pasa_asmbl_49055.p1, internal, 165476, 165591
Valid prediction for GlimmerHMM_glimmerT_16076-T1
Valid prediction for snap_scaffold_6-snap.3175-T1
Valid prediction for GlimmerHMM_glimmerT_16045-T1
Valid prediction for pasa_asmbl_49046.p1
Valid prediction for Augustus_model.g10785.t1
Valid prediction for Augustus_model.g10800.t1
Valid prediction for snap_scaffold_6-snap.3205-T1
Valid prediction for Augustus_model.g10793.t1
Valid prediction for GlimmerHMM_glimmerT_16070-T1
Valid prediction for snap_scaffold_6-snap.3210-T1
Valid prediction for HiQ_model.g10784.t1
Valid prediction for GlimmerHMM_glimmerT_16063-T1
Valid prediction for snap_scaffold_6-snap.3206-T1
Valid prediction for GlimmerHMM_glimmerT_16074-T1
Valid prediction for HiQ_model.g10788.t1
Valid prediction for snap_scaffold_6-snap.3194-T1
Valid prediction for GlimmerHMM_glimmerT_16077-T1
Valid prediction for GlimmerHMM_glimmerT_16067-T1
Valid prediction for CodingQuarry_transcript_55355-T1
Valid prediction for GlimmerHMM_glimmerT_16040-T1
Valid prediction for GlimmerHMM_glimmerT_16060-T1
Valid prediction for GlimmerHMM_glimmerT_16048-T1
Valid prediction for GlimmerHMM_glimmerT_16043-T1
Valid prediction for Augustus_model.g10802.t1
Valid prediction for Augustus_model.g10795.t1
Valid prediction for snap_scaffold_6-snap.3186-T1
Valid prediction for HiQ_model.g10782.t1
Valid prediction for GlimmerHMM_glimmerT_16068-T1
Valid prediction for GlimmerHMM_glimmerT_16064-T1
Valid prediction for snap_scaffold_6-snap.3196-T1
Valid prediction for Augustus_model.g10801.t1
Valid prediction for GlimmerHMM_glimmerT_16078-T1
Couldn't classify 179183, 179263
Sorry, prediction pasa_asmbl_49378.p1 fails validation.
(CAG)	 CT	179183-179263	GT	TGG
(GAG)	 AG	179548-179677	GT	CGG
(GCC)	 AG	179980-180046	GT	CTG
(GAG)	 AG	180155-180365	AC	AAA
-recovered pasa_asmbl_49378.p1, terminal, 180155, 180365
-recovered pasa_asmbl_49378.p1, internal, 179548, 179677
-recovered pasa_asmbl_49378.p1, internal, 179980, 180046
Valid prediction for snap_scaffold_6-snap.3181-T1
Couldn't classify 67914, 68037
Couldn't classify 69388, 69578
Sorry, prediction pasa_asmbl_49328.p2 fails validation.
(GGT)	 GA	67914-68037	GT	CGG
(AGG)	 AG	69388-69578	AG	TGA
Valid prediction for GlimmerHMM_glimmerT_16059-T1
Valid prediction for GlimmerHMM_glimmerT_16037-T1
Valid prediction for GlimmerHMM_glimmerT_16062-T1
Valid prediction for Augustus_model.g10796.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 16247, rend_intergenic: 16244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20750, rend_intergenic: 18889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43571, rend_intergenic: 40866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54001, rend_intergenic: 50367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59499, rend_intergenic: 54700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96666, rend_intergenic: 59590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100876, rend_intergenic: 97185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104308, rend_intergenic: 101720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110766, rend_intergenic: 105445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125938, rend_intergenic: 119026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127183, rend_intergenic: 126019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128151, rend_intergenic: 127451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145205, rend_intergenic: 130137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147652, rend_intergenic: 145621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150940, rend_intergenic: 147757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156829, rend_intergenic: 155021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159149, rend_intergenic: 157443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162968, rend_intergenic: 159311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167065, rend_intergenic: 163088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181393, rend_intergenic: 167098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195095, rend_intergenic: 184831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201441, rend_intergenic: 197026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213134
-exon list size: 461


building trellis

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-found 37 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 16247, rend_intergenic: 16244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20750, rend_intergenic: 18889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43571, rend_intergenic: 40866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54001, rend_intergenic: 50367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59499, rend_intergenic: 54700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96666, rend_intergenic: 59590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100876, rend_intergenic: 97185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104308, rend_intergenic: 101720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110766, rend_intergenic: 105445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125938, rend_intergenic: 119026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127183, rend_intergenic: 126019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128151, rend_intergenic: 127451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145205, rend_intergenic: 130137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147652, rend_intergenic: 145621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150940, rend_intergenic: 147757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156829, rend_intergenic: 155021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159149, rend_intergenic: 157443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162968, rend_intergenic: 159311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167065, rend_intergenic: 163088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181393, rend_intergenic: 167098  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195095, rend_intergenic: 184831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201441, rend_intergenic: 197026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 194292 - 213134
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 201442 - 213134
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 201661 - 213134