-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_5228373-5409672

-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_38340-T1
Valid prediction for Augustus_model.g25573.t1
Couldn't classify 149494, 149802
Sorry, prediction pasa_asmbl_17089.p1 fails validation.
(TCA)	 CC	149494-149802	AC	ACA
Valid prediction for Augustus_model.g25580.t1
Valid prediction for CodingQuarry_transcript_19965-T1
Valid prediction for GlimmerHMM_glimmerT_38329-T1
Valid prediction for snap_scaffold_16-snap.1010-T1
Valid prediction for snap_scaffold_16-snap.1021-T1
Valid prediction for snap_scaffold_16-snap.1031-T1
Valid prediction for GlimmerHMM_glimmerT_38342-T1
Valid prediction for Augustus_model.g25579.t1
Valid prediction for snap_scaffold_16-snap.1014-T1
Valid prediction for snap_scaffold_16-snap.1009-T1
Valid prediction for snap_scaffold_16-snap.1033-T1
Valid prediction for snap_scaffold_16-snap.1018-T1
Valid prediction for GlimmerHMM_glimmerT_38338-T1
Valid prediction for snap_scaffold_16-snap.1027-T1
Valid prediction for snap_scaffold_16-snap.1022-T1
Valid prediction for GlimmerHMM_glimmerT_38334-T1
Valid prediction for GlimmerHMM_glimmerT_38326-T1
Valid prediction for HiQ_model.g25588.t1
Valid prediction for snap_scaffold_16-snap.1011-T1
Valid prediction for Augustus_model.g25581.t1
Valid prediction for GlimmerHMM_glimmerT_38335-T1
Valid prediction for pasa_asmbl_16211.p2
Valid prediction for snap_scaffold_16-snap.1034-T1
Valid prediction for snap_scaffold_16-snap.1038-T1
Valid prediction for snap_scaffold_16-snap.1029-T1
Valid prediction for Augustus_model.g25574.t1
Valid prediction for snap_scaffold_16-snap.1015-T1
Valid prediction for Augustus_model.g25582.t1
Valid prediction for Augustus_model.g25586.t1
Valid prediction for GlimmerHMM_glimmerT_38337-T1
Valid prediction for snap_scaffold_16-snap.1041-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 3748, 3927
Sorry, prediction pasa_asmbl_17100.p1 fails validation.
(ATG)	 AC	2893-2912	GT	AGG
(GTG)	 AG	3467-3605	GT	AGG
(GCC)	 AG	3748-3927	AT	AGA
-recovered pasa_asmbl_17100.p1, initial, 2893, 2912
-recovered pasa_asmbl_17100.p1, internal, 3467, 3605
Valid prediction for snap_scaffold_16-snap.1042-T1
Valid prediction for snap_scaffold_16-snap.1030-T1
Valid prediction for snap_scaffold_16-snap.1037-T1
Valid prediction for snap_scaffold_16-snap.1036-T1
Valid prediction for snap_scaffold_16-snap.1012-T1
Valid prediction for CodingQuarry_transcript_19964-T1
Valid prediction for Augustus_model.g25584.t1
Valid prediction for GlimmerHMM_glimmerT_38327-T1
Valid prediction for snap_scaffold_16-snap.1025-T1
Valid prediction for snap_scaffold_16-snap.1013-T1
Valid prediction for HiQ_model.g25589.t1
Valid prediction for Augustus_model.g25585.t1
Valid prediction for snap_scaffold_16-snap.1023-T1
Valid prediction for GlimmerHMM_glimmerT_38328-T1
Valid prediction for GlimmerHMM_glimmerT_38341-T1
Couldn't classify 28341, 28394
Sorry, prediction pasa_asmbl_17091.p1 fails validation.
(ATG)	 CC	27294-27356	GT	AGG
(AAG)	 AG	27462-27635	GT	AGG
(GAA)	 AG	27921-28047	GT	AGG
(GTC)	 AG	28145-28236	GT	AGG
(GTT)	 AG	28341-28394	GT	AGG
-recovered pasa_asmbl_17091.p1, initial, 27294, 27356
-recovered pasa_asmbl_17091.p1, internal, 27462, 27635
-recovered pasa_asmbl_17091.p1, internal, 27921, 28047
-recovered pasa_asmbl_17091.p1, internal, 28145, 28236
-recovered pasa_asmbl_17091.p1, internal, 28341, 28394
Valid prediction for GlimmerHMM_glimmerT_38343-T1
Valid prediction for snap_scaffold_16-snap.1040-T1
Valid prediction for snap_scaffold_16-snap.1028-T1
Valid prediction for GlimmerHMM_glimmerT_38325-T1
Valid prediction for snap_scaffold_16-snap.1017-T1
Valid prediction for GlimmerHMM_glimmerT_38332-T1
Valid prediction for snap_scaffold_16-snap.1024-T1
Valid prediction for CodingQuarry_transcript_19962-T1
Valid prediction for pasa_asmbl_17092.p1
Couldn't classify 5894, 6193
Sorry, prediction pasa_asmbl_17098.p1 fails validation.
(TGC)	 AC	5894-6193	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_38331-T1
Valid prediction for CodingQuarry_transcript_19966-T1
Valid prediction for GlimmerHMM_glimmerT_38333-T1
Valid prediction for GlimmerHMM_glimmerT_38336-T1
Valid prediction for GlimmerHMM_glimmerT_38339-T1
Couldn't classify 4736, 4849
Couldn't classify 5545, 5692
Sorry, prediction pasa_asmbl_17099.p1 fails validation.
(TAC)	 TG	4736-4849	GT	AGG
(GTG)	 AG	4944-5153	GT	AGG
(GTG)	 AG	5255-5445	GT	AGG
(ATC)	 AG	5545-5692	CA	GCC
-recovered pasa_asmbl_17099.p1, internal, 4944, 5153
-recovered pasa_asmbl_17099.p1, internal, 5255, 5445
Valid prediction for snap_scaffold_16-snap.1026-T1
Valid prediction for snap_scaffold_16-snap.1039-T1
Valid prediction for GlimmerHMM_glimmerT_38330-T1
Valid prediction for snap_scaffold_16-snap.1019-T1
Valid prediction for HiQ_model.g25583.t1
Valid prediction for GlimmerHMM_glimmerT_38344-T1
Valid prediction for Augustus_model.g25578.t1
Valid prediction for snap_scaffold_16-snap.1035-T1
Valid prediction for HiQ_model.g25590.t1
Valid prediction for Augustus_model.g25575.t1
Valid prediction for snap_scaffold_16-snap.1020-T1
Valid prediction for snap_scaffold_16-snap.1032-T1
Valid prediction for Augustus_model.g25577.t1
Valid prediction for snap_scaffold_16-snap.1016-T1
Valid prediction for HiQ_model.g25587.t1
Couldn't classify 46136, 46252
Sorry, prediction pasa_asmbl_17088.p1 fails validation.
(GAG)	 AG	46136-46252	GT	AGG
(GTG)	 AG	46635-46716	GT	AGG
(TGC)	 AG	47324-47404	GT	TGG
(CAT)	 AG	48105-48184	GT	AGG
(GTG)	 AG	48469-48575	GT	AAG
(CAT)	 AG	48753-48790	GT	AGG
(ACT)	 AG	48957-49099	GT	TGG
(TTT)	 AG	49784-49854	GT	AAG
(GGC)	 AG	50806-50894	GT	AGG
(GAG)	 AG	51039-51103	GT	ACG
(AAA)	 AG	51524-51626	GT	AGG
(ATT)	 AG	51769-51881	GT	AGG
(CAG)	 AG	52063-52188	GT	AGG
(GTC)	 AG	52408-52497	GT	ATG
(GTG)	 AG	52618-52776	GT	GGG
(GTG)	 AG	52872-53033	GT	AGG
(GTA)	 AG	53232-53308	GT	GGG
(GTT)	 AG	53564-53681	GT	AGG
(GAC)	 AG	53795-53935	GT	AGG
(GGT)	 AG	54091-54213	CC	GAC
add_exon() Sorry, pasa_asmbl_17088.p1 50806-50894-terminal-2 is invalid.
-recovered pasa_asmbl_17088.p1, terminal, 50806, 50894
-recovered pasa_asmbl_17088.p1, terminal, 54091, 54213
-recovered pasa_asmbl_17088.p1, internal, 46136, 46252
-recovered pasa_asmbl_17088.p1, internal, 46635, 46716
-recovered pasa_asmbl_17088.p1, internal, 47324, 47404
-recovered pasa_asmbl_17088.p1, internal, 48105, 48184
-recovered pasa_asmbl_17088.p1, internal, 48469, 48575
-recovered pasa_asmbl_17088.p1, internal, 48753, 48790
-recovered pasa_asmbl_17088.p1, internal, 48957, 49099
-recovered pasa_asmbl_17088.p1, internal, 49784, 49854
-recovered pasa_asmbl_17088.p1, internal, 50806, 50894
-recovered pasa_asmbl_17088.p1, internal, 51039, 51103
-recovered pasa_asmbl_17088.p1, internal, 51524, 51626
-recovered pasa_asmbl_17088.p1, internal, 51769, 51881
-recovered pasa_asmbl_17088.p1, internal, 52063, 52188
-recovered pasa_asmbl_17088.p1, internal, 52408, 52497
-recovered pasa_asmbl_17088.p1, internal, 52618, 52776
-recovered pasa_asmbl_17088.p1, internal, 52872, 53033
-recovered pasa_asmbl_17088.p1, internal, 53232, 53308
-recovered pasa_asmbl_17088.p1, internal, 53564, 53681
-recovered pasa_asmbl_17088.p1, internal, 53795, 53935
Valid prediction for CodingQuarry_transcript_19963-T1
Couldn't classify 8247, 8291
Sorry, prediction pasa_asmbl_17096.p1 fails validation.
(AAA)	 AG	8247-8291	GT	TGG
(GTG)	 AG	8717-8818	GT	AGG
(TTG)	 AG	8931-9053	GT	AAG
(GAA)	 AG	9183-9215	GT	AGG
(GAG)	 AG	9462-9612	GT	AGG
(GCT)	 AG	9798-9889	GT	AGG
(GTG)	 AG	11024-11113	GT	ATG
(CCT)	 AG	11458-11502	GA	GAG
-recovered pasa_asmbl_17096.p1, terminal, 11458, 11502
-recovered pasa_asmbl_17096.p1, internal, 8247, 8291
-recovered pasa_asmbl_17096.p1, internal, 8717, 8818
-recovered pasa_asmbl_17096.p1, internal, 8931, 9053
-recovered pasa_asmbl_17096.p1, internal, 9183, 9215
-recovered pasa_asmbl_17096.p1, internal, 9462, 9612
-recovered pasa_asmbl_17096.p1, internal, 9798, 9889
-recovered pasa_asmbl_17096.p1, internal, 11024, 11113
Valid prediction for Augustus_model.g25576.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39249, rend_intergenic: 32982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59586, rend_intergenic: 51188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78528, rend_intergenic: 73627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88949, rend_intergenic: 80166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104758, rend_intergenic: 102223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111107, rend_intergenic: 110023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121168, rend_intergenic: 115328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131677, rend_intergenic: 125947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135649, rend_intergenic: 132076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154425, rend_intergenic: 135705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176366, rend_intergenic: 176365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178744, rend_intergenic: 176401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181300
-exon list size: 384


building trellis

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99.5    
99.7    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 39249, rend_intergenic: 32982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59586, rend_intergenic: 51188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78528, rend_intergenic: 73627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88949, rend_intergenic: 80166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104758, rend_intergenic: 102223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111107, rend_intergenic: 110023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121168, rend_intergenic: 115328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131677, rend_intergenic: 125947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135649, rend_intergenic: 132076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154425, rend_intergenic: 135705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176366, rend_intergenic: 176365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178744, rend_intergenic: 176401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 16602
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-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

-building DP trellis

-building trellis in range 1 - 11077
-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