-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_1710876-1847239

-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 snap_scaffold_27-snap.408-T1
Valid prediction for GlimmerHMM_glimmerT_56729-T1
Valid prediction for snap_scaffold_27-snap.412-T1
Valid prediction for GlimmerHMM_glimmerT_56721-T1
Valid prediction for GlimmerHMM_glimmerT_56715-T1
Valid prediction for GlimmerHMM_glimmerT_56713-T1
Valid prediction for Augustus_model.g37582.t1
Valid prediction for GlimmerHMM_glimmerT_56726-T1
Valid prediction for snap_scaffold_27-snap.414-T1
Valid prediction for Augustus_model.g37588.t1
Valid prediction for snap_scaffold_27-snap.397-T1
Valid prediction for GlimmerHMM_glimmerT_56727-T1
Valid prediction for snap_scaffold_27-snap.416-T1
Valid prediction for GlimmerHMM_glimmerT_56730-T1
Valid prediction for pasa_asmbl_36041.p1
Valid prediction for Augustus_model.g37587.t1
Valid prediction for snap_scaffold_27-snap.400-T1
Valid prediction for snap_scaffold_27-snap.411-T1
Valid prediction for GlimmerHMM_glimmerT_56728-T1
Valid prediction for snap_scaffold_27-snap.417-T1
Valid prediction for snap_scaffold_27-snap.418-T1
Valid prediction for snap_scaffold_27-snap.404-T1
Valid prediction for snap_scaffold_27-snap.401-T1
Valid prediction for snap_scaffold_27-snap.395-T1
Couldn't classify 49906, 49925
Couldn't classify 53675, 53743
Sorry, prediction pasa_asmbl_36035.p1 fails validation.
(ATC)	 AA	49906-49925	GT	AAG
(GAT)	 AG	50129-50283	GT	AGG
(ATC)	 AG	50796-50944	GC	AGG
(GCA)	 AG	51075-51140	GT	AGG
(GTG)	 AG	51447-51560	GT	AGG
(AAA)	 AG	52385-52576	GT	AGG
(AAC)	 AG	52973-53107	GT	AGG
(ACG)	 AG	53200-53275	GT	GGG
(CTC)	 AG	53458-53486	GT	AGG
(AGT)	 AG	53675-53743	GA	AGG
-recovered pasa_asmbl_36035.p1, internal, 50129, 50283
-recovered pasa_asmbl_36035.p1, internal, 50796, 50944
-recovered pasa_asmbl_36035.p1, internal, 51075, 51140
-recovered pasa_asmbl_36035.p1, internal, 51447, 51560
-recovered pasa_asmbl_36035.p1, internal, 52385, 52576
-recovered pasa_asmbl_36035.p1, internal, 52973, 53107
-recovered pasa_asmbl_36035.p1, internal, 53200, 53275
-recovered pasa_asmbl_36035.p1, internal, 53458, 53486
Valid prediction for HiQ_model.g37584.t1
Valid prediction for Augustus_model.g37589.t1
Valid prediction for snap_scaffold_27-snap.394-T1
Valid prediction for snap_scaffold_27-snap.409-T1
Couldn't classify 63909, 63990
Couldn't classify 64091, 64174
Sorry, prediction CodingQuarry_transcript_41788-T1 fails validation.
(ATG)	 AA	58747-58762	GT	AAG
(CTG)	 AG	59074-59140	GT	CAG
(GTC)	 AG	59269-59361	GT	GAG
(AAT)	 AG	59610-59669	GT	AGG
(CTA)	 AG	59848-60130	GT	AGG
(GTG)	 AG	61232-61302	GT	AAG
(GAG)	 AG	61483-61529	GT	GGG
(GAA)	 AG	61820-61983	GT	AGG
(GCC)	 AG	62110-62218	GT	GGG
(GTA)	 AG	62404-62443	GT	AGG
(CAT)	 AG	62910-63099	GT	AGG
(GCC)	 AG	63278-63296	GT	AGG
(CCC)	 AG	63909-63990	AT	ACA
(TGC)	 AC	64091-64174	GT	ACG
(TAT)	 AG	65040-65097	GT	AGG
(GGT)	 AG	65201-65289	GT	AAG
(AGC)	 AG	65744-65852	GT	CGG
(ATC)	 AG	65960-65994	GT	GGG
(GGT)	 AG	66200-66227	GA	GAG
-recovered CodingQuarry_transcript_41788-T1, initial, 58747, 58762
add_exon() Sorry, CodingQuarry_transcript_41788-T1 59269-59361-terminal-1 is invalid.
-recovered CodingQuarry_transcript_41788-T1, terminal, 59269, 59361
-recovered CodingQuarry_transcript_41788-T1, terminal, 66200, 66227
-recovered CodingQuarry_transcript_41788-T1, internal, 59074, 59140
-recovered CodingQuarry_transcript_41788-T1, internal, 59269, 59361
-recovered CodingQuarry_transcript_41788-T1, internal, 59610, 59669
-recovered CodingQuarry_transcript_41788-T1, internal, 59848, 60130
-recovered CodingQuarry_transcript_41788-T1, internal, 61232, 61302
-recovered CodingQuarry_transcript_41788-T1, internal, 61483, 61529
-recovered CodingQuarry_transcript_41788-T1, internal, 61820, 61983
-recovered CodingQuarry_transcript_41788-T1, internal, 62110, 62218
-recovered CodingQuarry_transcript_41788-T1, internal, 62404, 62443
-recovered CodingQuarry_transcript_41788-T1, internal, 62910, 63099
-recovered CodingQuarry_transcript_41788-T1, internal, 63278, 63296
-recovered CodingQuarry_transcript_41788-T1, internal, 65040, 65097
-recovered CodingQuarry_transcript_41788-T1, internal, 65201, 65289
-recovered CodingQuarry_transcript_41788-T1, internal, 65744, 65852
-recovered CodingQuarry_transcript_41788-T1, internal, 65960, 65994
Valid prediction for pasa_asmbl_36584.p1
Valid prediction for snap_scaffold_27-snap.406-T1
Couldn't classify 63909, 63990
Couldn't classify 64091, 64174
Sorry, prediction pasa_asmbl_36038.p1 fails validation.
(ATG)	 AA	58747-58762	GT	AAG
(CTG)	 AG	59074-59140	GT	CAG
(GTC)	 AG	59269-59361	GT	GAG
(AAT)	 AG	59610-59669	GT	AGG
(CTA)	 AG	59848-60130	GT	AGG
(GTG)	 AG	61232-61302	GT	AAG
(GAG)	 AG	61483-61529	GT	GGG
(GAA)	 AG	61820-61983	GT	AGG
(GCC)	 AG	62110-62218	GT	GGG
(GTA)	 AG	62404-62443	GT	AGG
(CAT)	 AG	62910-63099	GT	AGG
(GCC)	 AG	63278-63296	GT	AGG
(CCC)	 AG	63909-63990	AT	ACA
(TGC)	 AC	64091-64174	GT	ACG
(TAT)	 AG	65040-65097	GT	AGG
(GGT)	 AG	65201-65289	GT	AAG
(AGC)	 AG	65744-65852	GT	CGG
(ATC)	 AG	65960-65994	GT	GGG
(GGT)	 AG	66200-66227	GA	GAG
-recovered pasa_asmbl_36038.p1, initial, 58747, 58762
add_exon() Sorry, pasa_asmbl_36038.p1 59269-59361-terminal-1 is invalid.
-recovered pasa_asmbl_36038.p1, terminal, 59269, 59361
-recovered pasa_asmbl_36038.p1, terminal, 66200, 66227
-recovered pasa_asmbl_36038.p1, internal, 59074, 59140
-recovered pasa_asmbl_36038.p1, internal, 59269, 59361
-recovered pasa_asmbl_36038.p1, internal, 59610, 59669
-recovered pasa_asmbl_36038.p1, internal, 59848, 60130
-recovered pasa_asmbl_36038.p1, internal, 61232, 61302
-recovered pasa_asmbl_36038.p1, internal, 61483, 61529
-recovered pasa_asmbl_36038.p1, internal, 61820, 61983
-recovered pasa_asmbl_36038.p1, internal, 62110, 62218
-recovered pasa_asmbl_36038.p1, internal, 62404, 62443
-recovered pasa_asmbl_36038.p1, internal, 62910, 63099
-recovered pasa_asmbl_36038.p1, internal, 63278, 63296
-recovered pasa_asmbl_36038.p1, internal, 65040, 65097
-recovered pasa_asmbl_36038.p1, internal, 65201, 65289
-recovered pasa_asmbl_36038.p1, internal, 65744, 65852
-recovered pasa_asmbl_36038.p1, internal, 65960, 65994
Valid prediction for snap_scaffold_27-snap.398-T1
Valid prediction for snap_scaffold_27-snap.392-T1
Valid prediction for GlimmerHMM_glimmerT_56723-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 41827, 41845
Couldn't classify 45606, 45650
Sorry, prediction pasa_asmbl_36790.p1 fails validation.
(AAA)	 TG	41827-41845	GT	AGG
(CCC)	 AG	43951-44158	GT	AAG
(GGC)	 AG	44302-44440	GT	AGG
(TTG)	 AG	45127-45196	GT	GGG
(CTG)	 AG	45481-45527	GT	AGG
(ACC)	 AG	45606-45650	GA	AGG
-recovered pasa_asmbl_36790.p1, internal, 43951, 44158
-recovered pasa_asmbl_36790.p1, internal, 44302, 44440
-recovered pasa_asmbl_36790.p1, internal, 45127, 45196
-recovered pasa_asmbl_36790.p1, internal, 45481, 45527
Valid prediction for snap_scaffold_27-snap.396-T1
Valid prediction for snap_scaffold_27-snap.403-T1
Couldn't classify 77975, 78084
Sorry, prediction pasa_asmbl_36786.p1 fails validation.
(ATC)	 AA	77975-78084	GT	CGG
(GGA)	 AG	78627-78733	GT	CGG
(ACT)	 AG	78827-78912	AA	AGA
-recovered pasa_asmbl_36786.p1, terminal, 78827, 78912
-recovered pasa_asmbl_36786.p1, internal, 78627, 78733
Valid prediction for Augustus_model.g37586.t1
Couldn't classify 90844, 90968
Couldn't classify 92628, 92835
Sorry, prediction pasa_asmbl_37197.p1 fails validation.
(GGT)	 TC	90844-90968	GT	AGG
(GTA)	 AG	91940-92089	GT	AGG
(GCG)	 AG	92628-92835	AA	ACA
-recovered pasa_asmbl_37197.p1, internal, 91940, 92089
Valid prediction for pasa_asmbl_36779.p2
Valid prediction for Augustus_model.g37580.t1
Valid prediction for GlimmerHMM_glimmerT_56722-T1
Valid prediction for GlimmerHMM_glimmerT_56719-T1
Valid prediction for Augustus_model.g37590.t1
Valid prediction for snap_scaffold_27-snap.420-T1
Valid prediction for snap_scaffold_27-snap.405-T1
Valid prediction for GlimmerHMM_glimmerT_56732-T1
Valid prediction for Augustus_model.g37579.t1
Valid prediction for Augustus_model.g37581.t1
Valid prediction for snap_scaffold_27-snap.393-T1
Valid prediction for GlimmerHMM_glimmerT_56714-T1
Valid prediction for GlimmerHMM_glimmerT_56725-T1
Valid prediction for GlimmerHMM_glimmerT_56717-T1
Valid prediction for snap_scaffold_27-snap.391-T1
Valid prediction for snap_scaffold_27-snap.419-T1
Valid prediction for snap_scaffold_27-snap.410-T1
Valid prediction for Augustus_model.g37585.t1
Valid prediction for GlimmerHMM_glimmerT_56720-T1
Valid prediction for CodingQuarry_transcript_41789-T1
Valid prediction for GlimmerHMM_glimmerT_56724-T1
Valid prediction for GlimmerHMM_glimmerT_56716-T1
Valid prediction for GlimmerHMM_glimmerT_56718-T1
Valid prediction for snap_scaffold_27-snap.402-T1
Valid prediction for snap_scaffold_27-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_56712-T1
Couldn't classify 93259, 94215
Sorry, prediction pasa_asmbl_36785.p1 fails validation.
(GAG)	 CG	93259-94215	AG	GAA
Valid prediction for CodingQuarry_transcript_41787-T1
Valid prediction for GlimmerHMM_glimmerT_56731-T1
Valid prediction for snap_scaffold_27-snap.399-T1
Valid prediction for snap_scaffold_27-snap.407-T1
Valid prediction for HiQ_model.g37583.t1
Valid prediction for snap_scaffold_27-snap.415-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37121, rend_intergenic: 13377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45710, rend_intergenic: 39277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48819, rend_intergenic: 46396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55564, rend_intergenic: 53344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66227, rend_intergenic: 60816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69764, rend_intergenic: 67581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78459, rend_intergenic: 70146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86939, rend_intergenic: 79977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106414, rend_intergenic: 100053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130420, rend_intergenic: 114754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 136364
-exon list size: 386


building trellis

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97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 15 predictions from path traversal
Error with prediction: snap lend_intergenic: 37121, rend_intergenic: 13377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45710, rend_intergenic: 39277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48819, rend_intergenic: 46396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55564, rend_intergenic: 53344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66227, rend_intergenic: 60816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69764, rend_intergenic: 67581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78459, rend_intergenic: 70146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86939, rend_intergenic: 79977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106414, rend_intergenic: 100053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130420, rend_intergenic: 114754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support