-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_4882017-5078821

-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 Augustus_model.g9940.t1
Valid prediction for HiQ_model.g9949.t1
Valid prediction for GeneMark_model.25268_t
Valid prediction for snap_scaffold_6-snap.1173-T1
Valid prediction for snap_scaffold_6-snap.1165-T1
Couldn't classify 112559, 112708
Sorry, prediction pasa_asmbl_46844.p1 fails validation.
(ATG)	 CC	106211-106327	GT	ATG
(TTG)	 AG	106737-106815	GT	GAG
(GGT)	 AG	107033-107130	GT	AGG
(GCT)	 AG	107238-107366	GT	AGG
(ATG)	 AG	107836-107918	GT	GGG
(GTT)	 AG	108755-108881	GT	CTG
(GGT)	 AG	108977-109059	GT	GGG
(ATT)	 AG	109181-109274	GT	TGG
(GTG)	 AG	111167-111379	GT	CGG
(GAG)	 AG	112559-112708	GG	CAG
-recovered pasa_asmbl_46844.p1, initial, 106211, 106327
-recovered pasa_asmbl_46844.p1, initial, 107836, 107918
add_exon() Sorry, pasa_asmbl_46844.p1 106737-106815-terminal-3 is invalid.
-recovered pasa_asmbl_46844.p1, terminal, 106737, 106815
-recovered pasa_asmbl_46844.p1, internal, 106737, 106815
-recovered pasa_asmbl_46844.p1, internal, 107033, 107130
-recovered pasa_asmbl_46844.p1, internal, 107238, 107366
-recovered pasa_asmbl_46844.p1, internal, 107836, 107918
-recovered pasa_asmbl_46844.p1, internal, 108755, 108881
-recovered pasa_asmbl_46844.p1, internal, 108977, 109059
-recovered pasa_asmbl_46844.p1, internal, 109181, 109274
-recovered pasa_asmbl_46844.p1, internal, 111167, 111379
Valid prediction for snap_scaffold_6-snap.1188-T1
Valid prediction for GeneMark_model.25304_t
Valid prediction for snap_scaffold_6-snap.1186-T1
Valid prediction for snap_scaffold_6-snap.1175-T1
Valid prediction for HiQ_model.g9942.t1
Valid prediction for GlimmerHMM_glimmerT_14941-T1
Valid prediction for GeneMark_model.25292_t
Valid prediction for GeneMark_model.25286_t
Valid prediction for GlimmerHMM_glimmerT_14927-T1
Valid prediction for CodingQuarry_transcript_54891-T1
Valid prediction for snap_scaffold_6-snap.1176-T1
Valid prediction for snap_scaffold_6-snap.1166-T1
Valid prediction for GeneMark_model.25306_t
Valid prediction for Augustus_model.g9947.t1
Valid prediction for GeneMark_model.25284_t
Valid prediction for GeneMark_model.25312_t
Valid prediction for GlimmerHMM_glimmerT_14940-T1
Valid prediction for snap_scaffold_6-snap.1181-T1
Valid prediction for GeneMark_model.25269_t
Valid prediction for GeneMark_model.25309_t
Valid prediction for snap_scaffold_6-snap.1185-T1
Valid prediction for GeneMark_model.25293_t
Valid prediction for GeneMark_model.25276_t
Valid prediction for snap_scaffold_6-snap.1159-T1
Valid prediction for GlimmerHMM_glimmerT_14935-T1
Valid prediction for GeneMark_model.25280_t
Valid prediction for snap_scaffold_6-snap.1158-T1
Valid prediction for GeneMark_model.25308_t
Valid prediction for GlimmerHMM_glimmerT_14932-T1
Valid prediction for GlimmerHMM_glimmerT_14936-T1
Valid prediction for GeneMark_model.25271_t
Valid prediction for HiQ_model.g9948.t1
Valid prediction for pasa_asmbl_46856.p1
Valid prediction for GeneMark_model.25299_t
Valid prediction for GeneMark_model.25273_t
Valid prediction for snap_scaffold_6-snap.1174-T1
Valid prediction for pasa_asmbl_46847.p1
Valid prediction for snap_scaffold_6-snap.1183-T1
Couldn't classify 117993, 118080
Sorry, prediction GeneMark_model.25301_t fails validation.
(GCT)	 AG	117993-118080	GT	ACG
(AGC)	 AG	118196-118367	GT	TGG
(GGG)	 AG	119344-119527	AA	GAA
-recovered GeneMark_model.25301_t, terminal, 119344, 119527
-recovered GeneMark_model.25301_t, internal, 117993, 118080
-recovered GeneMark_model.25301_t, internal, 118196, 118367
Valid prediction for pasa_asmbl_46858.p1
Valid prediction for GeneMark_model.25282_t
Valid prediction for GeneMark_model.25275_t
Valid prediction for GeneMark_model.25290_t
Valid prediction for Augustus_model.g9937.t1
Valid prediction for GeneMark_model.25314_t
Valid prediction for Augustus_model.g9934.t1
Valid prediction for snap_scaffold_6-snap.1170-T1
Valid prediction for GeneMark_model.25296_t
Valid prediction for GeneMark_model.25297_t
Valid prediction for Augustus_model.g9945.t1
Valid prediction for GeneMark_model.25311_t
Valid prediction for GlimmerHMM_glimmerT_14934-T1
Valid prediction for CodingQuarry_transcript_54889-T1
Valid prediction for GlimmerHMM_glimmerT_14939-T1
Valid prediction for GeneMark_model.25295_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 snap_scaffold_6-snap.1162-T1
Valid prediction for CodingQuarry_transcript_54892-T1
Valid prediction for GlimmerHMM_glimmerT_14922-T1
Valid prediction for snap_scaffold_6-snap.1172-T1
Valid prediction for GeneMark_model.25291_t
Valid prediction for GeneMark_model.25287_t
Valid prediction for snap_scaffold_6-snap.1182-T1
Couldn't classify 64959, 65102
Sorry, prediction pasa_asmbl_48323.p1 fails validation.
(GCT)	 GT	64959-65102	GT	AGG
(CCC)	 AG	66047-66173	GT	TGG
(CTC)	 AG	66289-66337	GT	TGG
(GAG)	 AG	66633-66812	GT	AGG
(GAA)	 AG	67599-67884	GC	GAG
-recovered pasa_asmbl_48323.p1, terminal, 67599, 67884
-recovered pasa_asmbl_48323.p1, internal, 66047, 66173
-recovered pasa_asmbl_48323.p1, internal, 66289, 66337
-recovered pasa_asmbl_48323.p1, internal, 66633, 66812
-recovered pasa_asmbl_48323.p1, internal, 67599, 67884
Valid prediction for snap_scaffold_6-snap.1157-T1
Valid prediction for snap_scaffold_6-snap.1169-T1
Valid prediction for snap_scaffold_6-snap.1163-T1
Valid prediction for CodingQuarry_transcript_54884-T1
Valid prediction for snap_scaffold_6-snap.1187-T1
Valid prediction for GlimmerHMM_glimmerT_14924-T1
Valid prediction for GlimmerHMM_glimmerT_14921-T1
Valid prediction for pasa_asmbl_48332.p1
Valid prediction for GlimmerHMM_glimmerT_14938-T1
Valid prediction for GeneMark_model.25303_t
Valid prediction for GeneMark_model.25274_t
Valid prediction for HiQ_model.g9938.t1
Couldn't classify 93268, 93774
Sorry, prediction pasa_asmbl_48321.p2 fails validation.
(ATG)	 CC	93268-93774	GG	GGG
Valid prediction for GlimmerHMM_glimmerT_14933-T1
Valid prediction for snap_scaffold_6-snap.1179-T1
Valid prediction for GeneMark_model.25294_t
Valid prediction for snap_scaffold_6-snap.1160-T1
Valid prediction for snap_scaffold_6-snap.1155-T1
Valid prediction for Augustus_model.g9951.t1
Valid prediction for Augustus_model.g9936.t1
Valid prediction for Augustus_model.g9933.t1
Valid prediction for pasa_asmbl_48310.p1
Valid prediction for GlimmerHMM_glimmerT_14923-T1
Valid prediction for Augustus_model.g9946.t1
Valid prediction for GeneMark_model.25288_t
Valid prediction for GeneMark_model.25277_t
Valid prediction for GlimmerHMM_glimmerT_14926-T1
Valid prediction for snap_scaffold_6-snap.1177-T1
Valid prediction for GlimmerHMM_glimmerT_14937-T1
Valid prediction for GlimmerHMM_glimmerT_14929-T1
Valid prediction for GlimmerHMM_glimmerT_14943-T1
Valid prediction for GeneMark_model.25283_t
Valid prediction for GlimmerHMM_glimmerT_14920-T1
Valid prediction for pasa_asmbl_48336.p1
Valid prediction for GeneMark_model.25279_t
Valid prediction for GlimmerHMM_glimmerT_14928-T1
Valid prediction for CodingQuarry_transcript_54887-T1
Valid prediction for CodingQuarry_transcript_54885-T1
Valid prediction for GeneMark_model.25289_t
Valid prediction for GlimmerHMM_glimmerT_14925-T1
Valid prediction for snap_scaffold_6-snap.1178-T1
Valid prediction for snap_scaffold_6-snap.1168-T1
Valid prediction for GeneMark_model.25302_t
Valid prediction for snap_scaffold_6-snap.1184-T1
Valid prediction for GeneMark_model.25278_t
Valid prediction for GeneMark_model.25310_t
Valid prediction for snap_scaffold_6-snap.1190-T1
Valid prediction for GeneMark_model.25313_t
Valid prediction for HiQ_model.g9950.t1
Valid prediction for Augustus_model.g9943.t1
Valid prediction for GlimmerHMM_glimmerT_14944-T1
Valid prediction for snap_scaffold_6-snap.1164-T1
Valid prediction for CodingQuarry_transcript_54886-T1
Valid prediction for GlimmerHMM_glimmerT_14930-T1
Valid prediction for Augustus_model.g9935.t1
Valid prediction for pasa_asmbl_48314.p1
Valid prediction for snap_scaffold_6-snap.1189-T1
Valid prediction for Augustus_model.g9939.t1
Valid prediction for GeneMark_model.25307_t
Valid prediction for pasa_asmbl_48317.p1
Valid prediction for snap_scaffold_6-snap.1171-T1
Valid prediction for GeneMark_model.25298_t
Couldn't classify 61521, 61521
Sorry, prediction CodingQuarry_transcript_54890-T1 fails validation.
(ATG)	 GC	60506-60618	GT	TGG
(ACA)	 AG	61521-61521	CA	GAC
-recovered CodingQuarry_transcript_54890-T1, initial, 60506, 60618
Valid prediction for Augustus_model.g9944.t1
Valid prediction for snap_scaffold_6-snap.1161-T1
Valid prediction for Augustus_model.g9941.t1
Valid prediction for GeneMark_model.25285_t
Valid prediction for GlimmerHMM_glimmerT_14942-T1
Valid prediction for snap_scaffold_6-snap.1167-T1
Couldn't classify 78865, 79040
Sorry, prediction GeneMark_model.25300_t fails validation.
(AGA)	 AG	78865-79040	GT	AGG
(GAC)	 AG	79070-79118	GT	CAG
(GAG)	 AG	79156-79269	GT	CTG
(ACA)	 AG	79551-79584	GT	AGG
(GGC)	 AG	81329-81339	GT	CTG
(GAA)	 AG	81362-81430	GT	AGG
(GTG)	 AG	81469-81513	GT	GAG
(ACA)	 AG	81536-81556	GT	AGG
(GTG)	 AG	81577-81600	GT	GAG
(AGT)	 AG	81655-81835	GT	ATG
(AGG)	 AG	81963-82118	GA	GAG
-recovered GeneMark_model.25300_t, terminal, 81963, 82118
-recovered GeneMark_model.25300_t, internal, 78865, 79040
-recovered GeneMark_model.25300_t, internal, 79070, 79118
-recovered GeneMark_model.25300_t, internal, 79156, 79269
-recovered GeneMark_model.25300_t, internal, 79551, 79584
-recovered GeneMark_model.25300_t, internal, 81329, 81339
-recovered GeneMark_model.25300_t, internal, 81362, 81430
-recovered GeneMark_model.25300_t, internal, 81469, 81513
-recovered GeneMark_model.25300_t, internal, 81536, 81556
-recovered GeneMark_model.25300_t, internal, 81577, 81600
-recovered GeneMark_model.25300_t, internal, 81655, 81835
Valid prediction for GlimmerHMM_glimmerT_14931-T1
Valid prediction for GeneMark_model.25270_t
Valid prediction for GeneMark_model.25305_t
Valid prediction for snap_scaffold_6-snap.1180-T1
Valid prediction for snap_scaffold_6-snap.1156-T1
Valid prediction for Augustus_model.g9952.t1
Valid prediction for GeneMark_model.25272_t
Valid prediction for GeneMark_model.25281_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17995, rend_intergenic: 15260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28936, rend_intergenic: 22049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55101, rend_intergenic: 47213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93124, rend_intergenic: 90833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151489, rend_intergenic: 148233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162340, rend_intergenic: 160190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185766, rend_intergenic: 171420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196805
-exon list size: 636


building trellis

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92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 17995, rend_intergenic: 15260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28936, rend_intergenic: 22049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55101, rend_intergenic: 47213  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93124, rend_intergenic: 90833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151489, rend_intergenic: 148233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162340, rend_intergenic: 160190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185766, rend_intergenic: 171420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support