-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_6337777-6562220

-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 GeneMark_model.1088_t
Couldn't classify 82532, 82541
Sorry, prediction pasa_asmbl_1830.p1 fails validation.
(ATC)	 CC	82532-82541	GT	TGG
(GTG)	 AG	82640-82748	GT	AGG
(TGT)	 AG	82904-82972	GT	ATG
(CTT)	 AG	83083-83239	GG	AGG
-recovered pasa_asmbl_1830.p1, terminal, 83083, 83239
-recovered pasa_asmbl_1830.p1, internal, 82640, 82748
-recovered pasa_asmbl_1830.p1, internal, 82904, 82972
Valid prediction for snap_scaffold_1-snap.1072-T1
Couldn't classify 81714, 81748
Sorry, prediction pasa_asmbl_2776.p2 fails validation.
(ATG)	 GA	80521-80605	GT	AGG
(ACG)	 AG	81404-81589	GT	TGG
(GTG)	 AG	81714-81748	CG	AAC
-recovered pasa_asmbl_2776.p2, initial, 80521, 80605
-recovered pasa_asmbl_2776.p2, internal, 81404, 81589
Valid prediction for snap_scaffold_1-snap.1097-T1
Valid prediction for Augustus_model.g646.t1
Valid prediction for snap_scaffold_1-snap.1073-T1
Valid prediction for Augustus_model.g642.t1
Valid prediction for snap_scaffold_1-snap.1091-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g645.t1
Valid prediction for Augustus_model.g655.t1
Valid prediction for GeneMark_model.1076_t
Valid prediction for snap_scaffold_1-snap.1099-T1
Valid prediction for GlimmerHMM_glimmerT_882-T1
Valid prediction for snap_scaffold_1-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_866-T1
Valid prediction for GeneMark_model.1062_t
Valid prediction for GeneMark_model.1057_t
Valid prediction for GlimmerHMM_glimmerT_879-T1
Valid prediction for GlimmerHMM_glimmerT_876-T1
Valid prediction for GlimmerHMM_glimmerT_887-T1
Valid prediction for GeneMark_model.1066_t
Valid prediction for Augustus_model.g643.t1
Valid prediction for GeneMark_model.1098_t
Valid prediction for snap_scaffold_1-snap.1092-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.1068_t
Valid prediction for snap_scaffold_1-snap.1087-T1
Valid prediction for GlimmerHMM_glimmerT_885-T1
Valid prediction for GlimmerHMM_glimmerT_888-T1
Valid prediction for GlimmerHMM_glimmerT_880-T1
Valid prediction for GeneMark_model.1073_t
Valid prediction for GeneMark_model.1100_t
Valid prediction for GeneMark_model.1060_t
Valid prediction for Augustus_model.g658.t1
Valid prediction for Augustus_model.g665.t1
Valid prediction for GlimmerHMM_glimmerT_871-T1
Valid prediction for HiQ_model.g641.t1
Valid prediction for snap_scaffold_1-snap.1089-T1
Valid prediction for CodingQuarry_transcript_2651-T1
Valid prediction for snap_scaffold_1-snap.1066-T1
Valid prediction for snap_scaffold_1-snap.1100-T1
Valid prediction for Augustus_model.g657.t1
Valid prediction for snap_scaffold_1-snap.1068-T1
Valid prediction for GeneMark_model.1069_t
Valid prediction for snap_scaffold_1-snap.1104-T1
Valid prediction for GeneMark_model.1065_t
Valid prediction for snap_scaffold_1-snap.1084-T1
Valid prediction for GeneMark_model.1089_t
Valid prediction for snap_scaffold_1-snap.1080-T1
Valid prediction for GeneMark_model.1075_t
Valid prediction for snap_scaffold_1-snap.1078-T1
Valid prediction for snap_scaffold_1-snap.1070-T1
Valid prediction for Augustus_model.g644.t1
Valid prediction for snap_scaffold_1-snap.1106-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.1079_t
Valid prediction for GeneMark_model.1090_t
Valid prediction for Augustus_model.g661.t1
Valid prediction for snap_scaffold_1-snap.1081-T1
Valid prediction for Augustus_model.g652.t1
Valid prediction for GlimmerHMM_glimmerT_869-T1
Valid prediction for CodingQuarry_transcript_2653-T1
Valid prediction for GeneMark_model.1083_t
Valid prediction for snap_scaffold_1-snap.1090-T1
Valid prediction for snap_scaffold_1-snap.1093-T1
Valid prediction for Augustus_model.g649.t1
Valid prediction for GlimmerHMM_glimmerT_886-T1
Valid prediction for Augustus_model.g651.t1
Valid prediction for GeneMark_model.1053_t
Valid prediction for GeneMark_model.1077_t
Valid prediction for GlimmerHMM_glimmerT_897-T1
Valid prediction for snap_scaffold_1-snap.1083-T1
Valid prediction for GlimmerHMM_glimmerT_878-T1
Valid prediction for GeneMark_model.1094_t
Valid prediction for GlimmerHMM_glimmerT_883-T1
Valid prediction for pasa_asmbl_1824.p1
Valid prediction for GeneMark_model.1070_t
Valid prediction for GeneMark_model.1064_t
Valid prediction for snap_scaffold_1-snap.1082-T1
Valid prediction for GeneMark_model.1103_t
Valid prediction for GeneMark_model.1055_t
Valid prediction for GlimmerHMM_glimmerT_892-T1
Valid prediction for GeneMark_model.1081_t
Valid prediction for Augustus_model.g647.t1
Valid prediction for GeneMark_model.1105_t
Valid prediction for GeneMark_model.1107_t
Valid prediction for Augustus_model.g653.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 GeneMark_model.1058_t
Valid prediction for GlimmerHMM_glimmerT_872-T1
Valid prediction for pasa_asmbl_373.p1
Valid prediction for GeneMark_model.1102_t
Valid prediction for snap_scaffold_1-snap.1096-T1
Valid prediction for snap_scaffold_1-snap.1076-T1
Valid prediction for GeneMark_model.1056_t
Valid prediction for snap_scaffold_1-snap.1107-T1
Valid prediction for GlimmerHMM_glimmerT_881-T1
Valid prediction for GeneMark_model.1054_t
Valid prediction for snap_scaffold_1-snap.1079-T1
Valid prediction for CodingQuarry_transcript_2652-T1
Couldn't classify 2020, 2127
Couldn't classify 3188, 3403
Sorry, prediction pasa_asmbl_1339.p1 fails validation.
(GAG)	 TG	2020-2127	GT	AGG
(GTA)	 AG	2703-2798	GT	AGG
(GGG)	 AG	3188-3403	GA	ATG
-recovered pasa_asmbl_1339.p1, internal, 2703, 2798
Valid prediction for GlimmerHMM_glimmerT_870-T1
Valid prediction for GlimmerHMM_glimmerT_893-T1
Valid prediction for snap_scaffold_1-snap.1095-T1
Valid prediction for GeneMark_model.1108_t
Valid prediction for GlimmerHMM_glimmerT_877-T1
Valid prediction for GeneMark_model.1104_t
Valid prediction for snap_scaffold_1-snap.1067-T1
Valid prediction for GeneMark_model.1067_t
Valid prediction for snap_scaffold_1-snap.1101-T1
Valid prediction for GlimmerHMM_glimmerT_875-T1
Valid prediction for pasa_asmbl_376.p1
Valid prediction for GeneMark_model.1095_t
Valid prediction for GeneMark_model.1082_t
Valid prediction for CodingQuarry_transcript_2654-T1
Valid prediction for GeneMark_model.1086_t
Valid prediction for GlimmerHMM_glimmerT_890-T1
Valid prediction for Augustus_model.g664.t1
Valid prediction for GeneMark_model.1061_t
Valid prediction for snap_scaffold_1-snap.1105-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.1072_t
Valid prediction for GlimmerHMM_glimmerT_895-T1
Valid prediction for GeneMark_model.1063_t
Valid prediction for snap_scaffold_1-snap.1098-T1
Valid prediction for Augustus_model.g654.t1
Valid prediction for GlimmerHMM_glimmerT_884-T1
Valid prediction for GeneMark_model.1097_t
Valid prediction for GeneMark_model.1106_t
Valid prediction for GlimmerHMM_glimmerT_867-T1
Valid prediction for GlimmerHMM_glimmerT_865-T1
Valid prediction for GeneMark_model.1080_t
Valid prediction for snap_scaffold_1-snap.1103-T1
Valid prediction for Augustus_model.g648.t1
Valid prediction for GlimmerHMM_glimmerT_873-T1
Valid prediction for GlimmerHMM_glimmerT_889-T1
Valid prediction for snap_scaffold_1-snap.1074-T1
Valid prediction for snap_scaffold_1-snap.1108-T1
Valid prediction for snap_scaffold_1-snap.1077-T1
Valid prediction for GeneMark_model.1099_t
Valid prediction for GeneMark_model.1078_t
Valid prediction for snap_scaffold_1-snap.1069-T1
Valid prediction for snap_scaffold_1-snap.1094-T1
Valid prediction for Augustus_model.g650.t1
Valid prediction for GeneMark_model.1087_t
Valid prediction for GeneMark_model.1071_t
Valid prediction for HiQ_model.g659.t1
Valid prediction for snap_scaffold_1-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_896-T1
Valid prediction for snap_scaffold_1-snap.1085-T1
Valid prediction for GeneMark_model.1091_t
Valid prediction for GlimmerHMM_glimmerT_874-T1
Valid prediction for GlimmerHMM_glimmerT_868-T1
Valid prediction for Augustus_model.g660.t1
Valid prediction for GeneMark_model.1084_t
Valid prediction for Augustus_model.g666.t1
Valid prediction for Augustus_model.g656.t1
Valid prediction for Augustus_model.g662.t1
Valid prediction for snap_scaffold_1-snap.1102-T1
Valid prediction for GeneMark_model.1092_t
Valid prediction for GeneMark_model.1059_t
Valid prediction for GlimmerHMM_glimmerT_894-T1
Valid prediction for Augustus_model.g663.t1
Valid prediction for snap_scaffold_1-snap.1075-T1
Valid prediction for GlimmerHMM_glimmerT_891-T1
Valid prediction for snap_scaffold_1-snap.1086-T1
Valid prediction for GeneMark_model.1074_t
Valid prediction for GlimmerHMM_glimmerT_898-T1
Valid prediction for pasa_asmbl_368.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9179, rend_intergenic: 8785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22959, rend_intergenic: 9679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36347, rend_intergenic: 25211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128731, rend_intergenic: 120607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133461, rend_intergenic: 128997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139198, rend_intergenic: 134361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168970, rend_intergenic: 165395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171101, rend_intergenic: 169831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174852, rend_intergenic: 171341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214835, rend_intergenic: 208378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224444
-exon list size: 690


building trellis

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99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 9179, rend_intergenic: 8785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22959, rend_intergenic: 9679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36347, rend_intergenic: 25211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128731, rend_intergenic: 120607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133461, rend_intergenic: 128997  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139198, rend_intergenic: 134361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168970, rend_intergenic: 165395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171101, rend_intergenic: 169831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174852, rend_intergenic: 171341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214835, rend_intergenic: 208378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support