-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_5927601-6156237

-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.90747_t
Valid prediction for GeneMark_model.90745_t
Valid prediction for snap_scaffold_23-snap.1072-T1
Valid prediction for GeneMark_model.90744_t
Valid prediction for snap_scaffold_23-snap.1105-T1
Valid prediction for GeneMark_model.90751_t
Valid prediction for GeneMark_model.90719_t
Valid prediction for snap_scaffold_23-snap.1080-T1
Valid prediction for Augustus_model.g35216.t1
Valid prediction for GlimmerHMM_glimmerT_52333-T1
Valid prediction for GeneMark_model.90753_t
Valid prediction for snap_scaffold_23-snap.1087-T1
Valid prediction for GeneMark_model.90716_t
Valid prediction for GlimmerHMM_glimmerT_52354-T1
Valid prediction for GeneMark_model.90713_t
Valid prediction for Augustus_model.g35218.t1
Valid prediction for snap_scaffold_23-snap.1099-T1
Valid prediction for GlimmerHMM_glimmerT_52334-T1
Valid prediction for GeneMark_model.90733_t
Valid prediction for GlimmerHMM_glimmerT_52358-T1
Valid prediction for snap_scaffold_23-snap.1096-T1
Valid prediction for GeneMark_model.90721_t
Valid prediction for GeneMark_model.90723_t
Valid prediction for Augustus_model.g35209.t1
Valid prediction for GlimmerHMM_glimmerT_52347-T1
Valid prediction for snap_scaffold_23-snap.1093-T1
Valid prediction for GeneMark_model.90741_t
Valid prediction for GeneMark_model.90759_t
Valid prediction for GlimmerHMM_glimmerT_52335-T1
Valid prediction for GeneMark_model.90755_t
Valid prediction for GlimmerHMM_glimmerT_52353-T1
Valid prediction for GlimmerHMM_glimmerT_52360-T1
Valid prediction for GeneMark_model.90749_t
Valid prediction for snap_scaffold_23-snap.1106-T1
Valid prediction for GeneMark_model.90763_t
Valid prediction for snap_scaffold_23-snap.1076-T1
Valid prediction for Augustus_model.g35217.t1
Valid prediction for snap_scaffold_23-snap.1101-T1
Valid prediction for Augustus_model.g35214.t1
Valid prediction for snap_scaffold_23-snap.1074-T1
Valid prediction for GeneMark_model.90711_t
Valid prediction for snap_scaffold_23-snap.1078-T1
Valid prediction for GeneMark_model.90748_t
Valid prediction for GeneMark_model.90760_t
Valid prediction for GeneMark_model.90729_t
Valid prediction for GlimmerHMM_glimmerT_52350-T1
Valid prediction for snap_scaffold_23-snap.1098-T1
Valid prediction for GlimmerHMM_glimmerT_52338-T1
Valid prediction for snap_scaffold_23-snap.1107-T1
Valid prediction for snap_scaffold_23-snap.1084-T1
Valid prediction for GeneMark_model.90739_t
Valid prediction for GeneMark_model.90738_t
Valid prediction for snap_scaffold_23-snap.1077-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1104-T1
Valid prediction for GeneMark_model.90727_t
Valid prediction for GlimmerHMM_glimmerT_52328-T1
Valid prediction for GlimmerHMM_glimmerT_52357-T1
Valid prediction for GlimmerHMM_glimmerT_52348-T1
Valid prediction for GeneMark_model.90730_t
Valid prediction for Augustus_model.g35220.t1
Valid prediction for snap_scaffold_23-snap.1069-T1
Valid prediction for GlimmerHMM_glimmerT_52356-T1
Valid prediction for snap_scaffold_23-snap.1067-T1
Valid prediction for snap_scaffold_23-snap.1092-T1
Valid prediction for GeneMark_model.90731_t
Valid prediction for GlimmerHMM_glimmerT_52359-T1
Valid prediction for GeneMark_model.90750_t
Valid prediction for GeneMark_model.90722_t
Valid prediction for GeneMark_model.90728_t
Valid prediction for GeneMark_model.90725_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 Augustus_model.g35211.t1
Valid prediction for GlimmerHMM_glimmerT_52336-T1
Valid prediction for GlimmerHMM_glimmerT_52339-T1
Valid prediction for GlimmerHMM_glimmerT_52329-T1
Valid prediction for GeneMark_model.90718_t
Couldn't classify 149701, 149921
Couldn't classify 150046, 150139
Sorry, prediction pasa_asmbl_31683.p2 fails validation.
(AGC)	 TC	149701-149921	GT	CGG
(GTT)	 AG	150046-150139	GT	AGG
-recovered pasa_asmbl_31683.p2, internal, 150046, 150139
Valid prediction for GeneMark_model.90712_t
Valid prediction for Augustus_model.g35213.t1
Valid prediction for GeneMark_model.90715_t
Valid prediction for snap_scaffold_23-snap.1102-T1
Valid prediction for GlimmerHMM_glimmerT_52351-T1
Valid prediction for GlimmerHMM_glimmerT_52352-T1
Valid prediction for GeneMark_model.90754_t
Valid prediction for snap_scaffold_23-snap.1079-T1
Valid prediction for GeneMark_model.90736_t
Valid prediction for GeneMark_model.90737_t
Valid prediction for GeneMark_model.90735_t
Valid prediction for Augustus_model.g35215.t1
Valid prediction for snap_scaffold_23-snap.1082-T1
Valid prediction for snap_scaffold_23-snap.1103-T1
Valid prediction for GeneMark_model.90742_t
Valid prediction for GlimmerHMM_glimmerT_52344-T1
Valid prediction for GeneMark_model.90746_t
Valid prediction for GlimmerHMM_glimmerT_52330-T1
Valid prediction for Augustus_model.g35212.t1
Valid prediction for Augustus_model.g35208.t1
Valid prediction for GeneMark_model.90762_t
Valid prediction for GlimmerHMM_glimmerT_52331-T1
Valid prediction for GlimmerHMM_glimmerT_52343-T1
Valid prediction for GlimmerHMM_glimmerT_52341-T1
Valid prediction for GlimmerHMM_glimmerT_52332-T1
Valid prediction for GeneMark_model.90724_t
Valid prediction for snap_scaffold_23-snap.1075-T1
Valid prediction for GeneMark_model.90764_t
Valid prediction for snap_scaffold_23-snap.1066-T1
Valid prediction for snap_scaffold_23-snap.1073-T1
Valid prediction for GeneMark_model.90756_t
Valid prediction for GeneMark_model.90757_t
Valid prediction for GlimmerHMM_glimmerT_52340-T1
Valid prediction for GlimmerHMM_glimmerT_52355-T1
Valid prediction for snap_scaffold_23-snap.1089-T1
Valid prediction for snap_scaffold_23-snap.1086-T1
Valid prediction for snap_scaffold_23-snap.1090-T1
Valid prediction for GeneMark_model.90740_t
Valid prediction for GeneMark_model.90714_t
Valid prediction for GeneMark_model.90734_t
Valid prediction for GlimmerHMM_glimmerT_52346-T1
Valid prediction for snap_scaffold_23-snap.1065-T1
Couldn't classify 185271, 185422
Couldn't classify 187098, 187143
Sorry, prediction pasa_asmbl_31681.p1 fails validation.
(AGA)	 CC	185271-185422	GT	AGG
(GTC)	 AG	185757-185915	GT	AGG
(GGC)	 AG	187098-187143	TC	TCT
-recovered pasa_asmbl_31681.p1, internal, 185757, 185915
Valid prediction for GeneMark_model.90732_t
Valid prediction for GeneMark_model.90761_t
Valid prediction for snap_scaffold_23-snap.1071-T1
Valid prediction for GeneMark_model.90758_t
Valid prediction for snap_scaffold_23-snap.1070-T1
Valid prediction for snap_scaffold_23-snap.1097-T1
Valid prediction for GlimmerHMM_glimmerT_52342-T1
Valid prediction for Augustus_model.g35219.t1
Valid prediction for GeneMark_model.90720_t
Valid prediction for GeneMark_model.90717_t
Valid prediction for GeneMark_model.90726_t
Valid prediction for GeneMark_model.90752_t
Valid prediction for GlimmerHMM_glimmerT_52337-T1
Valid prediction for snap_scaffold_23-snap.1094-T1
Valid prediction for snap_scaffold_23-snap.1095-T1
Valid prediction for snap_scaffold_23-snap.1083-T1
Valid prediction for snap_scaffold_23-snap.1100-T1
Valid prediction for GlimmerHMM_glimmerT_52349-T1
Valid prediction for GeneMark_model.90743_t
Valid prediction for Augustus_model.g35210.t1
Valid prediction for snap_scaffold_23-snap.1085-T1
Valid prediction for GlimmerHMM_glimmerT_52345-T1
Valid prediction for snap_scaffold_23-snap.1068-T1
Couldn't classify 140947, 141024
Couldn't classify 144416, 144514
Sorry, prediction pasa_asmbl_31977.p1 fails validation.
(GAG)	 CA	140947-141024	GT	TGG
(CCG)	 AG	142512-142737	GT	GGG
(AAT)	 AG	143218-143315	GT	AGG
(CCT)	 AG	144416-144514	AC	CCA
-recovered pasa_asmbl_31977.p1, internal, 142512, 142737
-recovered pasa_asmbl_31977.p1, internal, 143218, 143315
Couldn't classify 137538, 137668
Sorry, prediction pasa_asmbl_31684.p1 fails validation.
(ATG)	 GA	134282-134481	GT	AGG
(GTA)	 AG	136011-136174	GT	AGG
(AGG)	 AG	137538-137668	GG	TGG
-recovered pasa_asmbl_31684.p1, initial, 134282, 134481
-recovered pasa_asmbl_31684.p1, internal, 136011, 136174
Valid prediction for snap_scaffold_23-snap.1091-T1
Valid prediction for snap_scaffold_23-snap.1081-T1
Valid prediction for snap_scaffold_23-snap.1088-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16347, rend_intergenic: 14261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23673, rend_intergenic: 18856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32936, rend_intergenic: 27088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40194, rend_intergenic: 39185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54305, rend_intergenic: 47271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73855, rend_intergenic: 61201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82607, rend_intergenic: 80360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91162, rend_intergenic: 86899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92653, rend_intergenic: 91957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179298, rend_intergenic: 177260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192672, rend_intergenic: 185154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200643, rend_intergenic: 194731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207887, rend_intergenic: 201916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228637
-exon list size: 769


building trellis

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90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 16347, rend_intergenic: 14261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23673, rend_intergenic: 18856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32936, rend_intergenic: 27088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40194, rend_intergenic: 39185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54305, rend_intergenic: 47271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73855, rend_intergenic: 61201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82607, rend_intergenic: 80360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91162, rend_intergenic: 86899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92653, rend_intergenic: 91957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179298, rend_intergenic: 177260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192672, rend_intergenic: 185154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200643, rend_intergenic: 194731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207887, rend_intergenic: 201916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support