-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_1695432-1903389

-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.14770_t
Valid prediction for snap_scaffold_4-snap.424-T1
Valid prediction for snap_scaffold_4-snap.390-T1
Valid prediction for snap_scaffold_4-snap.388-T1
Valid prediction for snap_scaffold_4-snap.427-T1
Valid prediction for GeneMark_model.14751_t
Valid prediction for snap_scaffold_4-snap.391-T1
Valid prediction for GeneMark_model.14742_t
Valid prediction for snap_scaffold_4-snap.395-T1
Valid prediction for GeneMark_model.14721_t
Couldn't classify 194691, 194813
Couldn't classify 195552, 195692
Sorry, prediction pasa_asmbl_42462.p1 fails validation.
(GTG)	 AC	194691-194813	GT	AGG
(ATC)	 AG	195147-195254	GT	AGG
(GTC)	 AG	195552-195692	CC	TGC
-recovered pasa_asmbl_42462.p1, internal, 195147, 195254
Valid prediction for GeneMark_model.14752_t
Valid prediction for GlimmerHMM_glimmerT_9013-T1
Valid prediction for GlimmerHMM_glimmerT_9006-T1
Couldn't classify 176020, 176213
Couldn't classify 177578, 177782
Sorry, prediction pasa_asmbl_42458.p1 fails validation.
(AGG)	 GA	176020-176213	GT	AGG
(CAA)	 AG	177578-177782	CC	TGC
Valid prediction for GlimmerHMM_glimmerT_9002-T1
Valid prediction for snap_scaffold_4-snap.402-T1
Valid prediction for snap_scaffold_4-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_9000-T1
Valid prediction for snap_scaffold_4-snap.399-T1
Couldn't classify 188229, 188496
Sorry, prediction pasa_asmbl_42461.p1 fails validation.
(CCC)	 CC	188229-188496	GT	AGG
(TGT)	 AG	189465-189508	TC	GAT
-recovered pasa_asmbl_42461.p1, terminal, 189465, 189508
Valid prediction for GeneMark_model.14745_t
Valid prediction for snap_scaffold_4-snap.401-T1
Valid prediction for GlimmerHMM_glimmerT_9007-T1
Valid prediction for GeneMark_model.14758_t
Valid prediction for snap_scaffold_4-snap.432-T1
Valid prediction for GeneMark_model.14772_t
Valid prediction for snap_scaffold_4-snap.393-T1
Valid prediction for GeneMark_model.14749_t
Valid prediction for Augustus_model.g5872.t1
Valid prediction for GlimmerHMM_glimmerT_8997-T1
Valid prediction for snap_scaffold_4-snap.419-T1
Valid prediction for GeneMark_model.14734_t
Valid prediction for snap_scaffold_4-snap.400-T1
Valid prediction for GeneMark_model.14756_t
Valid prediction for GlimmerHMM_glimmerT_9003-T1
Valid prediction for Augustus_model.g5866.t1
Valid prediction for GlimmerHMM_glimmerT_9005-T1
Valid prediction for snap_scaffold_4-snap.433-T1
Valid prediction for GeneMark_model.14720_t
Valid prediction for Augustus_model.g5868.t1
Valid prediction for GeneMark_model.14754_t
Valid prediction for snap_scaffold_4-snap.394-T1
Valid prediction for GeneMark_model.14724_t
Valid prediction for GeneMark_model.14731_t
Valid prediction for GeneMark_model.14764_t
Valid prediction for GlimmerHMM_glimmerT_9004-T1
Valid prediction for GeneMark_model.14737_t
Valid prediction for Augustus_model.g5867.t1
Valid prediction for snap_scaffold_4-snap.405-T1
Valid prediction for snap_scaffold_4-snap.418-T1
Valid prediction for snap_scaffold_4-snap.403-T1
Valid prediction for snap_scaffold_4-snap.412-T1
Valid prediction for GlimmerHMM_glimmerT_9001-T1
Valid prediction for Augustus_model.g5873.t1
Couldn't classify 181367, 181595
Couldn't classify 188103, 188153
Sorry, prediction pasa_asmbl_42459.p1 fails validation.
(AAA)	 AG	181367-181595	GT	AGG
(TTC)	 AG	182533-182577	GT	AGG
(AGT)	 AG	184186-184274	GT	AGG
(GGC)	 AG	185651-185836	GT	AGG
(TAC)	 AG	188103-188153	CC	CCC
add_exon() Sorry, pasa_asmbl_42459.p1 181367-181595-terminal-3 is invalid.
-recovered pasa_asmbl_42459.p1, terminal, 181367, 181595
-recovered pasa_asmbl_42459.p1, internal, 181367, 181595
-recovered pasa_asmbl_42459.p1, internal, 182533, 182577
-recovered pasa_asmbl_42459.p1, internal, 184186, 184274
-recovered pasa_asmbl_42459.p1, internal, 185651, 185836
Valid prediction for snap_scaffold_4-snap.415-T1
Valid prediction for Augustus_model.g5869.t1
Valid prediction for GeneMark_model.14739_t
Valid prediction for GeneMark_model.14776_t
Valid prediction for GeneMark_model.14773_t
Valid prediction for GeneMark_model.14759_t
Valid prediction for GlimmerHMM_glimmerT_8999-T1
Valid prediction for snap_scaffold_4-snap.417-T1
Valid prediction for GeneMark_model.14768_t
Valid prediction for snap_scaffold_4-snap.422-T1
Valid prediction for GlimmerHMM_glimmerT_9012-T1
Valid prediction for Augustus_model.g5865.t1
Valid prediction for GeneMark_model.14728_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 GeneMark_model.14769_t
Valid prediction for GlimmerHMM_glimmerT_8991-T1
Valid prediction for GeneMark_model.14732_t
Valid prediction for snap_scaffold_4-snap.428-T1
Valid prediction for GlimmerHMM_glimmerT_9009-T1
Valid prediction for GlimmerHMM_glimmerT_9014-T1
Valid prediction for Augustus_model.g5861.t1
Valid prediction for GlimmerHMM_glimmerT_9008-T1
Valid prediction for GeneMark_model.14755_t
Valid prediction for GeneMark_model.14740_t
Valid prediction for Augustus_model.g5862.t1
Valid prediction for GeneMark_model.14748_t
Valid prediction for GeneMark_model.14738_t
Valid prediction for GeneMark_model.14767_t
Valid prediction for snap_scaffold_4-snap.398-T1
Valid prediction for GeneMark_model.14743_t
Valid prediction for snap_scaffold_4-snap.407-T1
Valid prediction for snap_scaffold_4-snap.397-T1
Valid prediction for snap_scaffold_4-snap.411-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8995-T1
Valid prediction for GeneMark_model.14763_t
Valid prediction for GeneMark_model.14741_t
Valid prediction for GlimmerHMM_glimmerT_8990-T1
Valid prediction for GeneMark_model.14761_t
Valid prediction for snap_scaffold_4-snap.409-T1
Valid prediction for GeneMark_model.14735_t
Valid prediction for GeneMark_model.14746_t
Valid prediction for GlimmerHMM_glimmerT_8994-T1
Valid prediction for snap_scaffold_4-snap.430-T1
Valid prediction for GeneMark_model.14753_t
Valid prediction for snap_scaffold_4-snap.408-T1
Valid prediction for GlimmerHMM_glimmerT_8993-T1
Valid prediction for snap_scaffold_4-snap.396-T1
Valid prediction for snap_scaffold_4-snap.389-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8996-T1
Valid prediction for GeneMark_model.14736_t
Valid prediction for GlimmerHMM_glimmerT_8992-T1
Valid prediction for GeneMark_model.14727_t
Valid prediction for snap_scaffold_4-snap.392-T1
Valid prediction for GeneMark_model.14722_t
Valid prediction for snap_scaffold_4-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_8998-T1
Valid prediction for GeneMark_model.14723_t
Valid prediction for snap_scaffold_4-snap.431-T1
Valid prediction for GeneMark_model.14757_t
Valid prediction for GeneMark_model.14733_t
Valid prediction for snap_scaffold_4-snap.406-T1
Valid prediction for GeneMark_model.14730_t
Valid prediction for GeneMark_model.14725_t
Valid prediction for snap_scaffold_4-snap.420-T1
Valid prediction for GeneMark_model.14750_t
Valid prediction for snap_scaffold_4-snap.414-T1
Valid prediction for snap_scaffold_4-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_9011-T1
Valid prediction for GeneMark_model.14775_t
Valid prediction for Augustus_model.g5863.t1
Valid prediction for GeneMark_model.14760_t
Valid prediction for Augustus_model.g5871.t1
Valid prediction for snap_scaffold_4-snap.421-T1
Valid prediction for GeneMark_model.14777_t
Valid prediction for Augustus_model.g5870.t1
Valid prediction for GeneMark_model.14765_t
Valid prediction for snap_scaffold_4-snap.423-T1
Valid prediction for snap_scaffold_4-snap.426-T1
Valid prediction for snap_scaffold_4-snap.429-T1
Valid prediction for snap_scaffold_4-snap.416-T1
Valid prediction for GlimmerHMM_glimmerT_9010-T1
Valid prediction for GeneMark_model.14771_t
Valid prediction for GeneMark_model.14729_t
Valid prediction for snap_scaffold_4-snap.413-T1
Valid prediction for GeneMark_model.14762_t
Valid prediction for GeneMark_model.14744_t
Valid prediction for Augustus_model.g5864.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 105983, rend_intergenic: 105980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24341, rend_intergenic: 11384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31898, rend_intergenic: 25173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45920, rend_intergenic: 33095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47855, rend_intergenic: 45966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71195, rend_intergenic: 51574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73981, rend_intergenic: 72566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74608, rend_intergenic: 74420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100254, rend_intergenic: 95369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106359, rend_intergenic: 102337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107953, rend_intergenic: 106568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118374, rend_intergenic: 108154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121778, rend_intergenic: 120113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135203, rend_intergenic: 127438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140278, rend_intergenic: 135713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153436, rend_intergenic: 140938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194993, rend_intergenic: 169375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207958
-exon list size: 837


building trellis

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80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.6    
81.8    
81.9    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 25 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 105983, rend_intergenic: 105980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24341, rend_intergenic: 11384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31898, rend_intergenic: 25173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45920, rend_intergenic: 33095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47855, rend_intergenic: 45966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71195, rend_intergenic: 51574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73981, rend_intergenic: 72566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74608, rend_intergenic: 74420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100254, rend_intergenic: 95369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106359, rend_intergenic: 102337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107953, rend_intergenic: 106568  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118374, rend_intergenic: 108154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121778, rend_intergenic: 120113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135203, rend_intergenic: 127438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140278, rend_intergenic: 135713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153436, rend_intergenic: 140938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194993, rend_intergenic: 169375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support