-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_4377633-4586219

-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.g407.t1
Valid prediction for snap_scaffold_1-snap.651-T1
Valid prediction for GlimmerHMM_glimmerT_523-T1
Valid prediction for snap_scaffold_1-snap.659-T1
Valid prediction for snap_scaffold_1-snap.668-T1
Valid prediction for snap_scaffold_1-snap.634-T1
Valid prediction for Augustus_model.g411.t1
Valid prediction for snap_scaffold_1-snap.645-T1
Valid prediction for GlimmerHMM_glimmerT_514-T1
Valid prediction for snap_scaffold_1-snap.635-T1
Valid prediction for Augustus_model.g404.t1
Valid prediction for GlimmerHMM_glimmerT_518-T1
Valid prediction for GlimmerHMM_glimmerT_529-T1
Valid prediction for snap_scaffold_1-snap.650-T1
Valid prediction for snap_scaffold_1-snap.631-T1
Valid prediction for snap_scaffold_1-snap.638-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g410.t1
Valid prediction for snap_scaffold_1-snap.640-T1
Valid prediction for snap_scaffold_1-snap.642-T1
Valid prediction for Augustus_model.g420.t1
Valid prediction for snap_scaffold_1-snap.662-T1
Valid prediction for snap_scaffold_1-snap.649-T1
Valid prediction for Augustus_model.g409.t1
Valid prediction for GlimmerHMM_glimmerT_517-T1
Valid prediction for GlimmerHMM_glimmerT_524-T1
Valid prediction for GlimmerHMM_glimmerT_505-T1
Valid prediction for snap_scaffold_1-snap.641-T1
Valid prediction for snap_scaffold_1-snap.629-T1
Valid prediction for snap_scaffold_1-snap.644-T1
Valid prediction for Augustus_model.g414.t1
Valid prediction for snap_scaffold_1-snap.653-T1
Valid prediction for snap_scaffold_1-snap.667-T1
Valid prediction for GlimmerHMM_glimmerT_522-T1
Valid prediction for snap_scaffold_1-snap.652-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_2588-T1
Valid prediction for Augustus_model.g398.t1
Valid prediction for snap_scaffold_1-snap.658-T1
Valid prediction for snap_scaffold_1-snap.660-T1
Couldn't classify 142966, 143121
Sorry, prediction pasa_asmbl_1671.p3 fails validation.
(CTC)	 AG	142966-143121	GT	AGG
(ATC)	 AG	143746-143841	GT	AAG
(GAG)	 AG	144279-144404	GT	GGG
(CTG)	 AG	144981-145001	TG	GAT
-recovered pasa_asmbl_1671.p3, terminal, 144981, 145001
-recovered pasa_asmbl_1671.p3, internal, 142966, 143121
-recovered pasa_asmbl_1671.p3, internal, 143746, 143841
-recovered pasa_asmbl_1671.p3, internal, 144279, 144404
Valid prediction for Augustus_model.g415.t1
Valid prediction for GlimmerHMM_glimmerT_519-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 Augustus_model.g399.t1
Valid prediction for snap_scaffold_1-snap.664-T1
Valid prediction for snap_scaffold_1-snap.648-T1
Valid prediction for GlimmerHMM_glimmerT_525-T1
Couldn't classify 182625, 182703
Sorry, prediction pasa_asmbl_195.p1 fails validation.
(GGG)	 AA	182625-182703	GT	AGG
(AGT)	 AG	183107-183369	GT	AGG
(GCT)	 AG	183631-183711	GT	GTG
(GAG)	 AG	185304-185424	GT	TGG
(AGG)	 AG	185562-185614	GT	AGG
(ATT)	 AG	186352-186504	GT	TGG
(GCT)	 AG	187720-187911	AG	AGA
-recovered pasa_asmbl_195.p1, terminal, 187720, 187911
-recovered pasa_asmbl_195.p1, internal, 183107, 183369
-recovered pasa_asmbl_195.p1, internal, 183631, 183711
-recovered pasa_asmbl_195.p1, internal, 185304, 185424
-recovered pasa_asmbl_195.p1, internal, 185562, 185614
-recovered pasa_asmbl_195.p1, internal, 186352, 186504
Valid prediction for HiQ_model.g418.t1
Valid prediction for GlimmerHMM_glimmerT_528-T1
Valid prediction for pasa_asmbl_200.p1
Valid prediction for Augustus_model.g397.t1
Valid prediction for GlimmerHMM_glimmerT_526-T1
Valid prediction for snap_scaffold_1-snap.654-T1
Valid prediction for Augustus_model.g402.t1
Valid prediction for GlimmerHMM_glimmerT_508-T1
Valid prediction for GlimmerHMM_glimmerT_509-T1
Valid prediction for GlimmerHMM_glimmerT_527-T1
Valid prediction for pasa_asmbl_197.p1
Valid prediction for snap_scaffold_1-snap.655-T1
Valid prediction for snap_scaffold_1-snap.628-T1
Valid prediction for GlimmerHMM_glimmerT_506-T1
Valid prediction for CodingQuarry_transcript_2592-T1
Valid prediction for snap_scaffold_1-snap.637-T1
Valid prediction for Augustus_model.g403.t1
Valid prediction for snap_scaffold_1-snap.666-T1
Valid prediction for GlimmerHMM_glimmerT_512-T1
Valid prediction for snap_scaffold_1-snap.636-T1
Valid prediction for snap_scaffold_1-snap.630-T1
Valid prediction for CodingQuarry_transcript_2589-T1
Valid prediction for pasa_asmbl_198.p1
Valid prediction for Augustus_model.g413.t1
Valid prediction for GlimmerHMM_glimmerT_516-T1
Valid prediction for snap_scaffold_1-snap.632-T1
Valid prediction for CodingQuarry_transcript_2591-T1
Valid prediction for Augustus_model.g417.t1
Valid prediction for GlimmerHMM_glimmerT_511-T1
Valid prediction for GlimmerHMM_glimmerT_513-T1
Valid prediction for Augustus_model.g408.t1
Valid prediction for GlimmerHMM_glimmerT_504-T1
Valid prediction for CodingQuarry_transcript_2590-T1
Valid prediction for Augustus_model.g406.t1
Valid prediction for Augustus_model.g396.t1
Valid prediction for HiQ_model.g419.t1
Valid prediction for CodingQuarry_transcript_2587-T1
Valid prediction for pasa_asmbl_184.p1
Valid prediction for Augustus_model.g405.t1
Valid prediction for snap_scaffold_1-snap.647-T1
Valid prediction for Augustus_model.g401.t1
Valid prediction for snap_scaffold_1-snap.656-T1
Valid prediction for Augustus_model.g416.t1
Valid prediction for snap_scaffold_1-snap.665-T1
Valid prediction for Augustus_model.g400.t1
Valid prediction for HiQ_model.g395.t1
Valid prediction for snap_scaffold_1-snap.663-T1
Valid prediction for GlimmerHMM_glimmerT_507-T1
Valid prediction for Augustus_model.g412.t1
Valid prediction for snap_scaffold_1-snap.627-T1
Valid prediction for snap_scaffold_1-snap.646-T1
Valid prediction for snap_scaffold_1-snap.633-T1
Valid prediction for GlimmerHMM_glimmerT_520-T1
Valid prediction for snap_scaffold_1-snap.661-T1
Valid prediction for GlimmerHMM_glimmerT_515-T1
Valid prediction for snap_scaffold_1-snap.639-T1
Valid prediction for GlimmerHMM_glimmerT_521-T1
Valid prediction for snap_scaffold_1-snap.643-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.657-T1
Valid prediction for GlimmerHMM_glimmerT_510-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25455, rend_intergenic: 20677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27917, rend_intergenic: 26402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39991, rend_intergenic: 28101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46896, rend_intergenic: 44001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52878, rend_intergenic: 50723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57091, rend_intergenic: 53246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62894, rend_intergenic: 57388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76834, rend_intergenic: 63673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80059, rend_intergenic: 77993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96369, rend_intergenic: 84781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101943, rend_intergenic: 98273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145001, rend_intergenic: 138884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167572, rend_intergenic: 167288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170877, rend_intergenic: 167935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208587
-exon list size: 441


building trellis

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24.8    
25.1    
25.3    
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27.8    
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28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
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30.9    
31.2    
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31.6    
31.8    
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33.6    
33.9    
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34.5    
34.8    
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35.7    
35.9    
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36.6    
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40.6    
40.9    
41.1    
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41.8    
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42.9    
43.1    
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43.6    
43.8    
44.0    
44.2    
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44.9    
45.1    
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45.6    
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88.7    
88.9    
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89.4    
89.6    
89.8    
90.1    
90.3    
90.5    
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91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.2    
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93.7    
93.9    
94.1    
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94.6    
94.8    
95.0    
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95.9    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 25455, rend_intergenic: 20677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27917, rend_intergenic: 26402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39991, rend_intergenic: 28101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46896, rend_intergenic: 44001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52878, rend_intergenic: 50723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57091, rend_intergenic: 53246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62894, rend_intergenic: 57388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76834, rend_intergenic: 63673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80059, rend_intergenic: 77993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96369, rend_intergenic: 84781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101943, rend_intergenic: 98273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145001, rend_intergenic: 138884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167572, rend_intergenic: 167288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170877, rend_intergenic: 167935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support