-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_5833004-6020812

-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 GlimmerHMM_glimmerT_22251-T1
Valid prediction for GlimmerHMM_glimmerT_22250-T1
Valid prediction for snap_scaffold_9-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_22232-T1
Valid prediction for GlimmerHMM_glimmerT_22242-T1
Valid prediction for snap_scaffold_9-snap.1239-T1
Valid prediction for snap_scaffold_9-snap.1245-T1
Valid prediction for Augustus_model.g14796.t1
Valid prediction for Augustus_model.g14784.t1
Couldn't classify 28341, 28558
Sorry, prediction pasa_asmbl_54069.p1 fails validation.
(ACC)	 AC	28341-28558	GT	AGG
(CCT)	 AG	30059-30212	GA	AGG
-recovered pasa_asmbl_54069.p1, terminal, 30059, 30212
Valid prediction for GlimmerHMM_glimmerT_22229-T1
Valid prediction for snap_scaffold_9-snap.1231-T1
Valid prediction for snap_scaffold_9-snap.1262-T1
Couldn't classify 122270, 122729
Sorry, prediction pasa_asmbl_54680.p1 fails validation.
(ACC)	 CC	122270-122729	GT	TGG
(GTA)	 AG	122959-123104	GT	AGG
(CAC)	 AG	123220-123402	GT	AGG
(GCT)	 AG	124469-124795	GC	AAG
-recovered pasa_asmbl_54680.p1, terminal, 124469, 124795
-recovered pasa_asmbl_54680.p1, internal, 122959, 123104
-recovered pasa_asmbl_54680.p1, internal, 123220, 123402
-recovered pasa_asmbl_54680.p1, internal, 124469, 124795
Valid prediction for GlimmerHMM_glimmerT_22257-T1
Valid prediction for GlimmerHMM_glimmerT_22237-T1
Valid prediction for snap_scaffold_9-snap.1236-T1
Valid prediction for Augustus_model.g14788.t1
Valid prediction for snap_scaffold_9-snap.1254-T1
Valid prediction for snap_scaffold_9-snap.1238-T1
Valid prediction for Augustus_model.g14794.t1
Couldn't classify 117962, 118537
Sorry, prediction pasa_asmbl_54071.p1 fails validation.
(AAG)	 GG	117962-118537	CT	CAC
Valid prediction for snap_scaffold_9-snap.1253-T1
Valid prediction for snap_scaffold_9-snap.1232-T1
Valid prediction for snap_scaffold_9-snap.1250-T1
Valid prediction for GlimmerHMM_glimmerT_22247-T1
Valid prediction for GlimmerHMM_glimmerT_22245-T1
Valid prediction for snap_scaffold_9-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_22239-T1
Valid prediction for GlimmerHMM_glimmerT_22238-T1
Valid prediction for GlimmerHMM_glimmerT_22252-T1
Valid prediction for GlimmerHMM_glimmerT_22243-T1
Valid prediction for snap_scaffold_9-snap.1255-T1
Valid prediction for Augustus_model.g14780.t1
Valid prediction for GlimmerHMM_glimmerT_22241-T1
Valid prediction for GlimmerHMM_glimmerT_22227-T1
Valid prediction for snap_scaffold_9-snap.1233-T1
Valid prediction for GlimmerHMM_glimmerT_22233-T1
Valid prediction for snap_scaffold_9-snap.1235-T1
Valid prediction for snap_scaffold_9-snap.1258-T1
Valid prediction for Augustus_model.g14779.t1
Valid prediction for GlimmerHMM_glimmerT_22228-T1
Valid prediction for GlimmerHMM_glimmerT_22248-T1
Couldn't classify 118706, 119783
Couldn't classify 120977, 121000
Sorry, prediction pasa_asmbl_54072.p1 fails validation.
(CGC)	 GC	118706-119783	GT	AGG
(ACA)	 AG	119880-119987	GT	TGG
(GCC)	 AG	120547-120746	GT	TGG
(GTG)	 AG	120977-121000	TT	GTT
-recovered pasa_asmbl_54072.p1, internal, 119880, 119987
-recovered pasa_asmbl_54072.p1, internal, 120547, 120746
Valid prediction for GlimmerHMM_glimmerT_22230-T1
Valid prediction for Augustus_model.g14787.t1
Valid prediction for Augustus_model.g14793.t1
Valid prediction for GlimmerHMM_glimmerT_22231-T1
Valid prediction for Augustus_model.g14777.t1
Valid prediction for GlimmerHMM_glimmerT_22234-T1
Valid prediction for Augustus_model.g14782.t1
Valid prediction for Augustus_model.g14783.t1
Valid prediction for Augustus_model.g14789.t1
Valid prediction for Augustus_model.g14773.t1
Valid prediction for Augustus_model.g14781.t1
Valid prediction for snap_scaffold_9-snap.1249-T1
Valid prediction for Augustus_model.g14776.t1
Couldn't classify 121103, 121158
Couldn't classify 121884, 121894
Sorry, prediction pasa_asmbl_54073.p1 fails validation.
(ATC)	 AG	121103-121158	GT	GGG
(GTT)	 AG	121363-121528	GT	AGG
(CTG)	 AG	121625-121790	GT	AGG
(GTG)	 AG	121884-121894	AT	CCA
-recovered pasa_asmbl_54073.p1, terminal, 121625, 121790
-recovered pasa_asmbl_54073.p1, internal, 121103, 121158
-recovered pasa_asmbl_54073.p1, internal, 121363, 121528
-recovered pasa_asmbl_54073.p1, internal, 121625, 121790
Valid prediction for Augustus_model.g14790.t1
Valid prediction for Augustus_model.g14792.t1
Valid prediction for snap_scaffold_9-snap.1234-T1
Valid prediction for Augustus_model.g14791.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 snap_scaffold_9-snap.1242-T1
Valid prediction for GlimmerHMM_glimmerT_22226-T1
Valid prediction for snap_scaffold_9-snap.1259-T1
Valid prediction for GlimmerHMM_glimmerT_22253-T1
Valid prediction for Augustus_model.g14786.t1
Valid prediction for snap_scaffold_9-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_22254-T1
Valid prediction for Augustus_model.g14798.t1
Valid prediction for snap_scaffold_9-snap.1260-T1
Valid prediction for snap_scaffold_9-snap.1264-T1
Valid prediction for Augustus_model.g14795.t1
Valid prediction for GlimmerHMM_glimmerT_22258-T1
Valid prediction for GlimmerHMM_glimmerT_22225-T1
Valid prediction for GlimmerHMM_glimmerT_22255-T1
Valid prediction for GlimmerHMM_glimmerT_22259-T1
Valid prediction for snap_scaffold_9-snap.1244-T1
Valid prediction for Augustus_model.g14785.t1
Valid prediction for snap_scaffold_9-snap.1246-T1
Valid prediction for snap_scaffold_9-snap.1247-T1
Valid prediction for GlimmerHMM_glimmerT_22240-T1
Valid prediction for snap_scaffold_9-snap.1240-T1
Valid prediction for GlimmerHMM_glimmerT_22244-T1
Valid prediction for GlimmerHMM_glimmerT_22236-T1
Valid prediction for Augustus_model.g14778.t1
Valid prediction for GlimmerHMM_glimmerT_22249-T1
Valid prediction for GlimmerHMM_glimmerT_22246-T1
Valid prediction for snap_scaffold_9-snap.1230-T1
Valid prediction for Augustus_model.g14774.t1
Valid prediction for snap_scaffold_9-snap.1257-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1248-T1
Valid prediction for HiQ_model.g14775.t1
Valid prediction for snap_scaffold_9-snap.1261-T1
Valid prediction for snap_scaffold_9-snap.1252-T1
Valid prediction for Augustus_model.g14797.t1
Valid prediction for pasa_asmbl_55041.p1
Valid prediction for snap_scaffold_9-snap.1228-T1
Valid prediction for GlimmerHMM_glimmerT_22260-T1
Valid prediction for GlimmerHMM_glimmerT_22256-T1
Valid prediction for snap_scaffold_9-snap.1237-T1
Valid prediction for snap_scaffold_9-snap.1256-T1
Valid prediction for GlimmerHMM_glimmerT_22235-T1
Valid prediction for snap_scaffold_9-snap.1241-T1
Valid prediction for CodingQuarry_transcript_62192-T1
Valid prediction for snap_scaffold_9-snap.1263-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 58729, rend_intergenic: 54370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66419, rend_intergenic: 64712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84374, rend_intergenic: 67193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99531, rend_intergenic: 94904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135014, rend_intergenic: 132662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158616, rend_intergenic: 150629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162504, rend_intergenic: 160539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183255, rend_intergenic: 176196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 100106, rend_intergenic: 100103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187809
-exon list size: 415


building trellis

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32.9    
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33.6    
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36.9    
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37.6    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
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39.6    
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40.3    
40.5    
40.8    
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41.5    
41.7    
42.0    
42.2    
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42.7    
42.9    
43.2    
43.4    
43.6    
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44.4    
44.6    
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45.6    
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48.2    
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73.9    
74.1    
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77.9    
78.2    
78.4    
78.7    
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79.4    
79.6    
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80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.7    
83.0    
83.2    
83.5    
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83.9    
84.2    
84.4    
84.7    
84.9    
85.1    
85.4    
85.6    
85.9    
86.1    
86.3    
86.6    
86.8    
87.1    
87.3    
87.5    
87.8    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.4    
89.7    
89.9    
90.2    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 58729, rend_intergenic: 54370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66419, rend_intergenic: 64712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84374, rend_intergenic: 67193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99531, rend_intergenic: 94904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135014, rend_intergenic: 132662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158616, rend_intergenic: 150629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162504, rend_intergenic: 160539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183255, rend_intergenic: 176196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 100106, rend_intergenic: 100103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support