-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_1710431-1896563

-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.50928_t
Valid prediction for snap_scaffold_12-snap.371-T1
Valid prediction for HiQ_model.g19632.t1
Valid prediction for snap_scaffold_12-snap.369-T1
Valid prediction for GlimmerHMM_glimmerT_29515-T1
Valid prediction for snap_scaffold_12-snap.396-T1
Valid prediction for GlimmerHMM_glimmerT_29512-T1
Couldn't classify 23330, 23340
Sorry, prediction pasa_asmbl_8439.p1 fails validation.
(AAG)	 GC	23330-23340	GT	TGG
(GCA)	 AG	23759-23978	GT	AGG
(GTT)	 AG	24269-24529	GT	TGG
(AGG)	 AG	25316-25448	GT	AGG
(GTT)	 AG	25700-25838	GT	AGG
(CAT)	 AG	26001-26025	TG	GAT
-recovered pasa_asmbl_8439.p1, terminal, 26001, 26025
-recovered pasa_asmbl_8439.p1, internal, 23759, 23978
-recovered pasa_asmbl_8439.p1, internal, 24269, 24529
-recovered pasa_asmbl_8439.p1, internal, 25316, 25448
-recovered pasa_asmbl_8439.p1, internal, 25700, 25838
Valid prediction for snap_scaffold_12-snap.394-T1
Valid prediction for snap_scaffold_12-snap.364-T1
Valid prediction for GlimmerHMM_glimmerT_29501-T1
Valid prediction for snap_scaffold_12-snap.376-T1
Valid prediction for snap_scaffold_12-snap.380-T1
Valid prediction for snap_scaffold_12-snap.400-T1
Valid prediction for GlimmerHMM_glimmerT_29513-T1
Valid prediction for snap_scaffold_12-snap.392-T1
Valid prediction for GeneMark_model.50950_t
Valid prediction for snap_scaffold_12-snap.389-T1
Valid prediction for GeneMark_model.50932_t
Valid prediction for pasa_asmbl_8441.p1
Valid prediction for snap_scaffold_12-snap.372-T1
Valid prediction for snap_scaffold_12-snap.387-T1
Valid prediction for GeneMark_model.50957_t
Valid prediction for GeneMark_model.50946_t
Valid prediction for GeneMark_model.50961_t
Valid prediction for GlimmerHMM_glimmerT_29500-T1
Valid prediction for snap_scaffold_12-snap.382-T1
Valid prediction for GlimmerHMM_glimmerT_29518-T1
Valid prediction for GeneMark_model.50959_t
Valid prediction for GeneMark_model.50948_t
Valid prediction for snap_scaffold_12-snap.368-T1
Valid prediction for GeneMark_model.50941_t
Valid prediction for snap_scaffold_12-snap.386-T1
Valid prediction for Augustus_model.g19628.t1
Valid prediction for GeneMark_model.50930_t
Valid prediction for GeneMark_model.50960_t
Valid prediction for GeneMark_model.50939_t
Valid prediction for snap_scaffold_12-snap.385-T1
Valid prediction for GlimmerHMM_glimmerT_29502-T1
Valid prediction for GeneMark_model.50956_t
Valid prediction for snap_scaffold_12-snap.390-T1
Valid prediction for GeneMark_model.50944_t
Valid prediction for snap_scaffold_12-snap.378-T1
Valid prediction for Augustus_model.g19625.t1
Valid prediction for GeneMark_model.50964_t
Valid prediction for GeneMark_model.50951_t
Valid prediction for GeneMark_model.50935_t
Valid prediction for GeneMark_model.50962_t
Valid prediction for snap_scaffold_12-snap.365-T1
Valid prediction for Augustus_model.g19624.t1
Valid prediction for CodingQuarry_transcript_10104-T1
Valid prediction for GlimmerHMM_glimmerT_29506-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.g19626.t1
Valid prediction for Augustus_model.g19627.t1
Valid prediction for GeneMark_model.50963_t
Valid prediction for snap_scaffold_12-snap.362-T1
Valid prediction for GeneMark_model.50942_t
Valid prediction for GlimmerHMM_glimmerT_29511-T1
Valid prediction for snap_scaffold_12-snap.388-T1
Valid prediction for GlimmerHMM_glimmerT_29516-T1
Valid prediction for GeneMark_model.50927_t
Valid prediction for GlimmerHMM_glimmerT_29517-T1
Valid prediction for snap_scaffold_12-snap.367-T1
Valid prediction for GeneMark_model.50937_t
Valid prediction for GeneMark_model.50953_t
Couldn't classify 165344, 165436
Sorry, prediction pasa_asmbl_7438.p1 fails validation.
(ATG)	 AA	164636-164807	GT	TGG
(CAC)	 AG	164918-165072	GT	TTG
(TAT)	 AG	165185-165244	GT	AGG
(TTC)	 AG	165344-165436	AG	GGA
-recovered pasa_asmbl_7438.p1, initial, 164636, 164807
-recovered pasa_asmbl_7438.p1, internal, 164918, 165072
-recovered pasa_asmbl_7438.p1, internal, 165185, 165244
Valid prediction for snap_scaffold_12-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_29503-T1
Valid prediction for GeneMark_model.50929_t
Valid prediction for Augustus_model.g19623.t1
Valid prediction for GlimmerHMM_glimmerT_29499-T1
Valid prediction for GeneMark_model.50949_t
Valid prediction for GlimmerHMM_glimmerT_29510-T1
Valid prediction for GeneMark_model.50958_t
Valid prediction for GeneMark_model.50931_t
Valid prediction for snap_scaffold_12-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_29507-T1
Valid prediction for Augustus_model.g19629.t1
Valid prediction for GeneMark_model.50943_t
Valid prediction for snap_scaffold_12-snap.370-T1
Valid prediction for snap_scaffold_12-snap.395-T1
Valid prediction for GeneMark_model.50945_t
Valid prediction for GlimmerHMM_glimmerT_29504-T1
Valid prediction for GlimmerHMM_glimmerT_29514-T1
Valid prediction for GeneMark_model.50933_t
Valid prediction for snap_scaffold_12-snap.399-T1
Valid prediction for GeneMark_model.50940_t
Valid prediction for snap_scaffold_12-snap.391-T1
Valid prediction for GeneMark_model.50938_t
Valid prediction for snap_scaffold_12-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_29509-T1
Valid prediction for GeneMark_model.50947_t
Valid prediction for GeneMark_model.50955_t
Valid prediction for GeneMark_model.50952_t
Valid prediction for GeneMark_model.50965_t
Valid prediction for GeneMark_model.50936_t
Valid prediction for GlimmerHMM_glimmerT_29505-T1
Valid prediction for GeneMark_model.50934_t
Valid prediction for snap_scaffold_12-snap.398-T1
Valid prediction for snap_scaffold_12-snap.383-T1
Couldn't classify 167315, 167344
Sorry, prediction pasa_asmbl_7435.p1 fails validation.
(TGT)	 AG	167315-167344	GT	AAG
(GTC)	 AG	167902-168003	GT	AGG
(ATC)	 AG	168875-169016	GT	AGG
(GTG)	 AG	169155-169242	GT	AGG
(GGT)	 AG	169356-169575	GT	AGG
(GTT)	 AG	169779-170039	GT	TGG
(AGA)	 AG	170254-170389	GT	CGG
(GCT)	 AG	170734-170872	GT	AGG
(TAT)	 AG	170987-171011	AG	GAA
-recovered pasa_asmbl_7435.p1, terminal, 170987, 171011
-recovered pasa_asmbl_7435.p1, internal, 167315, 167344
-recovered pasa_asmbl_7435.p1, internal, 167902, 168003
-recovered pasa_asmbl_7435.p1, internal, 168875, 169016
-recovered pasa_asmbl_7435.p1, internal, 169155, 169242
-recovered pasa_asmbl_7435.p1, internal, 169356, 169575
-recovered pasa_asmbl_7435.p1, internal, 169779, 170039
-recovered pasa_asmbl_7435.p1, internal, 170254, 170389
-recovered pasa_asmbl_7435.p1, internal, 170734, 170872
Valid prediction for snap_scaffold_12-snap.373-T1
Valid prediction for snap_scaffold_12-snap.384-T1
Valid prediction for snap_scaffold_12-snap.379-T1
Valid prediction for Augustus_model.g19630.t1
Valid prediction for snap_scaffold_12-snap.375-T1
Valid prediction for HiQ_model.g19622.t1
Valid prediction for GeneMark_model.50954_t
Valid prediction for GlimmerHMM_glimmerT_29508-T1
Valid prediction for snap_scaffold_12-snap.377-T1
Valid prediction for snap_scaffold_12-snap.393-T1
Valid prediction for Augustus_model.g19631.t1
Valid prediction for snap_scaffold_12-snap.366-T1
Valid prediction for snap_scaffold_12-snap.397-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6129, rend_intergenic: 3574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36372, rend_intergenic: 33656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54283, rend_intergenic: 52421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59208, rend_intergenic: 57049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65405, rend_intergenic: 63609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97864, rend_intergenic: 96346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110575, rend_intergenic: 109107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150484, rend_intergenic: 148506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163689, rend_intergenic: 163129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186133
-exon list size: 485


building trellis

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32.9    
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34.3    
34.5    
34.7    
34.9    
35.1    
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35.5    
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35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
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38.4    
38.6    
38.8    
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39.6    
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40.2    
40.5    
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40.9    
41.1    
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42.9    
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43.3    
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45.6    
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80.7    
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81.3    
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83.4    
83.6    
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84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
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86.0    
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86.4    
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86.9    
87.1    
87.3    
87.5    
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87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.3    
94.5    
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94.9    
95.1    
95.3    
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95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 6129, rend_intergenic: 3574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36372, rend_intergenic: 33656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54283, rend_intergenic: 52421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59208, rend_intergenic: 57049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65405, rend_intergenic: 63609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97864, rend_intergenic: 96346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110575, rend_intergenic: 109107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150484, rend_intergenic: 148506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163689, rend_intergenic: 163129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support