-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_1918079-2237110

-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 snap_scaffold_12-snap.436-T1
Valid prediction for snap_scaffold_12-snap.454-T1
Valid prediction for snap_scaffold_12-snap.414-T1
Valid prediction for GlimmerHMM_glimmerT_28918-T1
Valid prediction for Augustus_model.g19087.t1
Valid prediction for snap_scaffold_12-snap.421-T1
Valid prediction for Augustus_model.g19093.t1
Valid prediction for GlimmerHMM_glimmerT_28934-T1
Valid prediction for snap_scaffold_12-snap.435-T1
Valid prediction for snap_scaffold_12-snap.438-T1
Valid prediction for Augustus_model.g19080.t1
Valid prediction for snap_scaffold_12-snap.453-T1
Valid prediction for snap_scaffold_12-snap.417-T1
Valid prediction for Augustus_model.g19092.t1
Valid prediction for snap_scaffold_12-snap.406-T1
Valid prediction for GlimmerHMM_glimmerT_28928-T1
Valid prediction for snap_scaffold_12-snap.441-T1
Valid prediction for snap_scaffold_12-snap.429-T1
Valid prediction for GlimmerHMM_glimmerT_28929-T1
Valid prediction for Augustus_model.g19084.t1
Valid prediction for GlimmerHMM_glimmerT_28931-T1
Valid prediction for snap_scaffold_12-snap.437-T1
Valid prediction for snap_scaffold_12-snap.432-T1
Valid prediction for snap_scaffold_12-snap.428-T1
Valid prediction for snap_scaffold_12-snap.449-T1
Valid prediction for Augustus_model.g19082.t1
Valid prediction for snap_scaffold_12-snap.446-T1
Valid prediction for snap_scaffold_12-snap.447-T1
Valid prediction for GlimmerHMM_glimmerT_28925-T1
Valid prediction for GlimmerHMM_glimmerT_28939-T1
Valid prediction for Augustus_model.g19094.t1
Valid prediction for snap_scaffold_12-snap.434-T1
Couldn't classify 186333, 186425
Couldn't classify 187245, 187802
Sorry, prediction pasa_asmbl_7482.p1 fails validation.
(CAC)	 TG	186333-186425	GT	CGG
(TCC)	 AG	187245-187802	GA	GGG
Valid prediction for GlimmerHMM_glimmerT_28937-T1
Valid prediction for GlimmerHMM_glimmerT_28938-T1
Valid prediction for Augustus_model.g19086.t1
Valid prediction for CodingQuarry_transcript_10135-T1
Valid prediction for snap_scaffold_12-snap.440-T1
Valid prediction for snap_scaffold_12-snap.426-T1
Valid prediction for GlimmerHMM_glimmerT_28930-T1
Valid prediction for Augustus_model.g19083.t1
Valid prediction for snap_scaffold_12-snap.430-T1
Couldn't classify 193414, 193484
Sorry, prediction pasa_asmbl_7484.p1 fails validation.
(GGA)	 GA	193414-193484	GT	CTG
(GTT)	 AG	193720-193825	GT	AGG
(TTG)	 AG	193949-194039	GT	AGG
(CGT)	 AG	194157-194227	GT	ATG
(GTC)	 AG	194532-194659	GT	AGG
(GGA)	 AG	194788-194974	GT	AGG
(GAG)	 AG	195446-195553	GT	AGG
(CTG)	 AG	195668-195779	GT	AGG
(GTG)	 AG	196012-196069	GT	AGG
(AGA)	 AG	196283-196362	GT	ATG
(ATA)	 AG	196699-196789	GT	AGG
(CGA)	 AG	197117-197270	GT	AGG
-recovered pasa_asmbl_7484.p1, terminal, 197117, 197270
-recovered pasa_asmbl_7484.p1, internal, 193720, 193825
-recovered pasa_asmbl_7484.p1, internal, 193949, 194039
-recovered pasa_asmbl_7484.p1, internal, 194157, 194227
-recovered pasa_asmbl_7484.p1, internal, 194532, 194659
-recovered pasa_asmbl_7484.p1, internal, 194788, 194974
-recovered pasa_asmbl_7484.p1, internal, 195446, 195553
-recovered pasa_asmbl_7484.p1, internal, 195668, 195779
-recovered pasa_asmbl_7484.p1, internal, 196012, 196069
-recovered pasa_asmbl_7484.p1, internal, 196283, 196362
-recovered pasa_asmbl_7484.p1, internal, 196699, 196789
-recovered pasa_asmbl_7484.p1, internal, 197117, 197270
Valid prediction for GlimmerHMM_glimmerT_28920-T1
Valid prediction for snap_scaffold_12-snap.452-T1
Valid prediction for snap_scaffold_12-snap.451-T1
Valid prediction for HiQ_model.g19088.t1
Valid prediction for snap_scaffold_12-snap.448-T1
Valid prediction for snap_scaffold_12-snap.420-T1
Valid prediction for snap_scaffold_12-snap.422-T1
Valid prediction for snap_scaffold_12-snap.443-T1
Valid prediction for snap_scaffold_12-snap.427-T1
Valid prediction for Augustus_model.g19085.t1
Valid prediction for snap_scaffold_12-snap.424-T1
Valid prediction for snap_scaffold_12-snap.410-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.g19089.t1
Valid prediction for Augustus_model.g19077.t1
Valid prediction for Augustus_model.g19091.t1
Valid prediction for HiQ_model.g19079.t1
Valid prediction for Augustus_model.g19090.t1
Valid prediction for GlimmerHMM_glimmerT_28932-T1
Valid prediction for CodingQuarry_transcript_10133-T1
Valid prediction for snap_scaffold_12-snap.431-T1
Valid prediction for snap_scaffold_12-snap.418-T1
Valid prediction for snap_scaffold_12-snap.416-T1
Valid prediction for GlimmerHMM_glimmerT_28922-T1
Valid prediction for pasa_asmbl_8312.p1
Valid prediction for snap_scaffold_12-snap.408-T1
Valid prediction for CodingQuarry_transcript_10134-T1
Valid prediction for snap_scaffold_12-snap.450-T1
Valid prediction for Augustus_model.g19073.t1
Valid prediction for snap_scaffold_12-snap.433-T1
Valid prediction for snap_scaffold_12-snap.409-T1
Valid prediction for snap_scaffold_12-snap.415-T1
Valid prediction for CodingQuarry_transcript_10132-T1
Valid prediction for snap_scaffold_12-snap.442-T1
Valid prediction for GlimmerHMM_glimmerT_28926-T1
Valid prediction for GlimmerHMM_glimmerT_28924-T1
Valid prediction for GlimmerHMM_glimmerT_28933-T1
Valid prediction for snap_scaffold_12-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_28921-T1
Valid prediction for GlimmerHMM_glimmerT_28927-T1
Valid prediction for GlimmerHMM_glimmerT_28919-T1
Couldn't classify 263551, 263669
Sorry, prediction pasa_asmbl_8308.p1 fails validation.
(CTT)	 AG	263551-263669	GT	AGG
(GAT)	 AG	264608-264828	GT	CAG
(AGC)	 AG	265123-265233	GT	GAG
(AGT)	 AG	265409-265500	AA	AAA
add_exon() Sorry, pasa_asmbl_8308.p1 265123-265233-terminal-1 is invalid.
-recovered pasa_asmbl_8308.p1, terminal, 265123, 265233
-recovered pasa_asmbl_8308.p1, terminal, 265409, 265500
-recovered pasa_asmbl_8308.p1, internal, 263551, 263669
-recovered pasa_asmbl_8308.p1, internal, 264608, 264828
-recovered pasa_asmbl_8308.p1, internal, 265123, 265233
Valid prediction for snap_scaffold_12-snap.419-T1
Valid prediction for snap_scaffold_12-snap.439-T1
Valid prediction for snap_scaffold_12-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_28936-T1
Valid prediction for GlimmerHMM_glimmerT_28923-T1
Valid prediction for snap_scaffold_12-snap.423-T1
Valid prediction for snap_scaffold_12-snap.407-T1
Valid prediction for Augustus_model.g19078.t1
Valid prediction for Augustus_model.g19074.t1
Valid prediction for Augustus_model.g19075.t1
Valid prediction for Augustus_model.g19076.t1
Valid prediction for HiQ_model.g19081.t1
Valid prediction for pasa_asmbl_8317.p1
Valid prediction for snap_scaffold_12-snap.413-T1
Valid prediction for snap_scaffold_12-snap.412-T1
Couldn't classify 279306, 279490
Sorry, prediction pasa_asmbl_8305.p1 fails validation.
(GAG)	 TG	279306-279490	GT	ATG
(GAT)	 AG	279884-280040	GT	GGG
(TTC)	 AG	280306-280459	GT	CGG
(GGA)	 AG	280931-281007	GT	AGG
(CTG)	 AG	281285-281350	GT	TGG
(ATC)	 AG	282816-282968	GA	AAG
-recovered pasa_asmbl_8305.p1, terminal, 282816, 282968
-recovered pasa_asmbl_8305.p1, internal, 279884, 280040
-recovered pasa_asmbl_8305.p1, internal, 280306, 280459
-recovered pasa_asmbl_8305.p1, internal, 280931, 281007
-recovered pasa_asmbl_8305.p1, internal, 281285, 281350
Valid prediction for snap_scaffold_12-snap.444-T1
Valid prediction for GlimmerHMM_glimmerT_28917-T1
Valid prediction for GlimmerHMM_glimmerT_28935-T1
Couldn't classify 301986, 302071
Couldn't classify 302280, 302502
Sorry, prediction pasa_asmbl_9210.p1 fails validation.
(AGC)	 GC	301986-302071	GT	AAG
(GAA)	 AG	302280-302502	GG	TAG
Valid prediction for snap_scaffold_12-snap.411-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13716, rend_intergenic: 8780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116668, rend_intergenic: 115358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167487, rend_intergenic: 166749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236910, rend_intergenic: 235204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 319032
-exon list size: 358


building trellis

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50.6    
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54.4    
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65.3    
65.6    
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66.1    
66.4    
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67.2    
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70.3    
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77.8    
78.1    
78.3    
78.6    
78.9    
79.2    
79.4    
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80.0    
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80.6    
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84.2    
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84.7    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.7    
86.9    
87.2    
87.5    
87.8    
88.1    
88.3    
88.6    
88.9    
89.2    
89.4    
89.7    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.7    
91.9    
92.2    
92.5    
92.8    
93.1    
93.3    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.3    
95.6    
95.8    
96.1    
96.4    
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96.9    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 13716, rend_intergenic: 8780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116668, rend_intergenic: 115358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167487, rend_intergenic: 166749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236910, rend_intergenic: 235204  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