-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_10567027-10770078

-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_49778-T1
Valid prediction for GeneMark_model.86214_t
Valid prediction for snap_scaffold_21-snap.2319-T1
Valid prediction for GeneMark_model.86218_t
Valid prediction for snap_scaffold_21-snap.2336-T1
Valid prediction for GlimmerHMM_glimmerT_49773-T1
Valid prediction for GlimmerHMM_glimmerT_49776-T1
Valid prediction for Augustus_model.g33393.t1
Valid prediction for GeneMark_model.86213_t
Valid prediction for snap_scaffold_21-snap.2316-T1
Valid prediction for snap_scaffold_21-snap.2339-T1
Valid prediction for GeneMark_model.86202_t
Valid prediction for GeneMark_model.86197_t
Valid prediction for GeneMark_model.86229_t
Valid prediction for snap_scaffold_21-snap.2328-T1
Valid prediction for GeneMark_model.86238_t
Valid prediction for snap_scaffold_21-snap.2347-T1
Valid prediction for GeneMark_model.86222_t
Valid prediction for GeneMark_model.86234_t
Valid prediction for Augustus_model.g33392.t1
Valid prediction for snap_scaffold_21-snap.2342-T1
Valid prediction for snap_scaffold_21-snap.2335-T1
Valid prediction for Augustus_model.g33398.t1
Valid prediction for GeneMark_model.86216_t
Valid prediction for snap_scaffold_21-snap.2344-T1
Valid prediction for GeneMark_model.86209_t
Valid prediction for snap_scaffold_21-snap.2329-T1
Valid prediction for GeneMark_model.86205_t
Valid prediction for GeneMark_model.86230_t
Valid prediction for GeneMark_model.86207_t
Valid prediction for GeneMark_model.86200_t
Valid prediction for GlimmerHMM_glimmerT_49770-T1
Valid prediction for GeneMark_model.86224_t
Couldn't classify 75276, 75321
Sorry, prediction pasa_asmbl_28892.p1 fails validation.
(TAC)	 GA	75276-75321	GT	AGG
(GGT)	 AG	76593-77686	CA	AGC
-recovered pasa_asmbl_28892.p1, terminal, 76593, 77686
Valid prediction for snap_scaffold_21-snap.2320-T1
Valid prediction for GeneMark_model.86236_t
Valid prediction for snap_scaffold_21-snap.2350-T1
Valid prediction for snap_scaffold_21-snap.2317-T1
Valid prediction for GeneMark_model.86211_t
Valid prediction for GeneMark_model.86204_t
Valid prediction for Augustus_model.g33394.t1
Valid prediction for snap_scaffold_21-snap.2322-T1
Valid prediction for snap_scaffold_21-snap.2324-T1
Valid prediction for GlimmerHMM_glimmerT_49772-T1
Valid prediction for GlimmerHMM_glimmerT_49774-T1
Valid prediction for snap_scaffold_21-snap.2340-T1
Valid prediction for GeneMark_model.86199_t
Valid prediction for Augustus_model.g33390.t1
Valid prediction for GlimmerHMM_glimmerT_49766-T1
Valid prediction for GeneMark_model.86240_t
Valid prediction for snap_scaffold_21-snap.2331-T1
Valid prediction for snap_scaffold_21-snap.2348-T1
Valid prediction for snap_scaffold_21-snap.2353-T1
Valid prediction for GeneMark_model.86232_t
Valid prediction for GeneMark_model.86227_t
Valid prediction for GeneMark_model.86237_t
Valid prediction for snap_scaffold_21-snap.2333-T1
Valid prediction for Augustus_model.g33386.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 GeneMark_model.86226_t
Valid prediction for GeneMark_model.86210_t
Valid prediction for GeneMark_model.86241_t
Valid prediction for snap_scaffold_21-snap.2315-T1
Valid prediction for GeneMark_model.86228_t
Couldn't classify 109309, 109460
Sorry, prediction pasa_asmbl_28098.p1 fails validation.
(GGC)	 CG	109309-109460	GT	GAG
(GTA)	 AG	110301-110673	GC	GAG
-recovered pasa_asmbl_28098.p1, terminal, 110301, 110673
-recovered pasa_asmbl_28098.p1, internal, 110301, 110673
Valid prediction for GeneMark_model.86239_t
Valid prediction for Augustus_model.g33400.t1
Valid prediction for GlimmerHMM_glimmerT_49783-T1
Valid prediction for snap_scaffold_21-snap.2332-T1
Valid prediction for snap_scaffold_21-snap.2325-T1
Valid prediction for snap_scaffold_21-snap.2355-T1
Valid prediction for GeneMark_model.86196_t
Valid prediction for snap_scaffold_21-snap.2352-T1
Valid prediction for GeneMark_model.86235_t
Valid prediction for GeneMark_model.86203_t
Valid prediction for HiQ_model.g33388.t1
Valid prediction for GlimmerHMM_glimmerT_49779-T1
Valid prediction for snap_scaffold_21-snap.2345-T1
Couldn't classify 188358, 188927
Sorry, prediction pasa_asmbl_28093.p1 fails validation.
(TGT)	 CG	188358-188927	CA	GAC
Valid prediction for GeneMark_model.86233_t
Valid prediction for GlimmerHMM_glimmerT_49777-T1
Valid prediction for snap_scaffold_21-snap.2349-T1
Valid prediction for GlimmerHMM_glimmerT_49780-T1
Valid prediction for Augustus_model.g33401.t1
Couldn't classify 179185, 179266
Couldn't classify 179901, 179965
Sorry, prediction pasa_asmbl_28255.p1 fails validation.
(CCC)	 CT	179185-179266	GT	CGG
(GCG)	 AG	179563-179712	GT	TGG
(GTG)	 AG	179901-179965	GG	AGG
-recovered pasa_asmbl_28255.p1, internal, 179563, 179712
Valid prediction for snap_scaffold_21-snap.2327-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49781-T1
Valid prediction for snap_scaffold_21-snap.2351-T1
Valid prediction for GeneMark_model.86231_t
Valid prediction for GeneMark_model.86208_t
Valid prediction for snap_scaffold_21-snap.2318-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.2341-T1
Valid prediction for GeneMark_model.86201_t
Valid prediction for GeneMark_model.86223_t
Valid prediction for Augustus_model.g33402.t1
Valid prediction for Augustus_model.g33396.t1
Valid prediction for HiQ_model.g33385.t1
Valid prediction for GeneMark_model.86212_t
Valid prediction for Augustus_model.g33387.t1
Valid prediction for snap_scaffold_21-snap.2323-T1
Valid prediction for snap_scaffold_21-snap.2337-T1
Valid prediction for Augustus_model.g33391.t1
Valid prediction for snap_scaffold_21-snap.2338-T1
Valid prediction for Augustus_model.g33389.t1
Couldn't classify 184018, 184079
Couldn't classify 184917, 184954
Sorry, prediction pasa_asmbl_28094.p1 fails validation.
(GAA)	 TC	184018-184079	GT	CAG
(GTG)	 AG	184273-184334	GT	AGG
(CTG)	 AG	184548-184703	GT	AGG
(ATG)	 AG	184917-184954	GA	GTG
add_exon() Sorry, pasa_asmbl_28094.p1 184548-184703-terminal-1 is invalid.
-recovered pasa_asmbl_28094.p1, terminal, 184548, 184703
-recovered pasa_asmbl_28094.p1, internal, 184273, 184334
-recovered pasa_asmbl_28094.p1, internal, 184548, 184703
Valid prediction for snap_scaffold_21-snap.2321-T1
Valid prediction for GlimmerHMM_glimmerT_49782-T1
Valid prediction for GeneMark_model.86217_t
Valid prediction for pasa_asmbl_28090.p1
Valid prediction for snap_scaffold_21-snap.2334-T1
Valid prediction for GlimmerHMM_glimmerT_49769-T1
Valid prediction for GeneMark_model.86220_t
Valid prediction for snap_scaffold_21-snap.2343-T1
Valid prediction for GeneMark_model.86206_t
Valid prediction for GeneMark_model.86225_t
Valid prediction for GeneMark_model.86215_t
Valid prediction for Augustus_model.g33395.t1
Valid prediction for CodingQuarry_transcript_32668-T1
Valid prediction for Augustus_model.g33397.t1
Valid prediction for GlimmerHMM_glimmerT_49767-T1
Valid prediction for GlimmerHMM_glimmerT_49768-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49771-T1
Valid prediction for Augustus_model.g33399.t1
Valid prediction for snap_scaffold_21-snap.2326-T1
Valid prediction for snap_scaffold_21-snap.2330-T1
Valid prediction for CodingQuarry_transcript_32669-T1
Valid prediction for snap_scaffold_21-snap.2346-T1
Valid prediction for snap_scaffold_21-snap.2354-T1
Valid prediction for GlimmerHMM_glimmerT_49775-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_32667-T1
Valid prediction for GeneMark_model.86221_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28535, rend_intergenic: 14172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38044, rend_intergenic: 36789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43531, rend_intergenic: 39446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61312, rend_intergenic: 47054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64077, rend_intergenic: 61347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70406, rend_intergenic: 68547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90089, rend_intergenic: 86899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101291, rend_intergenic: 96238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117394, rend_intergenic: 112218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122685, rend_intergenic: 118679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126453, rend_intergenic: 124612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134186, rend_intergenic: 128932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142495, rend_intergenic: 139820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203052
-exon list size: 632


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 28535, rend_intergenic: 14172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38044, rend_intergenic: 36789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43531, rend_intergenic: 39446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61312, rend_intergenic: 47054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64077, rend_intergenic: 61347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70406, rend_intergenic: 68547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90089, rend_intergenic: 86899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101291, rend_intergenic: 96238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117394, rend_intergenic: 112218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122685, rend_intergenic: 118679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126453, rend_intergenic: 124612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134186, rend_intergenic: 128932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142495, rend_intergenic: 139820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 186672 - 203052
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 186672 - 198803
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support