-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_1986667-2164306

-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_7-snap.498-T1
Valid prediction for GeneMark_model.29259_t
Valid prediction for GeneMark_model.29244_t
Valid prediction for GlimmerHMM_glimmerT_17388-T1
Valid prediction for GlimmerHMM_glimmerT_17384-T1
Valid prediction for Augustus_model.g11629.t1
Valid prediction for GlimmerHMM_glimmerT_17375-T1
Valid prediction for GlimmerHMM_glimmerT_17394-T1
Valid prediction for GeneMark_model.29257_t
Valid prediction for GeneMark_model.29238_t
Valid prediction for snap_scaffold_7-snap.507-T1
Valid prediction for Augustus_model.g11633.t1
Valid prediction for snap_scaffold_7-snap.475-T1
Valid prediction for GlimmerHMM_glimmerT_17379-T1
Valid prediction for snap_scaffold_7-snap.482-T1
Valid prediction for snap_scaffold_7-snap.497-T1
Valid prediction for GlimmerHMM_glimmerT_17382-T1
Valid prediction for Augustus_model.g11631.t1
Valid prediction for GeneMark_model.29263_t
Valid prediction for GeneMark_model.29254_t
Valid prediction for GlimmerHMM_glimmerT_17396-T1
Valid prediction for GlimmerHMM_glimmerT_17392-T1
Couldn't classify 169340, 169462
Couldn't classify 172251, 172301
Sorry, prediction pasa_asmbl_50506.p1 fails validation.
(CTG)	 GG	169340-169462	GT	AGG
(GTG)	 AG	169932-170207	GT	ATG
(GTG)	 AG	170756-170836	GT	AGG
(TGC)	 AG	171731-171871	GT	AGG
(GGG)	 AG	172251-172301	AC	ACA
-recovered pasa_asmbl_50506.p1, internal, 169932, 170207
-recovered pasa_asmbl_50506.p1, internal, 170756, 170836
-recovered pasa_asmbl_50506.p1, internal, 171731, 171871
Valid prediction for HiQ_model.g11645.t1
Valid prediction for Augustus_model.g11638.t1
Valid prediction for snap_scaffold_7-snap.472-T1
Valid prediction for snap_scaffold_7-snap.502-T1
Valid prediction for snap_scaffold_7-snap.500-T1
Valid prediction for GeneMark_model.29252_t
Valid prediction for GeneMark_model.29266_t
Valid prediction for GeneMark_model.29260_t
Valid prediction for snap_scaffold_7-snap.478-T1
Valid prediction for snap_scaffold_7-snap.469-T1
Valid prediction for GeneMark_model.29225_t
Valid prediction for GlimmerHMM_glimmerT_17387-T1
Valid prediction for GlimmerHMM_glimmerT_17398-T1
Valid prediction for GeneMark_model.29264_t
Valid prediction for GeneMark_model.29236_t
Valid prediction for snap_scaffold_7-snap.504-T1
Valid prediction for Augustus_model.g11630.t1
Valid prediction for snap_scaffold_7-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_17385-T1
Valid prediction for snap_scaffold_7-snap.505-T1
Valid prediction for snap_scaffold_7-snap.473-T1
Valid prediction for snap_scaffold_7-snap.467-T1
Valid prediction for GeneMark_model.29247_t
Valid prediction for GeneMark_model.29248_t
Valid prediction for GeneMark_model.29249_t
Valid prediction for GeneMark_model.29246_t
Valid prediction for GlimmerHMM_glimmerT_17376-T1
Valid prediction for Augustus_model.g11635.t1
Valid prediction for Augustus_model.g11636.t1
Valid prediction for GlimmerHMM_glimmerT_17373-T1
Valid prediction for GlimmerHMM_glimmerT_17369-T1
Valid prediction for Augustus_model.g11634.t1
Valid prediction for GeneMark_model.29243_t
Valid prediction for GeneMark_model.29233_t
Valid prediction for GlimmerHMM_glimmerT_17390-T1
Valid prediction for GlimmerHMM_glimmerT_17389-T1
Valid prediction for GlimmerHMM_glimmerT_17371-T1
Valid prediction for GeneMark_model.29269_t
Valid prediction for GeneMark_model.29227_t
Valid prediction for GeneMark_model.29261_t
Valid prediction for GeneMark_model.29229_t
Valid prediction for GeneMark_model.29255_t
Valid prediction for GlimmerHMM_glimmerT_17397-T1
Valid prediction for Augustus_model.g11628.t1
Valid prediction for snap_scaffold_7-snap.495-T1
Valid prediction for Augustus_model.g11646.t1
Valid prediction for GlimmerHMM_glimmerT_17393-T1
Valid prediction for GeneMark_model.29241_t
Valid prediction for snap_scaffold_7-snap.490-T1
Valid prediction for snap_scaffold_7-snap.477-T1
Valid prediction for GeneMark_model.29230_t
Valid prediction for snap_scaffold_7-snap.492-T1
Valid prediction for GlimmerHMM_glimmerT_17383-T1
Valid prediction for Augustus_model.g11640.t1
Valid prediction for GeneMark_model.29235_t
Valid prediction for snap_scaffold_7-snap.491-T1
Valid prediction for Augustus_model.g11637.t1
Valid prediction for GlimmerHMM_glimmerT_17368-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.29253_t
Valid prediction for Augustus_model.g11642.t1
Valid prediction for Augustus_model.g11643.t1
Valid prediction for snap_scaffold_7-snap.468-T1
Couldn't classify 24405, 24467
Sorry, prediction pasa_asmbl_49563.p1 fails validation.
(ATG)	 AG	21344-21409	GT	TGG
(GTG)	 AG	22626-22802	GT	AGG
(GAT)	 AG	24405-24467	AG	ACA
-recovered pasa_asmbl_49563.p1, initial, 21344, 21409
-recovered pasa_asmbl_49563.p1, internal, 21344, 21409
-recovered pasa_asmbl_49563.p1, internal, 22626, 22802
Valid prediction for snap_scaffold_7-snap.474-T1
Valid prediction for snap_scaffold_7-snap.501-T1
Valid prediction for snap_scaffold_7-snap.488-T1
Valid prediction for GlimmerHMM_glimmerT_17399-T1
Valid prediction for GlimmerHMM_glimmerT_17386-T1
Valid prediction for snap_scaffold_7-snap.496-T1
Valid prediction for GeneMark_model.29270_t
Valid prediction for snap_scaffold_7-snap.470-T1
Couldn't classify 60508, 60603
Couldn't classify 62034, 62141
Sorry, prediction pasa_asmbl_49562.p2 fails validation.
(CTG)	 CT	60508-60603	GT	AGG
(CTG)	 AG	60870-61019	GT	AGG
(ACG)	 AG	62034-62141	CA	GGC
-recovered pasa_asmbl_49562.p2, internal, 60870, 61019
Valid prediction for GeneMark_model.29231_t
Valid prediction for snap_scaffold_7-snap.471-T1
Valid prediction for GeneMark_model.29256_t
Valid prediction for snap_scaffold_7-snap.494-T1
Valid prediction for GeneMark_model.29268_t
Valid prediction for Augustus_model.g11632.t1
Valid prediction for GeneMark_model.29226_t
Valid prediction for snap_scaffold_7-snap.484-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.29242_t
Valid prediction for GlimmerHMM_glimmerT_17378-T1
Valid prediction for snap_scaffold_7-snap.503-T1
Valid prediction for snap_scaffold_7-snap.499-T1
Valid prediction for GeneMark_model.29234_t
Valid prediction for GlimmerHMM_glimmerT_17370-T1
Valid prediction for snap_scaffold_7-snap.481-T1
Valid prediction for GeneMark_model.29239_t
Valid prediction for GlimmerHMM_glimmerT_17377-T1
Valid prediction for snap_scaffold_7-snap.506-T1
Valid prediction for snap_scaffold_7-snap.493-T1
Valid prediction for GeneMark_model.29245_t
Valid prediction for snap_scaffold_7-snap.487-T1
Valid prediction for Augustus_model.g11641.t1
Valid prediction for snap_scaffold_7-snap.489-T1
Valid prediction for snap_scaffold_7-snap.486-T1
Valid prediction for GeneMark_model.29262_t
Valid prediction for GeneMark_model.29267_t
Valid prediction for snap_scaffold_7-snap.476-T1
Valid prediction for GlimmerHMM_glimmerT_17380-T1
Valid prediction for GlimmerHMM_glimmerT_17395-T1
Valid prediction for snap_scaffold_7-snap.483-T1
Valid prediction for GeneMark_model.29258_t
Valid prediction for snap_scaffold_7-snap.508-T1
Valid prediction for snap_scaffold_7-snap.480-T1
Valid prediction for GeneMark_model.29251_t
Valid prediction for GlimmerHMM_glimmerT_17374-T1
Valid prediction for GeneMark_model.29265_t
Valid prediction for GlimmerHMM_glimmerT_17372-T1
Valid prediction for GeneMark_model.29228_t
Valid prediction for GeneMark_model.29232_t
Valid prediction for GlimmerHMM_glimmerT_17391-T1
Valid prediction for GeneMark_model.29240_t
Valid prediction for GlimmerHMM_glimmerT_17381-T1
Valid prediction for Augustus_model.g11639.t1
Valid prediction for snap_scaffold_7-snap.485-T1
Valid prediction for Augustus_model.g11644.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6617, rend_intergenic: 3229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23570, rend_intergenic: 18297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30545, rend_intergenic: 24278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49121, rend_intergenic: 43849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50627, rend_intergenic: 49516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64680, rend_intergenic: 61868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85122, rend_intergenic: 65674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124170, rend_intergenic: 123118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134533, rend_intergenic: 125001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141552, rend_intergenic: 134622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142393, rend_intergenic: 141852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145724, rend_intergenic: 143649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149746, rend_intergenic: 146841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165719, rend_intergenic: 163659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175455, rend_intergenic: 173774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177640
-exon list size: 750


building trellis

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94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 6617, rend_intergenic: 3229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23570, rend_intergenic: 18297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30545, rend_intergenic: 24278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49121, rend_intergenic: 43849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50627, rend_intergenic: 49516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64680, rend_intergenic: 61868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85122, rend_intergenic: 65674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124170, rend_intergenic: 123118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134533, rend_intergenic: 125001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141552, rend_intergenic: 134622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142393, rend_intergenic: 141852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145724, rend_intergenic: 143649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149746, rend_intergenic: 146841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165719, rend_intergenic: 163659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175455, rend_intergenic: 173774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support