-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_4755081-4975069

-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_39112-T1
Valid prediction for snap_scaffold_16-snap.956-T1
Valid prediction for GlimmerHMM_glimmerT_39120-T1
Valid prediction for snap_scaffold_16-snap.936-T1
Valid prediction for GeneMark_model.66984_t
Valid prediction for GlimmerHMM_glimmerT_39111-T1
Valid prediction for GeneMark_model.66963_t
Valid prediction for Augustus_model.g26278.t1
Valid prediction for Augustus_model.g26284.t1
Couldn't classify 131719, 131816
Couldn't classify 131950, 132214
Sorry, prediction pasa_asmbl_16994.p1 fails validation.
(GTG)	 TT	131719-131816	GT	AGG
(ATG)	 AG	131950-132214	CC	AGC
Couldn't classify 192404, 192437
Couldn't classify 193596, 193807
Sorry, prediction pasa_asmbl_16997.p1 fails validation.
(AAA)	 AG	192404-192437	GT	GAG
(TGG)	 AG	193162-193359	GT	CAG
(GTC)	 AG	193596-193807	AT	AGA
-recovered pasa_asmbl_16997.p1, internal, 192404, 192437
-recovered pasa_asmbl_16997.p1, internal, 193162, 193359
Couldn't classify 146365, 146590
Couldn't classify 147356, 147615
Sorry, prediction pasa_asmbl_16995.p1 fails validation.
(GTG)	 GG	146365-146590	GT	AGG
(GGT)	 AG	147356-147615	TG	ACT
Valid prediction for snap_scaffold_16-snap.935-T1
Valid prediction for GeneMark_model.66989_t
Valid prediction for GlimmerHMM_glimmerT_39108-T1
Valid prediction for snap_scaffold_16-snap.944-T1
Valid prediction for GlimmerHMM_glimmerT_39126-T1
Valid prediction for GlimmerHMM_glimmerT_39106-T1
Valid prediction for GeneMark_model.66956_t
Valid prediction for GeneMark_model.66959_t
Valid prediction for GeneMark_model.66973_t
Valid prediction for snap_scaffold_16-snap.940-T1
Valid prediction for GlimmerHMM_glimmerT_39127-T1
Valid prediction for GlimmerHMM_glimmerT_39119-T1
Valid prediction for GeneMark_model.66980_t
Valid prediction for GeneMark_model.66991_t
Valid prediction for Augustus_model.g26275.t1
Valid prediction for GeneMark_model.66988_t
Valid prediction for GlimmerHMM_glimmerT_39121-T1
Valid prediction for snap_scaffold_16-snap.931-T1
Valid prediction for snap_scaffold_16-snap.953-T1
Valid prediction for Augustus_model.g26279.t1
Valid prediction for snap_scaffold_16-snap.951-T1
Valid prediction for snap_scaffold_16-snap.948-T1
Valid prediction for GeneMark_model.66949_t
Valid prediction for GeneMark_model.66985_t
Valid prediction for GeneMark_model.66964_t
Valid prediction for GeneMark_model.66970_t
Valid prediction for GeneMark_model.66958_t
Valid prediction for snap_scaffold_16-snap.929-T1
Valid prediction for snap_scaffold_16-snap.937-T1
Valid prediction for GeneMark_model.66992_t
Valid prediction for snap_scaffold_16-snap.930-T1
Valid prediction for GeneMark_model.66982_t
Valid prediction for snap_scaffold_16-snap.933-T1
Valid prediction for snap_scaffold_16-snap.957-T1
Valid prediction for GeneMark_model.66960_t
Valid prediction for GlimmerHMM_glimmerT_39128-T1
Valid prediction for GeneMark_model.66968_t
Valid prediction for GeneMark_model.66971_t
Valid prediction for snap_scaffold_16-snap.928-T1
Valid prediction for GeneMark_model.66954_t
Valid prediction for GlimmerHMM_glimmerT_39107-T1
Valid prediction for GlimmerHMM_glimmerT_39117-T1
Valid prediction for GlimmerHMM_glimmerT_39124-T1
Valid prediction for snap_scaffold_16-snap.950-T1
Valid prediction for GeneMark_model.66986_t
Valid prediction for Augustus_model.g26283.t1
Valid prediction for snap_scaffold_16-snap.943-T1
Couldn't classify 200873, 200906
Sorry, prediction pasa_asmbl_16998.p1 fails validation.
(GAA)	 CA	200873-200906	GT	AGG
(GTC)	 AG	201062-201233	GT	AGG
(GTG)	 AG	202286-202481	GT	AGG
(GAC)	 AG	204350-204560	GT	AGG
(GGG)	 AG	204659-204732	GT	AAG
(CTC)	 AG	205629-205784	GT	AGG
(ATT)	 AG	206834-207055	GC	AGG
-recovered pasa_asmbl_16998.p1, terminal, 206834, 207055
-recovered pasa_asmbl_16998.p1, internal, 201062, 201233
-recovered pasa_asmbl_16998.p1, internal, 202286, 202481
-recovered pasa_asmbl_16998.p1, internal, 204350, 204560
-recovered pasa_asmbl_16998.p1, internal, 204659, 204732
-recovered pasa_asmbl_16998.p1, internal, 205629, 205784
-recovered pasa_asmbl_16998.p1, internal, 206834, 207055
Valid prediction for GlimmerHMM_glimmerT_39116-T1
Valid prediction for snap_scaffold_16-snap.941-T1
Valid prediction for snap_scaffold_16-snap.942-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_16-snap.949-T1
Valid prediction for GlimmerHMM_glimmerT_39109-T1
Valid prediction for GlimmerHMM_glimmerT_39110-T1
Valid prediction for Augustus_model.g26280.t1
Valid prediction for CodingQuarry_transcript_19917-T1
Valid prediction for GlimmerHMM_glimmerT_39123-T1
Valid prediction for GeneMark_model.66990_t
Valid prediction for snap_scaffold_16-snap.947-T1
Valid prediction for HiQ_model.g26276.t1
Valid prediction for GeneMark_model.66978_t
Valid prediction for CodingQuarry_transcript_19918-T1
Valid prediction for snap_scaffold_16-snap.955-T1
Valid prediction for GlimmerHMM_glimmerT_39114-T1
Valid prediction for Augustus_model.g26274.t1
Valid prediction for CodingQuarry_transcript_19916-T1
Valid prediction for snap_scaffold_16-snap.939-T1
Valid prediction for snap_scaffold_16-snap.927-T1
Valid prediction for pasa_asmbl_16250.p1
Valid prediction for GeneMark_model.66967_t
Valid prediction for GeneMark_model.66972_t
Valid prediction for snap_scaffold_16-snap.938-T1
Valid prediction for CodingQuarry_transcript_19919-T1
Valid prediction for GlimmerHMM_glimmerT_39115-T1
Valid prediction for snap_scaffold_16-snap.946-T1
Valid prediction for GlimmerHMM_glimmerT_39125-T1
Couldn't classify 71716, 72087
Sorry, prediction pasa_asmbl_16996.p2 fails validation.
(ATG)	 AA	71716-72087	CC	GGC
Valid prediction for GeneMark_model.66955_t
Valid prediction for HiQ_model.g26277.t1
Valid prediction for GeneMark_model.66962_t
Valid prediction for GlimmerHMM_glimmerT_39118-T1
Valid prediction for GeneMark_model.66987_t
Valid prediction for GeneMark_model.66976_t
Valid prediction for pasa_asmbl_16254.p1
Couldn't classify 68222, 68263
Sorry, prediction pasa_asmbl_16252.p1 fails validation.
(GCA)	 GG	68222-68263	GT	AGG
(GTC)	 AG	68478-68606	GT	AGG
(TGG)	 AG	68739-68864	GT	AGG
(GTC)	 AG	69144-69221	GT	AGG
(GCC)	 AG	69534-69659	GT	AGG
(CTC)	 AG	69767-69895	CC	AAC
-recovered pasa_asmbl_16252.p1, terminal, 69767, 69895
-recovered pasa_asmbl_16252.p1, internal, 68478, 68606
-recovered pasa_asmbl_16252.p1, internal, 68739, 68864
-recovered pasa_asmbl_16252.p1, internal, 69144, 69221
-recovered pasa_asmbl_16252.p1, internal, 69534, 69659
Valid prediction for GeneMark_model.66953_t
Valid prediction for GlimmerHMM_glimmerT_39113-T1
Valid prediction for GeneMark_model.66950_t
Valid prediction for Augustus_model.g26273.t1
Valid prediction for GeneMark_model.66952_t
Valid prediction for snap_scaffold_16-snap.945-T1
Valid prediction for CodingQuarry_transcript_19920-T1
Valid prediction for snap_scaffold_16-snap.954-T1
Valid prediction for GeneMark_model.66969_t
Valid prediction for GeneMark_model.66951_t
Valid prediction for GeneMark_model.66979_t
Valid prediction for GlimmerHMM_glimmerT_39122-T1
Valid prediction for Augustus_model.g26282.t1
Valid prediction for GeneMark_model.66965_t
Valid prediction for GlimmerHMM_glimmerT_39129-T1
Valid prediction for GeneMark_model.66977_t
Valid prediction for HiQ_model.g26281.t1
Couldn't classify 101694, 101905
Couldn't classify 104919, 105100
Sorry, prediction pasa_asmbl_16765.p1 fails validation.
(AAG)	 AC	101694-101905	GT	AGG
(CTT)	 AG	102033-102191	GT	AAG
(GAT)	 AG	102315-102454	GT	AGG
(CTG)	 AG	102709-102879	GT	AGG
(GTG)	 AG	103003-103192	GT	AAG
(GGG)	 AG	103346-103402	GT	AGG
(CCG)	 AG	103582-103683	GT	GGG
(GTG)	 AG	103913-103990	GT	AGG
(TCG)	 AG	104130-104246	GT	TTG
(TAT)	 AG	104356-104487	GT	GAG
(TCT)	 AG	104630-104826	GT	AGG
(ACC)	 AG	104919-105100	CC	CCC
add_exon() Sorry, pasa_asmbl_16765.p1 104356-104487-terminal-1 is invalid.
-recovered pasa_asmbl_16765.p1, terminal, 104356, 104487
-recovered pasa_asmbl_16765.p1, terminal, 104630, 104826
-recovered pasa_asmbl_16765.p1, internal, 102033, 102191
-recovered pasa_asmbl_16765.p1, internal, 102315, 102454
-recovered pasa_asmbl_16765.p1, internal, 102709, 102879
-recovered pasa_asmbl_16765.p1, internal, 103003, 103192
-recovered pasa_asmbl_16765.p1, internal, 103346, 103402
-recovered pasa_asmbl_16765.p1, internal, 103582, 103683
-recovered pasa_asmbl_16765.p1, internal, 103913, 103990
-recovered pasa_asmbl_16765.p1, internal, 104130, 104246
-recovered pasa_asmbl_16765.p1, internal, 104356, 104487
-recovered pasa_asmbl_16765.p1, internal, 104630, 104826
Valid prediction for GlimmerHMM_glimmerT_39105-T1
Valid prediction for GeneMark_model.66974_t
Valid prediction for GeneMark_model.66993_t
Valid prediction for GeneMark_model.66975_t
Valid prediction for snap_scaffold_16-snap.934-T1
Valid prediction for snap_scaffold_16-snap.932-T1
Valid prediction for GeneMark_model.66983_t
Valid prediction for GeneMark_model.66957_t
Valid prediction for GeneMark_model.66966_t
Valid prediction for GeneMark_model.66961_t
Valid prediction for snap_scaffold_16-snap.952-T1
Valid prediction for snap_scaffold_16-snap.926-T1
Couldn't classify 105752, 106084
Sorry, prediction pasa_asmbl_16246.p1 fails validation.
(TAC)	 GC	105752-106084	CC	CCC
Valid prediction for GeneMark_model.66981_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 113875, rend_intergenic: 113774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165279, rend_intergenic: 162527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182835, rend_intergenic: 178868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207299, rend_intergenic: 186850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214720, rend_intergenic: 207398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219989
-exon list size: 486


building trellis

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-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 113875, rend_intergenic: 113774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165279, rend_intergenic: 162527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182835, rend_intergenic: 178868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207299, rend_intergenic: 186850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214720, rend_intergenic: 207398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 208413 - 219989
-exon list size: 24


building trellis

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65.4    
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73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-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