-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_3190255-3311229

-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.70455_t
Valid prediction for snap_scaffold_17-snap.672-T1
Valid prediction for GlimmerHMM_glimmerT_40912-T1
Valid prediction for Augustus_model.g27401.t1
Valid prediction for snap_scaffold_17-snap.684-T1
Couldn't classify 28687, 28824
Sorry, prediction pasa_asmbl_17836.p3 fails validation.
(CAG)	 TC	28687-28824	GT	CTG
(GCC)	 AG	29054-29151	GT	AGG
(CCG)	 AG	30005-30119	AT	GAA
-recovered pasa_asmbl_17836.p3, terminal, 30005, 30119
-recovered pasa_asmbl_17836.p3, internal, 29054, 29151
Valid prediction for GeneMark_model.70459_t
Valid prediction for GeneMark_model.70444_t
Valid prediction for GeneMark_model.70478_t
Valid prediction for GlimmerHMM_glimmerT_40924-T1
Valid prediction for Augustus_model.g27402.t1
Valid prediction for snap_scaffold_17-snap.679-T1
Valid prediction for snap_scaffold_17-snap.681-T1
Valid prediction for GlimmerHMM_glimmerT_40918-T1
Valid prediction for Augustus_model.g27396.t1
Valid prediction for GlimmerHMM_glimmerT_40919-T1
Valid prediction for Augustus_model.g27397.t1
Valid prediction for GeneMark_model.70469_t
Valid prediction for GeneMark_model.70464_t
Valid prediction for GeneMark_model.70467_t
Valid prediction for snap_scaffold_17-snap.674-T1
Valid prediction for GlimmerHMM_glimmerT_40926-T1
Valid prediction for HiQ_model.g27403.t1
Valid prediction for GlimmerHMM_glimmerT_40914-T1
Couldn't classify 71121, 71222
Sorry, prediction pasa_asmbl_17841.p1 fails validation.
(CTA)	 CA	71121-71222	GT	TGG
(GTG)	 AG	71652-71963	CC	AGC
-recovered pasa_asmbl_17841.p1, terminal, 71652, 71963
Valid prediction for snap_scaffold_17-snap.682-T1
Valid prediction for GeneMark_model.70450_t
Valid prediction for snap_scaffold_17-snap.688-T1
Couldn't classify 59669, 60184
Sorry, prediction pasa_asmbl_17839.p2 fails validation.
(ATG)	 AA	59669-60184	AA	AGA
Valid prediction for pasa_asmbl_17842.p1
Valid prediction for GeneMark_model.70458_t
Couldn't classify 22705, 22801
Couldn't classify 23541, 23785
Sorry, prediction pasa_asmbl_18555.p2 fails validation.
(GAG)	 CG	22705-22801	GT	CGG
(AGG)	 AG	23541-23785	CC	AGC
Valid prediction for GeneMark_model.70476_t
Valid prediction for snap_scaffold_17-snap.687-T1
Valid prediction for snap_scaffold_17-snap.677-T1
Valid prediction for GlimmerHMM_glimmerT_40922-T1
Valid prediction for Augustus_model.g27394.t1
Valid prediction for GeneMark_model.70446_t
Valid prediction for snap_scaffold_17-snap.695-T1
Valid prediction for GeneMark_model.70471_t
Valid prediction for GeneMark_model.70473_t
Valid prediction for snap_scaffold_17-snap.693-T1
Valid prediction for snap_scaffold_17-snap.676-T1
Valid prediction for snap_scaffold_17-snap.696-T1
Couldn't classify 67253, 67580
Couldn't classify 69533, 69549
Sorry, prediction pasa_asmbl_18649.p2 fails validation.
(GGT)	 TG	67253-67580	GT	AGG
(AGC)	 AG	69533-69549	CA	TCC
Valid prediction for GeneMark_model.70461_t
Valid prediction for GeneMark_model.70463_t
Valid prediction for GeneMark_model.70475_t
Valid prediction for GeneMark_model.70449_t
Valid prediction for GeneMark_model.70442_t
Valid prediction for GlimmerHMM_glimmerT_40915-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_17-snap.673-T1
Valid prediction for GeneMark_model.70448_t
Valid prediction for GlimmerHMM_glimmerT_40920-T1
Valid prediction for GeneMark_model.70451_t
Valid prediction for GeneMark_model.70477_t
Valid prediction for GlimmerHMM_glimmerT_40921-T1
Valid prediction for snap_scaffold_17-snap.692-T1
Valid prediction for snap_scaffold_17-snap.689-T1
Valid prediction for Augustus_model.g27399.t1
Valid prediction for GlimmerHMM_glimmerT_40910-T1
Valid prediction for GlimmerHMM_glimmerT_40917-T1
Valid prediction for snap_scaffold_17-snap.680-T1
Valid prediction for GeneMark_model.70470_t
Valid prediction for GlimmerHMM_glimmerT_40927-T1
Valid prediction for Augustus_model.g27404.t1
Valid prediction for GlimmerHMM_glimmerT_40925-T1
Valid prediction for Augustus_model.g27395.t1
Valid prediction for snap_scaffold_17-snap.678-T1
Valid prediction for snap_scaffold_17-snap.694-T1
Valid prediction for snap_scaffold_17-snap.686-T1
Valid prediction for GeneMark_model.70466_t
Valid prediction for snap_scaffold_17-snap.690-T1
Valid prediction for GeneMark_model.70454_t
Valid prediction for GeneMark_model.70452_t
Valid prediction for GeneMark_model.70445_t
Valid prediction for GlimmerHMM_glimmerT_40909-T1
Valid prediction for GeneMark_model.70443_t
Valid prediction for Augustus_model.g27398.t1
Valid prediction for GeneMark_model.70472_t
Valid prediction for GlimmerHMM_glimmerT_40911-T1
Valid prediction for GlimmerHMM_glimmerT_40913-T1
Valid prediction for GlimmerHMM_glimmerT_40916-T1
Couldn't classify 73745, 73855
Sorry, prediction pasa_asmbl_18852.p1 fails validation.
(GGT)	 CA	73745-73855	GT	AGG
(GTG)	 AG	74068-74216	GT	GCG
(CTA)	 AG	75425-75526	GT	AGG
(GAA)	 AG	77467-77515	GT	AGG
(ACG)	 AG	77943-78065	GA	GAG
-recovered pasa_asmbl_18852.p1, terminal, 77943, 78065
-recovered pasa_asmbl_18852.p1, internal, 74068, 74216
-recovered pasa_asmbl_18852.p1, internal, 75425, 75526
-recovered pasa_asmbl_18852.p1, internal, 77467, 77515
Valid prediction for Augustus_model.g27400.t1
Valid prediction for GeneMark_model.70460_t
Valid prediction for GeneMark_model.70457_t
Valid prediction for GeneMark_model.70462_t
Valid prediction for GeneMark_model.70441_t
Valid prediction for GeneMark_model.70474_t
Valid prediction for snap_scaffold_17-snap.685-T1
Valid prediction for GeneMark_model.70456_t
Valid prediction for snap_scaffold_17-snap.675-T1
Valid prediction for snap_scaffold_17-snap.691-T1
Valid prediction for GeneMark_model.70447_t
Valid prediction for GlimmerHMM_glimmerT_40923-T1
Valid prediction for GeneMark_model.70468_t
Valid prediction for GeneMark_model.70453_t
Valid prediction for snap_scaffold_17-snap.683-T1
Valid prediction for GeneMark_model.70465_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11185, rend_intergenic: 9040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18045, rend_intergenic: 11403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20155, rend_intergenic: 18129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28192, rend_intergenic: 24960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52347, rend_intergenic: 48508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71963, rend_intergenic: 64580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79935, rend_intergenic: 75199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101784, rend_intergenic: 82452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103861, rend_intergenic: 102262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112177, rend_intergenic: 110336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 120975
-exon list size: 428


building trellis

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98.8    
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99.5    
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-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 11185, rend_intergenic: 9040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18045, rend_intergenic: 11403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20155, rend_intergenic: 18129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28192, rend_intergenic: 24960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52347, rend_intergenic: 48508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71963, rend_intergenic: 64580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79935, rend_intergenic: 75199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101784, rend_intergenic: 82452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103861, rend_intergenic: 102262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112177, rend_intergenic: 110336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support