-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_1320986-1471402

-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 Augustus_model.g36685.t1
Valid prediction for GeneMark_model.95698_t
Valid prediction for snap_scaffold_25-snap.284-T1
Valid prediction for GeneMark_model.95700_t
Valid prediction for snap_scaffold_25-snap.279-T1
Valid prediction for snap_scaffold_25-snap.288-T1
Valid prediction for snap_scaffold_25-snap.275-T1
Valid prediction for GeneMark_model.95704_t
Valid prediction for GeneMark_model.95685_t
Valid prediction for GlimmerHMM_glimmerT_54912-T1
Valid prediction for snap_scaffold_25-snap.290-T1
Valid prediction for GlimmerHMM_glimmerT_54909-T1
Valid prediction for snap_scaffold_25-snap.282-T1
Valid prediction for GlimmerHMM_glimmerT_54902-T1
Valid prediction for GlimmerHMM_glimmerT_54917-T1
Valid prediction for GeneMark_model.95694_t
Valid prediction for GeneMark_model.95682_t
Valid prediction for GeneMark_model.95677_t
Valid prediction for snap_scaffold_25-snap.270-T1
Couldn't classify 136546, 136752
Sorry, prediction pasa_asmbl_33373.p1 fails validation.
(ATG)	 TG	124039-124234	GT	CGG
(ACA)	 AG	126881-127004	GT	CGG
(GTT)	 AG	128516-128669	GT	AGG
(GGC)	 AG	130670-130833	GT	AGG
(CTA)	 AG	131273-131642	GT	ATG
(GAC)	 AG	132084-132269	GT	TGG
(GAG)	 AG	132929-133086	GT	AGG
(TAC)	 AG	133439-133553	GT	AGG
(ATG)	 AG	136546-136752	AC	GCA
-recovered pasa_asmbl_33373.p1, initial, 124039, 124234
-recovered pasa_asmbl_33373.p1, internal, 126881, 127004
-recovered pasa_asmbl_33373.p1, internal, 128516, 128669
-recovered pasa_asmbl_33373.p1, internal, 130670, 130833
-recovered pasa_asmbl_33373.p1, internal, 131273, 131642
-recovered pasa_asmbl_33373.p1, internal, 132084, 132269
-recovered pasa_asmbl_33373.p1, internal, 132929, 133086
-recovered pasa_asmbl_33373.p1, internal, 133439, 133553
Valid prediction for snap_scaffold_25-snap.277-T1
Valid prediction for GeneMark_model.95687_t
Valid prediction for snap_scaffold_25-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_54905-T1
Valid prediction for GeneMark_model.95671_t
Valid prediction for snap_scaffold_25-snap.299-T1
Valid prediction for GeneMark_model.95699_t
Valid prediction for GlimmerHMM_glimmerT_54908-T1
Valid prediction for GeneMark_model.95697_t
Valid prediction for snap_scaffold_25-snap.268-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.95692_t
Valid prediction for GlimmerHMM_glimmerT_54916-T1
Valid prediction for GeneMark_model.95703_t
Valid prediction for snap_scaffold_25-snap.295-T1
Valid prediction for snap_scaffold_25-snap.292-T1
Valid prediction for snap_scaffold_25-snap.291-T1
Valid prediction for GeneMark_model.95690_t
Valid prediction for GlimmerHMM_glimmerT_54914-T1
Valid prediction for snap_scaffold_25-snap.278-T1
Couldn't classify 138364, 138441
Sorry, prediction pasa_asmbl_33374.p3 fails validation.
(GAT)	 AC	138364-138441	GT	TGG
(GCC)	 AG	139042-139129	GT	GAG
(ACA)	 AG	139607-139740	GT	TGG
(GAG)	 AG	141677-141817	GT	GGG
(AGT)	 AG	142272-142313	AG	GAA
-recovered pasa_asmbl_33374.p3, terminal, 142272, 142313
-recovered pasa_asmbl_33374.p3, internal, 139042, 139129
-recovered pasa_asmbl_33374.p3, internal, 139607, 139740
-recovered pasa_asmbl_33374.p3, internal, 141677, 141817
Valid prediction for CodingQuarry_transcript_38562-T1
Valid prediction for GeneMark_model.95689_t
Valid prediction for GeneMark_model.95678_t
Valid prediction for GlimmerHMM_glimmerT_54918-T1
Valid prediction for snap_scaffold_25-snap.296-T1
Valid prediction for snap_scaffold_25-snap.285-T1
Valid prediction for GeneMark_model.95675_t
Valid prediction for snap_scaffold_25-snap.271-T1
Valid prediction for GeneMark_model.95706_t
Valid prediction for GeneMark_model.95668_t
Valid prediction for GeneMark_model.95669_t

-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_25-snap.298-T1
Valid prediction for GeneMark_model.95688_t
Valid prediction for GeneMark_model.95701_t
Valid prediction for snap_scaffold_25-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_54904-T1
Couldn't classify 87705, 87825
Sorry, prediction pasa_asmbl_34020.p1 fails validation.
(GAG)	 CA	87705-87825	GT	TGG
(GGT)	 AG	89451-89621	GT	AGG
(GGC)	 AG	90090-90100	CC	GAC
-recovered pasa_asmbl_34020.p1, terminal, 90090, 90100
-recovered pasa_asmbl_34020.p1, internal, 89451, 89621
Valid prediction for snap_scaffold_25-snap.294-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.95670_t
Valid prediction for snap_scaffold_25-snap.283-T1
Valid prediction for Augustus_model.g36682.t1
Valid prediction for Augustus_model.g36684.t1
Valid prediction for snap_scaffold_25-snap.274-T1
Valid prediction for GeneMark_model.95676_t
Valid prediction for snap_scaffold_25-snap.301-T1
Valid prediction for GeneMark_model.95667_t
Valid prediction for GeneMark_model.95705_t
Valid prediction for Augustus_model.g36683.t1
Valid prediction for GlimmerHMM_glimmerT_54906-T1
Valid prediction for snap_scaffold_25-snap.276-T1
Valid prediction for GeneMark_model.95683_t
Valid prediction for GeneMark_model.95674_t
Valid prediction for snap_scaffold_25-snap.302-T1
Valid prediction for GeneMark_model.95707_t
Valid prediction for GeneMark_model.95672_t
Valid prediction for GeneMark_model.95681_t
Valid prediction for Augustus_model.g36678.t1
Valid prediction for snap_scaffold_25-snap.303-T1
Valid prediction for GeneMark_model.95693_t
Valid prediction for Augustus_model.g36680.t1
Valid prediction for snap_scaffold_25-snap.287-T1
Valid prediction for snap_scaffold_25-snap.293-T1
Valid prediction for GlimmerHMM_glimmerT_54911-T1
Valid prediction for snap_scaffold_25-snap.297-T1
Valid prediction for GlimmerHMM_glimmerT_54913-T1
Valid prediction for snap_scaffold_25-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_54915-T1
Valid prediction for GeneMark_model.95679_t
Valid prediction for GlimmerHMM_glimmerT_54907-T1
Valid prediction for GeneMark_model.95695_t
Valid prediction for snap_scaffold_25-snap.300-T1
Valid prediction for GeneMark_model.95696_t
Valid prediction for Augustus_model.g36681.t1
Valid prediction for snap_scaffold_25-snap.280-T1
Valid prediction for pasa_asmbl_34515.p1
Valid prediction for GlimmerHMM_glimmerT_54903-T1
Valid prediction for GeneMark_model.95673_t
Valid prediction for CodingQuarry_transcript_38561-T1
Valid prediction for GeneMark_model.95691_t
Valid prediction for CodingQuarry_transcript_38560-T1
Valid prediction for snap_scaffold_25-snap.269-T1
Valid prediction for GeneMark_model.95686_t
Valid prediction for snap_scaffold_25-snap.281-T1
Valid prediction for snap_scaffold_25-snap.273-T1
Valid prediction for Augustus_model.g36679.t1
Valid prediction for GeneMark_model.95684_t
Valid prediction for GlimmerHMM_glimmerT_54910-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 59894, rend_intergenic: 59891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 111997, rend_intergenic: 111994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 4851, rend_intergenic: 2350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20084, rend_intergenic: 12733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25266, rend_intergenic: 22873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30908, rend_intergenic: 26667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44078, rend_intergenic: 36646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46820, rend_intergenic: 44148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65331, rend_intergenic: 59937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74611, rend_intergenic: 66049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89054, rend_intergenic: 74725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91149, rend_intergenic: 89425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102318, rend_intergenic: 93292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115989, rend_intergenic: 112040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126361, rend_intergenic: 122525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127851, rend_intergenic: 126533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145760, rend_intergenic: 128238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150417
-exon list size: 625


building trellis

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99.4    
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99.8    
-found 29 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 59894, rend_intergenic: 59891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 111997, rend_intergenic: 111994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 4851, rend_intergenic: 2350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20084, rend_intergenic: 12733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25266, rend_intergenic: 22873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30908, rend_intergenic: 26667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44078, rend_intergenic: 36646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46820, rend_intergenic: 44148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65331, rend_intergenic: 59937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74611, rend_intergenic: 66049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89054, rend_intergenic: 74725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91149, rend_intergenic: 89425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102318, rend_intergenic: 93292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115989, rend_intergenic: 112040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126361, rend_intergenic: 122525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127851, rend_intergenic: 126533  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145760, rend_intergenic: 128238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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