-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_15686291-15793458

-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.g22615.t1
Valid prediction for snap_scaffold_13-snap.3049-T1
Valid prediction for GeneMark_model.57842_t
Couldn't classify 18602, 19069
Sorry, prediction pasa_asmbl_11511.p2 fails validation.
(GTC)	 CG	18602-19069	CT	GAC
Valid prediction for snap_scaffold_13-snap.3067-T1
Valid prediction for GeneMark_model.57816_t
Valid prediction for snap_scaffold_13-snap.3056-T1
Valid prediction for GlimmerHMM_glimmerT_33691-T1
Valid prediction for CodingQuarry_transcript_13304-T1
Valid prediction for Augustus_model.g22626.t1
Valid prediction for GeneMark_model.57845_t
Valid prediction for Augustus_model.g22625.t1
Valid prediction for snap_scaffold_13-snap.3061-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.57844_t
Valid prediction for Augustus_model.g22624.t1
Valid prediction for GlimmerHMM_glimmerT_33688-T1
Valid prediction for snap_scaffold_13-snap.3058-T1
Valid prediction for GeneMark_model.57846_t
Valid prediction for GeneMark_model.57829_t
Valid prediction for GlimmerHMM_glimmerT_33693-T1
Valid prediction for GeneMark_model.57840_t
Valid prediction for GeneMark_model.57814_t
Valid prediction for pasa_asmbl_11512.p1
Valid prediction for snap_scaffold_13-snap.3059-T1
Valid prediction for snap_scaffold_13-snap.3052-T1
Valid prediction for GeneMark_model.57827_t
Valid prediction for snap_scaffold_13-snap.3070-T1
Valid prediction for GlimmerHMM_glimmerT_33694-T1
Valid prediction for GlimmerHMM_glimmerT_33692-T1
Valid prediction for GlimmerHMM_glimmerT_33683-T1
Valid prediction for GeneMark_model.57831_t
Valid prediction for GeneMark_model.57819_t
Couldn't classify 63650, 63738
Sorry, prediction CodingQuarry_transcript_13305-T1 fails validation.
(ATG)	 TC	62592-62983	GT	CTG
(GAC)	 CA	63650-63738	GT	AGG
(GGG)	 AG	63856-64229	GT	AGG
(GTA)	 AG	64337-64666	GT	AGG
(CAT)	 AG	65015-65468	GT	AGG
(CTA)	 AG	65769-65802	GT	AGG
(AGT)	 AG	66230-66242	TA	AAT
-recovered CodingQuarry_transcript_13305-T1, initial, 62592, 62983
-recovered CodingQuarry_transcript_13305-T1, terminal, 66230, 66242
-recovered CodingQuarry_transcript_13305-T1, internal, 63856, 64229
-recovered CodingQuarry_transcript_13305-T1, internal, 64337, 64666
-recovered CodingQuarry_transcript_13305-T1, internal, 65015, 65468
-recovered CodingQuarry_transcript_13305-T1, internal, 65769, 65802
Valid prediction for GeneMark_model.57848_t
Valid prediction for Augustus_model.g22623.t1
Valid prediction for snap_scaffold_13-snap.3054-T1
Couldn't classify 94432, 94455
Couldn't classify 95734, 95796
Sorry, prediction pasa_asmbl_11517.p1 fails validation.
(GAC)	 AT	94432-94455	GT	AGG
(AGC)	 AG	94915-95034	GT	AGG
(GTG)	 AG	95229-95321	GT	TGG
(TCA)	 AG	95734-95796	AG	CAA
-recovered pasa_asmbl_11517.p1, internal, 94915, 95034
-recovered pasa_asmbl_11517.p1, internal, 95229, 95321
Valid prediction for snap_scaffold_13-snap.3064-T1
Valid prediction for GlimmerHMM_glimmerT_33690-T1
Valid prediction for GeneMark_model.57833_t
Valid prediction for snap_scaffold_13-snap.3068-T1
Valid prediction for GeneMark_model.57825_t
Valid prediction for snap_scaffold_13-snap.3071-T1
Valid prediction for GlimmerHMM_glimmerT_33695-T1
Valid prediction for GeneMark_model.57821_t
Valid prediction for GeneMark_model.57838_t
Valid prediction for GeneMark_model.57836_t
Valid prediction for snap_scaffold_13-snap.3066-T1
Valid prediction for snap_scaffold_13-snap.3062-T1
Valid prediction for Augustus_model.g22622.t1
Valid prediction for HiQ_model.g22621.t1
Valid prediction for GeneMark_model.57823_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 Augustus_model.g22617.t1
Valid prediction for GeneMark_model.57820_t
Valid prediction for GeneMark_model.57817_t
Valid prediction for snap_scaffold_13-snap.3065-T1
Valid prediction for GeneMark_model.57847_t
Valid prediction for snap_scaffold_13-snap.3069-T1
Valid prediction for GeneMark_model.57832_t
Valid prediction for GeneMark_model.57834_t
Valid prediction for GeneMark_model.57839_t
Valid prediction for GeneMark_model.57822_t
Valid prediction for GeneMark_model.57841_t
Valid prediction for GlimmerHMM_glimmerT_33696-T1
Valid prediction for HiQ_model.g22616.t1
Valid prediction for GlimmerHMM_glimmerT_33689-T1
Valid prediction for HiQ_model.g22620.t1
Valid prediction for GeneMark_model.57843_t
Valid prediction for GeneMark_model.57830_t
Valid prediction for GlimmerHMM_glimmerT_33687-T1
Valid prediction for snap_scaffold_13-snap.3072-T1
Valid prediction for GeneMark_model.57828_t
Valid prediction for GlimmerHMM_glimmerT_33684-T1
Valid prediction for snap_scaffold_13-snap.3057-T1
Valid prediction for snap_scaffold_13-snap.3055-T1
Valid prediction for snap_scaffold_13-snap.3063-T1
Valid prediction for Augustus_model.g22618.t1
Couldn't classify 77268, 77352
Couldn't classify 79271, 79395
Couldn't classify 79700, 79798
Sorry, prediction pasa_asmbl_10217.p1 fails validation.
(GAG)	 GA	77268-77352	GT	AGG
(TCC)	 AG	77536-77591	GT	AGG
(CTG)	 AG	78341-78482	GT	TGG
(AGA)	 AG	78711-78810	GT	AGG
(CTT)	 AG	79271-79395	AT	TTA
(GTG)	 AC	79700-79798	GT	AGG
(TCT)	 AG	80177-80355	GT	TGG
(GCG)	 AG	80868-81030	GT	AGG
(ATG)	 AG	81680-81780	GT	AGG
(CTG)	 AG	82225-82333	GT	AGG
(GTA)	 AG	82654-82766	GT	TTG
(GAC)	 AG	82985-83150	GT	AGG
(GCT)	 AG	83362-83487	GT	CGG
(CCC)	 AG	84520-84618	GT	GCG
(AGG)	 AG	84823-84908	GT	CCG
(GAG)	 AG	85261-85417	GT	TGG
(ATG)	 AG	85870-85948	GT	GGG
(TGA)	 AG	86327-86435	AC	GAA
add_exon() Sorry, pasa_asmbl_10217.p1 81680-81780-initial-1 is invalid.
-recovered pasa_asmbl_10217.p1, initial, 81680, 81780
-recovered pasa_asmbl_10217.p1, initial, 85870, 85948
add_exon() Sorry, pasa_asmbl_10217.p1 80868-81030-terminal-3 is invalid.
-recovered pasa_asmbl_10217.p1, terminal, 80868, 81030
-recovered pasa_asmbl_10217.p1, terminal, 86327, 86435
-recovered pasa_asmbl_10217.p1, internal, 77536, 77591
-recovered pasa_asmbl_10217.p1, internal, 78341, 78482
-recovered pasa_asmbl_10217.p1, internal, 78711, 78810
-recovered pasa_asmbl_10217.p1, internal, 80177, 80355
-recovered pasa_asmbl_10217.p1, internal, 80868, 81030
-recovered pasa_asmbl_10217.p1, internal, 81680, 81780
-recovered pasa_asmbl_10217.p1, internal, 82225, 82333
-recovered pasa_asmbl_10217.p1, internal, 82654, 82766
-recovered pasa_asmbl_10217.p1, internal, 82985, 83150
-recovered pasa_asmbl_10217.p1, internal, 83362, 83487
-recovered pasa_asmbl_10217.p1, internal, 84520, 84618
-recovered pasa_asmbl_10217.p1, internal, 84823, 84908
-recovered pasa_asmbl_10217.p1, internal, 85261, 85417
-recovered pasa_asmbl_10217.p1, internal, 85870, 85948
Valid prediction for CodingQuarry_transcript_13303-T1
Valid prediction for GeneMark_model.57826_t
Valid prediction for snap_scaffold_13-snap.3053-T1
Valid prediction for snap_scaffold_13-snap.3051-T1
Couldn't classify 56232, 56456
Couldn't classify 58162, 58247
Sorry, prediction pasa_asmbl_10223.p1 fails validation.
(AGA)	 AG	56232-56456	GT	TGG
(GAG)	 AG	56939-57008	GT	AGG
(AGG)	 AG	57332-57480	GT	TGG
(ATC)	 AG	57796-58030	GT	AGG
(AAC)	 AG	58162-58247	GT	AGG
-recovered pasa_asmbl_10223.p1, internal, 56232, 56456
-recovered pasa_asmbl_10223.p1, internal, 56939, 57008
-recovered pasa_asmbl_10223.p1, internal, 57332, 57480
-recovered pasa_asmbl_10223.p1, internal, 57796, 58030
-recovered pasa_asmbl_10223.p1, internal, 58162, 58247
Valid prediction for GeneMark_model.57815_t
Valid prediction for GeneMark_model.57849_t
Valid prediction for Augustus_model.g22619.t1
Valid prediction for snap_scaffold_13-snap.3060-T1
Couldn't classify 58569, 58593
Sorry, prediction pasa_asmbl_10221.p2 fails validation.
(GAG)	 TC	58569-58593	GT	AGG
(AGA)	 AG	59136-59281	GT	TGG
(CCC)	 AG	59535-59618	GT	AGG
(GTG)	 AG	60941-61047	GT	AAG
(GTG)	 AG	62001-62052	GG	GAG
-recovered pasa_asmbl_10221.p2, terminal, 62001, 62052
-recovered pasa_asmbl_10221.p2, internal, 59136, 59281
-recovered pasa_asmbl_10221.p2, internal, 59535, 59618
-recovered pasa_asmbl_10221.p2, internal, 60941, 61047
Valid prediction for GlimmerHMM_glimmerT_33686-T1
Valid prediction for GlimmerHMM_glimmerT_33685-T1
Valid prediction for GeneMark_model.57824_t
Valid prediction for snap_scaffold_13-snap.3050-T1
Valid prediction for GeneMark_model.57835_t
Valid prediction for GeneMark_model.57837_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19069, rend_intergenic: 3963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27208, rend_intergenic: 19642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27431, rend_intergenic: 27281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30268, rend_intergenic: 27709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40427, rend_intergenic: 31947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47330, rend_intergenic: 43257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52157, rend_intergenic: 47809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56645, rend_intergenic: 53814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87246, rend_intergenic: 72094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105421, rend_intergenic: 92323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 107168
-exon list size: 514


building trellis

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28.9    
29.1    
29.3    
29.5    
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29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.8    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
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38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.1    
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40.9    
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42.6    
42.8    
43.0    
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48.3    
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64.3    
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98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 19069, rend_intergenic: 3963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27208, rend_intergenic: 19642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27431, rend_intergenic: 27281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30268, rend_intergenic: 27709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40427, rend_intergenic: 31947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47330, rend_intergenic: 43257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52157, rend_intergenic: 47809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56645, rend_intergenic: 53814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87246, rend_intergenic: 72094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105421, rend_intergenic: 92323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support