-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_1345434-1627797

-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_25-snap.282-T1
Valid prediction for snap_scaffold_25-snap.299-T1
Valid prediction for snap_scaffold_25-snap.303-T1
Valid prediction for GlimmerHMM_glimmerT_53613-T1
Couldn't classify 113916, 113993
Sorry, prediction pasa_asmbl_33911.p3 fails validation.
(GAT)	 AC	113916-113993	GT	TGG
(GCC)	 AG	114594-114681	GT	GAG
(ACA)	 AG	115159-115292	GT	TGG
(GAG)	 AG	117229-117369	GT	GGG
(AGT)	 AG	117824-117865	AG	GAA
-recovered pasa_asmbl_33911.p3, terminal, 117824, 117865
-recovered pasa_asmbl_33911.p3, internal, 114594, 114681
-recovered pasa_asmbl_33911.p3, internal, 115159, 115292
-recovered pasa_asmbl_33911.p3, internal, 117229, 117369
Valid prediction for GlimmerHMM_glimmerT_53607-T1
Valid prediction for snap_scaffold_25-snap.313-T1
Valid prediction for snap_scaffold_25-snap.283-T1
Valid prediction for GlimmerHMM_glimmerT_53617-T1
Valid prediction for snap_scaffold_25-snap.314-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.305-T1
Valid prediction for snap_scaffold_25-snap.300-T1
Valid prediction for CodingQuarry_transcript_38644-T1
Valid prediction for snap_scaffold_25-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_53624-T1
Valid prediction for snap_scaffold_25-snap.297-T1
Valid prediction for GlimmerHMM_glimmerT_53629-T1
Couldn't classify 112098, 112304
Sorry, prediction pasa_asmbl_33379.p1 fails validation.
(ATG)	 TG	99591-99786	GT	CGG
(ACA)	 AG	102433-102556	GT	CGG
(GTT)	 AG	104068-104221	GT	AGG
(GGC)	 AG	106222-106385	GT	AGG
(CTA)	 AG	106825-107194	GT	ATG
(GAC)	 AG	107636-107821	GT	TGG
(GAG)	 AG	108481-108638	GT	AGG
(TAC)	 AG	108991-109105	GT	AGG
(ATG)	 AG	112098-112304	AC	GCA
-recovered pasa_asmbl_33379.p1, initial, 99591, 99786
-recovered pasa_asmbl_33379.p1, internal, 102433, 102556
-recovered pasa_asmbl_33379.p1, internal, 104068, 104221
-recovered pasa_asmbl_33379.p1, internal, 106222, 106385
-recovered pasa_asmbl_33379.p1, internal, 106825, 107194
-recovered pasa_asmbl_33379.p1, internal, 107636, 107821
-recovered pasa_asmbl_33379.p1, internal, 108481, 108638
-recovered pasa_asmbl_33379.p1, internal, 108991, 109105
Valid prediction for snap_scaffold_25-snap.276-T1
Couldn't classify 244657, 245151
Sorry, prediction pasa_asmbl_34600.p1 fails validation.
(CTC)	 GC	244657-245151	AA	AGA
Valid prediction for snap_scaffold_25-snap.281-T1
Valid prediction for snap_scaffold_25-snap.269-T1
Valid prediction for snap_scaffold_25-snap.268-T1
Valid prediction for snap_scaffold_25-snap.290-T1
Valid prediction for snap_scaffold_25-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_53609-T1
Valid prediction for snap_scaffold_25-snap.288-T1
Valid prediction for snap_scaffold_25-snap.270-T1
Valid prediction for Augustus_model.g35634.t1
Valid prediction for snap_scaffold_25-snap.295-T1
Valid prediction for snap_scaffold_25-snap.286-T1
Valid prediction for GlimmerHMM_glimmerT_53618-T1
Valid prediction for GlimmerHMM_glimmerT_53606-T1
Valid prediction for GlimmerHMM_glimmerT_53614-T1
Valid prediction for GlimmerHMM_glimmerT_53603-T1
Valid prediction for snap_scaffold_25-snap.301-T1
Valid prediction for snap_scaffold_25-snap.278-T1
Valid prediction for snap_scaffold_25-snap.306-T1
Valid prediction for snap_scaffold_25-snap.280-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 Augustus_model.g35632.t1
Valid prediction for Augustus_model.g35633.t1
Couldn't classify 244100, 244220
Sorry, prediction pasa_asmbl_34031.p1 fails validation.
(GAG)	 CA	244100-244220	GT	TGG
(GGT)	 AG	245846-246016	GT	AGG
(GGC)	 AG	246485-246495	CC	GAC
-recovered pasa_asmbl_34031.p1, terminal, 246485, 246495
-recovered pasa_asmbl_34031.p1, internal, 245846, 246016
Valid prediction for GlimmerHMM_glimmerT_53605-T1
Valid prediction for GlimmerHMM_glimmerT_53623-T1
Valid prediction for snap_scaffold_25-snap.275-T1
Valid prediction for snap_scaffold_25-snap.291-T1
Valid prediction for snap_scaffold_25-snap.289-T1
Valid prediction for GlimmerHMM_glimmerT_53626-T1
Valid prediction for snap_scaffold_25-snap.311-T1
Valid prediction for pasa_asmbl_34033.p1
Valid prediction for GlimmerHMM_glimmerT_53616-T1
Valid prediction for GlimmerHMM_glimmerT_53615-T1
Valid prediction for snap_scaffold_25-snap.312-T1
Valid prediction for CodingQuarry_transcript_38642-T1
Valid prediction for snap_scaffold_25-snap.309-T1
Valid prediction for snap_scaffold_25-snap.271-T1
Valid prediction for GlimmerHMM_glimmerT_53612-T1
Valid prediction for snap_scaffold_25-snap.296-T1
Valid prediction for Augustus_model.g35635.t1
Valid prediction for snap_scaffold_25-snap.292-T1
Valid prediction for snap_scaffold_25-snap.277-T1
Valid prediction for Augustus_model.g35638.t1
Valid prediction for Augustus_model.g35639.t1
Valid prediction for snap_scaffold_25-snap.284-T1
Valid prediction for GlimmerHMM_glimmerT_53602-T1
Valid prediction for GlimmerHMM_glimmerT_53620-T1
Valid prediction for snap_scaffold_25-snap.307-T1
Valid prediction for snap_scaffold_25-snap.273-T1
Valid prediction for Augustus_model.g35636.t1
Valid prediction for Augustus_model.g35637.t1
Valid prediction for GlimmerHMM_glimmerT_53610-T1
Couldn't classify 77885, 78010
Couldn't classify 79314, 79505
Sorry, prediction pasa_asmbl_34618.p1 fails validation.
(CAG)	 TC	77885-78010	GT	AGG
(GAC)	 AG	79314-79505	GT	ATG
-recovered pasa_asmbl_34618.p1, internal, 79314, 79505
Valid prediction for snap_scaffold_25-snap.267-T1
Valid prediction for snap_scaffold_25-snap.287-T1
Valid prediction for snap_scaffold_25-snap.274-T1
Valid prediction for GlimmerHMM_glimmerT_53619-T1
Valid prediction for GlimmerHMM_glimmerT_53611-T1
Valid prediction for GlimmerHMM_glimmerT_53627-T1
Valid prediction for GlimmerHMM_glimmerT_53608-T1
Valid prediction for GlimmerHMM_glimmerT_53628-T1
Valid prediction for GlimmerHMM_glimmerT_53622-T1
Valid prediction for Augustus_model.g35628.t1
Valid prediction for GlimmerHMM_glimmerT_53604-T1
Valid prediction for Augustus_model.g35630.t1
Valid prediction for Augustus_model.g35629.t1
Valid prediction for snap_scaffold_25-snap.298-T1
Valid prediction for snap_scaffold_25-snap.285-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53621-T1
Valid prediction for snap_scaffold_25-snap.294-T1
Valid prediction for Augustus_model.g35640.t1
Valid prediction for snap_scaffold_25-snap.302-T1
Valid prediction for snap_scaffold_25-snap.308-T1
Valid prediction for snap_scaffold_25-snap.293-T1
Valid prediction for GlimmerHMM_glimmerT_53625-T1
Couldn't classify 36745, 36812
Sorry, prediction pasa_asmbl_34044.p1 fails validation.
(ATG)	 AC	33130-33268	GT	GGG
(AGA)	 AG	33777-33854	GT	AAG
(TCA)	 AG	34041-34142	GT	CGG
(GTT)	 AG	36745-36812	GG	CCG
-recovered pasa_asmbl_34044.p1, initial, 33130, 33268
-recovered pasa_asmbl_34044.p1, terminal, 33777, 33854
-recovered pasa_asmbl_34044.p1, internal, 33777, 33854
-recovered pasa_asmbl_34044.p1, internal, 34041, 34142
Couldn't classify 75145, 75352
Couldn't classify 76301, 76429
Sorry, prediction pasa_asmbl_34553.p1 fails validation.
(CTC)	 GC	75145-75352	GT	TGG
(GTC)	 AG	75709-75764	GT	AGG
(CTG)	 AG	76301-76429	CC	ACC
-recovered pasa_asmbl_34553.p1, internal, 75709, 75764
Valid prediction for CodingQuarry_transcript_38643-T1
Valid prediction for snap_scaffold_25-snap.304-T1
Valid prediction for snap_scaffold_25-snap.279-T1
Valid prediction for Augustus_model.g35631.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6460, rend_intergenic: 2219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19630, rend_intergenic: 12198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22372, rend_intergenic: 19700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49143, rend_intergenic: 41614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50163, rend_intergenic: 50063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63769, rend_intergenic: 50277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66701, rend_intergenic: 64977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77870, rend_intergenic: 67085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91578, rend_intergenic: 87592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99428, rend_intergenic: 99117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101913, rend_intergenic: 99513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103403, rend_intergenic: 102085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121312, rend_intergenic: 103790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127844, rend_intergenic: 125970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128075, rend_intergenic: 127971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170258, rend_intergenic: 133659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176483, rend_intergenic: 170677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195803, rend_intergenic: 177183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212145, rend_intergenic: 195900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240404, rend_intergenic: 212152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250089, rend_intergenic: 240505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265740, rend_intergenic: 251546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272903, rend_intergenic: 265800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 35446, rend_intergenic: 35443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 282364
-exon list size: 410


building trellis

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29.6    
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30.6    
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33.3    
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34.2    
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36.2    
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37.1    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
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39.6    
39.8    
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40.3    
40.5    
40.8    
41.0    
41.3    
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42.0    
42.2    
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43.2    
43.4    
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43.9    
44.2    
44.4    
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45.4    
45.6    
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99.5    
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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 6460, rend_intergenic: 2219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19630, rend_intergenic: 12198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22372, rend_intergenic: 19700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49143, rend_intergenic: 41614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50163, rend_intergenic: 50063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63769, rend_intergenic: 50277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66701, rend_intergenic: 64977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77870, rend_intergenic: 67085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91578, rend_intergenic: 87592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99428, rend_intergenic: 99117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101913, rend_intergenic: 99513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103403, rend_intergenic: 102085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121312, rend_intergenic: 103790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127844, rend_intergenic: 125970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128075, rend_intergenic: 127971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170258, rend_intergenic: 133659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176483, rend_intergenic: 170677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195803, rend_intergenic: 177183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212145, rend_intergenic: 195900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240404, rend_intergenic: 212152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250089, rend_intergenic: 240505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 265740, rend_intergenic: 251546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272903, rend_intergenic: 265800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 35446, rend_intergenic: 35443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support