-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_518535-727676

-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.g11205.t1
Valid prediction for snap_scaffold_7-snap.167-T1
Valid prediction for snap_scaffold_7-snap.183-T1
Valid prediction for snap_scaffold_7-snap.155-T1
Valid prediction for GlimmerHMM_glimmerT_16768-T1
Valid prediction for GlimmerHMM_glimmerT_16778-T1
Valid prediction for snap_scaffold_7-snap.173-T1
Valid prediction for CodingQuarry_transcript_57423-T1
Valid prediction for snap_scaffold_7-snap.141-T1
Valid prediction for snap_scaffold_7-snap.169-T1
Valid prediction for snap_scaffold_7-snap.176-T1
Valid prediction for GlimmerHMM_glimmerT_16754-T1
Valid prediction for CodingQuarry_transcript_57424-T1
Valid prediction for snap_scaffold_7-snap.138-T1
Valid prediction for GlimmerHMM_glimmerT_16753-T1
Valid prediction for GlimmerHMM_glimmerT_16757-T1
Valid prediction for snap_scaffold_7-snap.146-T1
Valid prediction for GlimmerHMM_glimmerT_16762-T1
Valid prediction for snap_scaffold_7-snap.140-T1
Valid prediction for snap_scaffold_7-snap.162-T1
Valid prediction for GlimmerHMM_glimmerT_16759-T1
Valid prediction for snap_scaffold_7-snap.172-T1
Valid prediction for GlimmerHMM_glimmerT_16765-T1
Valid prediction for snap_scaffold_7-snap.161-T1
Valid prediction for GlimmerHMM_glimmerT_16779-T1
Valid prediction for Augustus_model.g11204.t1
Valid prediction for GlimmerHMM_glimmerT_16766-T1
Valid prediction for Augustus_model.g11202.t1
Valid prediction for GlimmerHMM_glimmerT_16774-T1
Valid prediction for snap_scaffold_7-snap.164-T1
Valid prediction for Augustus_model.g11194.t1
Valid prediction for snap_scaffold_7-snap.151-T1
Valid prediction for GlimmerHMM_glimmerT_16782-T1
Valid prediction for GlimmerHMM_glimmerT_16784-T1
Valid prediction for snap_scaffold_7-snap.152-T1
Valid prediction for Augustus_model.g11201.t1
Valid prediction for snap_scaffold_7-snap.156-T1
Valid prediction for snap_scaffold_7-snap.154-T1
Valid prediction for snap_scaffold_7-snap.145-T1
Valid prediction for pasa_asmbl_49556.p1
Valid prediction for snap_scaffold_7-snap.159-T1
Valid prediction for GlimmerHMM_glimmerT_16751-T1
Valid prediction for Augustus_model.g11197.t1
Valid prediction for snap_scaffold_7-snap.180-T1
Valid prediction for snap_scaffold_7-snap.148-T1
Valid prediction for GlimmerHMM_glimmerT_16781-T1
Valid prediction for GlimmerHMM_glimmerT_16760-T1
Valid prediction for snap_scaffold_7-snap.179-T1
Valid prediction for snap_scaffold_7-snap.144-T1
Valid prediction for GlimmerHMM_glimmerT_16761-T1
Valid prediction for HiQ_model.g11198.t1
Valid prediction for CodingQuarry_transcript_57422-T1
Valid prediction for snap_scaffold_7-snap.143-T1
Valid prediction for snap_scaffold_7-snap.157-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_7-snap.177-T1
Valid prediction for GlimmerHMM_glimmerT_16783-T1
Valid prediction for CodingQuarry_transcript_57425-T1
Valid prediction for GlimmerHMM_glimmerT_16755-T1
Valid prediction for GlimmerHMM_glimmerT_16750-T1
Valid prediction for GlimmerHMM_glimmerT_16756-T1
Valid prediction for GlimmerHMM_glimmerT_16752-T1
Valid prediction for snap_scaffold_7-snap.153-T1
Valid prediction for snap_scaffold_7-snap.165-T1
Valid prediction for snap_scaffold_7-snap.168-T1
Valid prediction for GlimmerHMM_glimmerT_16758-T1
Valid prediction for GlimmerHMM_glimmerT_16771-T1
Valid prediction for snap_scaffold_7-snap.174-T1
Valid prediction for GlimmerHMM_glimmerT_16776-T1
Valid prediction for GlimmerHMM_glimmerT_16763-T1
Valid prediction for snap_scaffold_7-snap.181-T1
Valid prediction for GlimmerHMM_glimmerT_16775-T1
Valid prediction for Augustus_model.g11196.t1
Valid prediction for snap_scaffold_7-snap.170-T1
Valid prediction for Augustus_model.g11195.t1
Valid prediction for snap_scaffold_7-snap.158-T1
Valid prediction for snap_scaffold_7-snap.147-T1
Valid prediction for HiQ_model.g11203.t1
Valid prediction for snap_scaffold_7-snap.178-T1
Valid prediction for Augustus_model.g11192.t1
Valid prediction for Augustus_model.g11200.t1
Valid prediction for snap_scaffold_7-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_16767-T1
Valid prediction for GlimmerHMM_glimmerT_16777-T1
Couldn't classify 22863, 23139
Couldn't classify 23315, 23658
Sorry, prediction CodingQuarry_transcript_57426-T1 fails validation.
(ATG)	 TC	20756-20945	GT	AGG
(TGC)	 AG	21595-21680	GT	AGG
(ATT)	 AG	21991-22119	GT	AGG
(ATC)	 AG	22863-23139	CT	CTC
(TGC)	 CT	23315-23658	TC	GAT
-recovered CodingQuarry_transcript_57426-T1, initial, 20756, 20945
-recovered CodingQuarry_transcript_57426-T1, internal, 21595, 21680
-recovered CodingQuarry_transcript_57426-T1, internal, 21991, 22119
Valid prediction for snap_scaffold_7-snap.163-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g11199.t1
Valid prediction for GlimmerHMM_glimmerT_16770-T1
Valid prediction for GlimmerHMM_glimmerT_16772-T1
Valid prediction for snap_scaffold_7-snap.139-T1
Valid prediction for GlimmerHMM_glimmerT_16764-T1
Valid prediction for GlimmerHMM_glimmerT_16769-T1
Couldn't classify 7825, 7920
Couldn't classify 15979, 16068
Sorry, prediction pasa_asmbl_50693.p1 fails validation.
(CTG)	 AG	7825-7920	GT	AGG
(GTG)	 AG	8957-9088	GT	AGG
(GGT)	 AG	9349-9558	GT	CTG
(ATC)	 AG	10004-10140	GT	AGG
(GAG)	 AG	11119-11172	GT	ATG
(GCC)	 AG	11350-11479	GT	AGG
(GTG)	 AG	12240-12321	GT	CTG
(GTG)	 AG	12627-12780	GT	CGG
(GAA)	 AG	13043-13112	GT	AGG
(AGT)	 AG	14783-14908	GT	AGG
(GGT)	 AG	15022-15174	GT	AGG
(GTG)	 AG	15612-15716	GT	GCG
(GAG)	 AG	15979-16068	TG	CAT
-recovered pasa_asmbl_50693.p1, internal, 7825, 7920
-recovered pasa_asmbl_50693.p1, internal, 8957, 9088
-recovered pasa_asmbl_50693.p1, internal, 9349, 9558
-recovered pasa_asmbl_50693.p1, internal, 10004, 10140
-recovered pasa_asmbl_50693.p1, internal, 11119, 11172
-recovered pasa_asmbl_50693.p1, internal, 11350, 11479
-recovered pasa_asmbl_50693.p1, internal, 12240, 12321
-recovered pasa_asmbl_50693.p1, internal, 12627, 12780
-recovered pasa_asmbl_50693.p1, internal, 13043, 13112
-recovered pasa_asmbl_50693.p1, internal, 14783, 14908
-recovered pasa_asmbl_50693.p1, internal, 15022, 15174
-recovered pasa_asmbl_50693.p1, internal, 15612, 15716
Valid prediction for snap_scaffold_7-snap.175-T1
Valid prediction for snap_scaffold_7-snap.166-T1
Valid prediction for snap_scaffold_7-snap.142-T1
Valid prediction for pasa_asmbl_50686.p1
Valid prediction for GlimmerHMM_glimmerT_16773-T1
Valid prediction for GlimmerHMM_glimmerT_16780-T1
Valid prediction for snap_scaffold_7-snap.150-T1
Valid prediction for snap_scaffold_7-snap.171-T1
Valid prediction for CodingQuarry_transcript_57427-T1
Valid prediction for Augustus_model.g11193.t1
Valid prediction for snap_scaffold_7-snap.160-T1
Sorry, intron length (5) is less than minimum required (10)
Couldn't classify 22863, 23021
Sorry, prediction pasa_asmbl_50691.p1 fails validation.
(ATG)	 TC	20756-20945	GT	AGG
(TGC)	 AG	21595-21680	GT	AGG
(ATT)	 AG	21991-22119	GT	AGG
(ATC)	 AG	22863-23021	TC	TAT
-recovered pasa_asmbl_50691.p1, initial, 20756, 20945
-recovered pasa_asmbl_50691.p1, internal, 21595, 21680
-recovered pasa_asmbl_50691.p1, internal, 21991, 22119
Valid prediction for snap_scaffold_7-snap.182-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13337, rend_intergenic: 8739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16341, rend_intergenic: 13740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19555, rend_intergenic: 16679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21543, rend_intergenic: 20110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41369, rend_intergenic: 30244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68446, rend_intergenic: 55509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87954, rend_intergenic: 73332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105832, rend_intergenic: 100066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109865, rend_intergenic: 107118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118946, rend_intergenic: 112101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119260, rend_intergenic: 118952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121752, rend_intergenic: 119312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124953, rend_intergenic: 122116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133598, rend_intergenic: 128346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161965, rend_intergenic: 161462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174273, rend_intergenic: 167600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187552, rend_intergenic: 179271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201994, rend_intergenic: 190690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 113968, rend_intergenic: 113965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209142
-exon list size: 366


building trellis

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29.3    
29.6    
29.9    
30.2    
30.4    
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32.3    
32.6    
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33.4    
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35.3    
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38.0    
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38.9    
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40.8    
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41.3    
41.6    
41.8    
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42.4    
42.7    
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43.2    
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44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
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48.4    
48.6    
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54.6    
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88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
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90.8    
91.0    
91.3    
91.6    
91.8    
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97.3    
97.6    
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98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 13337, rend_intergenic: 8739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16341, rend_intergenic: 13740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19555, rend_intergenic: 16679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21543, rend_intergenic: 20110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41369, rend_intergenic: 30244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68446, rend_intergenic: 55509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87954, rend_intergenic: 73332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105832, rend_intergenic: 100066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109865, rend_intergenic: 107118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118946, rend_intergenic: 112101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119260, rend_intergenic: 118952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121752, rend_intergenic: 119312  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124953, rend_intergenic: 122116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133598, rend_intergenic: 128346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161965, rend_intergenic: 161462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174273, rend_intergenic: 167600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187552, rend_intergenic: 179271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201994, rend_intergenic: 190690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 113968, rend_intergenic: 113965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11949
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support