-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_16020423-16186226

-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: +)Couldn't classify 28265, 28400
Sorry, prediction pasa_asmbl_47906.p1 fails validation.
(GAG)	 CA	28265-28400	GT	CAG
(AAA)	 AG	28547-28652	GT	AAG
(GGT)	 AG	29012-29189	GA	GAG
-recovered pasa_asmbl_47906.p1, terminal, 29012, 29189
-recovered pasa_asmbl_47906.p1, internal, 28547, 28652
Valid prediction for snap_scaffold_6-snap.3382-T1
Valid prediction for snap_scaffold_6-snap.3420-T1
Valid prediction for snap_scaffold_6-snap.3419-T1
Valid prediction for GlimmerHMM_glimmerT_16227-T1
Valid prediction for snap_scaffold_6-snap.3413-T1
Valid prediction for GlimmerHMM_glimmerT_16200-T1
Valid prediction for Augustus_model.g10876.t1
Valid prediction for snap_scaffold_6-snap.3386-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16208-T1
Valid prediction for Augustus_model.g10889.t1
Valid prediction for snap_scaffold_6-snap.3418-T1
Valid prediction for snap_scaffold_6-snap.3401-T1
Valid prediction for snap_scaffold_6-snap.3416-T1
Valid prediction for GlimmerHMM_glimmerT_16218-T1
Valid prediction for GlimmerHMM_glimmerT_16225-T1
Valid prediction for GlimmerHMM_glimmerT_16201-T1
Valid prediction for GlimmerHMM_glimmerT_16219-T1
Valid prediction for GlimmerHMM_glimmerT_16199-T1
Couldn't classify 30534, 30729
Sorry, prediction pasa_asmbl_47685.p1 fails validation.
(AAA)	 TA	30534-30729	GT	GTG
(TCA)	 AG	31158-31264	TG	AAT
-recovered pasa_asmbl_47685.p1, terminal, 31158, 31264
Valid prediction for GlimmerHMM_glimmerT_16210-T1
Valid prediction for snap_scaffold_6-snap.3390-T1
Valid prediction for snap_scaffold_6-snap.3410-T1
Valid prediction for snap_scaffold_6-snap.3391-T1
Valid prediction for GlimmerHMM_glimmerT_16207-T1
Valid prediction for Augustus_model.g10877.t1
Valid prediction for GlimmerHMM_glimmerT_16214-T1
Valid prediction for snap_scaffold_6-snap.3397-T1
Valid prediction for snap_scaffold_6-snap.3411-T1
Valid prediction for GlimmerHMM_glimmerT_16209-T1
Valid prediction for snap_scaffold_6-snap.3395-T1
Valid prediction for Augustus_model.g10887.t1
Valid prediction for GlimmerHMM_glimmerT_16197-T1
Couldn't classify 22698, 22769
Couldn't classify 27710, 27789
Sorry, prediction pasa_asmbl_47986.p1 fails validation.
(CTG)	 CA	22698-22769	GT	CGG
(AAG)	 AG	23520-23600	GT	CGG
(AGC)	 AG	24681-24748	GT	AGG
(GAA)	 AG	25882-25969	GT	CTG
(AAC)	 AG	26237-26338	GT	AGG
(CTG)	 AG	26472-26612	GT	AGG
(GAG)	 AG	26886-26973	GT	CTG
(CCA)	 AG	27092-27214	GT	AGG
(ATA)	 AG	27469-27567	GT	AGG
(GTC)	 AG	27710-27789	GT	ACG
-recovered pasa_asmbl_47986.p1, internal, 23520, 23600
-recovered pasa_asmbl_47986.p1, internal, 24681, 24748
-recovered pasa_asmbl_47986.p1, internal, 25882, 25969
-recovered pasa_asmbl_47986.p1, internal, 26237, 26338
-recovered pasa_asmbl_47986.p1, internal, 26472, 26612
-recovered pasa_asmbl_47986.p1, internal, 26886, 26973
-recovered pasa_asmbl_47986.p1, internal, 27092, 27214
-recovered pasa_asmbl_47986.p1, internal, 27469, 27567
-recovered pasa_asmbl_47986.p1, internal, 27710, 27789
Couldn't classify 21355, 21795
Couldn't classify 21909, 22046
Sorry, prediction pasa_asmbl_47684.p1 fails validation.
(CCC)	 CC	21355-21795	GT	CGG
(CCC)	 AG	21909-22046	CT	CTC
Valid prediction for snap_scaffold_6-snap.3388-T1
Valid prediction for Augustus_model.g10875.t1
Valid prediction for Augustus_model.g10883.t1
Valid prediction for GlimmerHMM_glimmerT_16217-T1
Valid prediction for snap_scaffold_6-snap.3393-T1
Valid prediction for GlimmerHMM_glimmerT_16226-T1
Valid prediction for snap_scaffold_6-snap.3408-T1
Valid prediction for GlimmerHMM_glimmerT_16223-T1
Valid prediction for HiQ_model.g10878.t1
Valid prediction for snap_scaffold_6-snap.3384-T1
Valid prediction for GlimmerHMM_glimmerT_16211-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 GlimmerHMM_glimmerT_16212-T1
Valid prediction for GlimmerHMM_glimmerT_16224-T1
Valid prediction for snap_scaffold_6-snap.3387-T1
Valid prediction for snap_scaffold_6-snap.3407-T1
Valid prediction for GlimmerHMM_glimmerT_16203-T1
Valid prediction for GlimmerHMM_glimmerT_16215-T1
Valid prediction for snap_scaffold_6-snap.3421-T1
Valid prediction for snap_scaffold_6-snap.3396-T1
Valid prediction for snap_scaffold_6-snap.3403-T1
Valid prediction for snap_scaffold_6-snap.3402-T1
Valid prediction for GlimmerHMM_glimmerT_16221-T1
Valid prediction for Augustus_model.g10882.t1
Valid prediction for snap_scaffold_6-snap.3406-T1
Valid prediction for Augustus_model.g10888.t1
Valid prediction for snap_scaffold_6-snap.3415-T1
Valid prediction for snap_scaffold_6-snap.3417-T1
Valid prediction for snap_scaffold_6-snap.3381-T1
Valid prediction for snap_scaffold_6-snap.3389-T1
Valid prediction for snap_scaffold_6-snap.3412-T1
Valid prediction for Augustus_model.g10879.t1
Valid prediction for snap_scaffold_6-snap.3398-T1
Valid prediction for GlimmerHMM_glimmerT_16205-T1
Valid prediction for snap_scaffold_6-snap.3385-T1
Valid prediction for GlimmerHMM_glimmerT_16220-T1
Valid prediction for snap_scaffold_6-snap.3405-T1
Valid prediction for GlimmerHMM_glimmerT_16213-T1
Valid prediction for snap_scaffold_6-snap.3394-T1
Valid prediction for GlimmerHMM_glimmerT_16216-T1
Valid prediction for Augustus_model.g10880.t1
Valid prediction for GlimmerHMM_glimmerT_16206-T1
Valid prediction for Augustus_model.g10885.t1
Valid prediction for snap_scaffold_6-snap.3383-T1
Valid prediction for Augustus_model.g10884.t1
Valid prediction for GlimmerHMM_glimmerT_16196-T1
Valid prediction for Augustus_model.g10881.t1
Valid prediction for GlimmerHMM_glimmerT_16222-T1
Valid prediction for snap_scaffold_6-snap.3409-T1
Valid prediction for snap_scaffold_6-snap.3392-T1
Valid prediction for GlimmerHMM_glimmerT_16202-T1
Valid prediction for snap_scaffold_6-snap.3400-T1
Valid prediction for Augustus_model.g10886.t1
Couldn't classify 106271, 106446
Sorry, prediction pasa_asmbl_49385.p1 fails validation.
(CAG)	 CT	106271-106446	GT	ACG
(GTA)	 AG	107832-108052	GT	AGG
(GTA)	 AG	109029-109273	GT	GAG
add_exon() Sorry, pasa_asmbl_49385.p1 107832-108052-terminal-2 is invalid.
-recovered pasa_asmbl_49385.p1, terminal, 107832, 108052
-recovered pasa_asmbl_49385.p1, terminal, 109029, 109273
-recovered pasa_asmbl_49385.p1, internal, 107832, 108052
-recovered pasa_asmbl_49385.p1, internal, 109029, 109273
Valid prediction for GlimmerHMM_glimmerT_16198-T1
Valid prediction for snap_scaffold_6-snap.3404-T1
Couldn't classify 129613, 130329
Sorry, prediction pasa_asmbl_49097.p1 fails validation.
(TCC)	 CC	129613-130329	GT	CGG
(GTC)	 AG	130756-130849	GT	GGG
(AGA)	 AG	131095-131647	GT	AGG
(ACA)	 AG	131905-132110	GT	AGG
(GTA)	 AG	132357-132451	GT	TGG
(TGA)	 AG	132606-132608	GA	GAG
-recovered pasa_asmbl_49097.p1, terminal, 132606, 132608
-recovered pasa_asmbl_49097.p1, internal, 130756, 130849
-recovered pasa_asmbl_49097.p1, internal, 131095, 131647
-recovered pasa_asmbl_49097.p1, internal, 131905, 132110
-recovered pasa_asmbl_49097.p1, internal, 132357, 132451
Couldn't classify 82282, 82851
Sorry, prediction pasa_asmbl_49103.p1 fails validation.
(ATG)	 AT	82282-82851	CT	GCC
Valid prediction for snap_scaffold_6-snap.3414-T1
Valid prediction for snap_scaffold_6-snap.3399-T1
Couldn't classify 120211, 120299
Couldn't classify 126927, 127046
Sorry, prediction pasa_asmbl_49099.p1 fails validation.
(GGC)	 AG	120211-120299	GT	AGG
(GTA)	 AG	121820-122039	GT	TGG
(GTG)	 AG	122479-122875	GT	CTG
(CGG)	 AG	124175-124383	GT	CGG
(AGC)	 AG	124833-124906	GT	AGG
(CTA)	 AG	125812-125947	GT	GGG
(TTA)	 AG	126295-126411	GT	TGG
(GTG)	 AG	126927-127046	CT	CCC
-recovered pasa_asmbl_49099.p1, internal, 120211, 120299
-recovered pasa_asmbl_49099.p1, internal, 121820, 122039
-recovered pasa_asmbl_49099.p1, internal, 122479, 122875
-recovered pasa_asmbl_49099.p1, internal, 124175, 124383
-recovered pasa_asmbl_49099.p1, internal, 124833, 124906
-recovered pasa_asmbl_49099.p1, internal, 125812, 125947
-recovered pasa_asmbl_49099.p1, internal, 126295, 126411
Valid prediction for GlimmerHMM_glimmerT_16204-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7640, rend_intergenic: 6318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10634, rend_intergenic: 7871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29189, rend_intergenic: 26197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42524, rend_intergenic: 35951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43320, rend_intergenic: 42871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46249, rend_intergenic: 43821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51043, rend_intergenic: 46542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56736, rend_intergenic: 52849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61889, rend_intergenic: 60453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69468, rend_intergenic: 62604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76800, rend_intergenic: 74982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98062, rend_intergenic: 97298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104113, rend_intergenic: 98763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108592, rend_intergenic: 104194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113930, rend_intergenic: 109111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116332, rend_intergenic: 114206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117273, rend_intergenic: 116432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127188, rend_intergenic: 123528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143684, rend_intergenic: 129898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164830, rend_intergenic: 144775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165804
-exon list size: 346


building trellis

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31.0    
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31.6    
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48.9    
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97.1    
97.4    
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98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 7640, rend_intergenic: 6318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10634, rend_intergenic: 7871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29189, rend_intergenic: 26197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42524, rend_intergenic: 35951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43320, rend_intergenic: 42871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46249, rend_intergenic: 43821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51043, rend_intergenic: 46542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56736, rend_intergenic: 52849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61889, rend_intergenic: 60453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69468, rend_intergenic: 62604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76800, rend_intergenic: 74982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98062, rend_intergenic: 97298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104113, rend_intergenic: 98763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108592, rend_intergenic: 104194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113930, rend_intergenic: 109111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116332, rend_intergenic: 114206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117273, rend_intergenic: 116432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127188, rend_intergenic: 123528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143684, rend_intergenic: 129898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164830, rend_intergenic: 144775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support