-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_1554662-1769354

-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 GeneMark_model.5348_t
Valid prediction for GeneMark_model.5351_t
Valid prediction for GeneMark_model.5337_t
Valid prediction for snap_scaffold_2-snap.392-T1
Valid prediction for GeneMark_model.5320_t
Valid prediction for snap_scaffold_2-snap.381-T1
Valid prediction for Augustus_model.g2224.t1
Valid prediction for GeneMark_model.5327_t
Valid prediction for snap_scaffold_2-snap.358-T1
Valid prediction for Augustus_model.g2228.t1
Valid prediction for snap_scaffold_2-snap.360-T1
Valid prediction for snap_scaffold_2-snap.406-T1
Valid prediction for GlimmerHMM_glimmerT_3322-T1
Valid prediction for snap_scaffold_2-snap.385-T1
Valid prediction for snap_scaffold_2-snap.397-T1
Valid prediction for snap_scaffold_2-snap.404-T1
Valid prediction for snap_scaffold_2-snap.396-T1
Valid prediction for GeneMark_model.5354_t
Valid prediction for snap_scaffold_2-snap.389-T1
Valid prediction for pasa_asmbl_24237.p1
Valid prediction for GeneMark_model.5356_t
Valid prediction for snap_scaffold_2-snap.362-T1
Valid prediction for GlimmerHMM_glimmerT_3303-T1
Valid prediction for snap_scaffold_2-snap.379-T1
Valid prediction for snap_scaffold_2-snap.384-T1
Valid prediction for snap_scaffold_2-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_3320-T1
Valid prediction for snap_scaffold_2-snap.376-T1
Valid prediction for GeneMark_model.5358_t
Valid prediction for GeneMark_model.5339_t
Valid prediction for GeneMark_model.5344_t
Valid prediction for GeneMark_model.5335_t
Valid prediction for GeneMark_model.5319_t
Valid prediction for GeneMark_model.5359_t
Valid prediction for GeneMark_model.5321_t
Valid prediction for GlimmerHMM_glimmerT_3321-T1
Valid prediction for GlimmerHMM_glimmerT_3309-T1
Valid prediction for GeneMark_model.5346_t
Valid prediction for GlimmerHMM_glimmerT_3315-T1
Valid prediction for Augustus_model.g2231.t1
Valid prediction for Augustus_model.g2229.t1
Valid prediction for GlimmerHMM_glimmerT_3324-T1
Valid prediction for GeneMark_model.5326_t
Valid prediction for snap_scaffold_2-snap.388-T1
Valid prediction for snap_scaffold_2-snap.367-T1
Valid prediction for snap_scaffold_2-snap.383-T1
Valid prediction for GeneMark_model.5343_t
Valid prediction for GeneMark_model.5324_t
Valid prediction for snap_scaffold_2-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_3323-T1
Valid prediction for GlimmerHMM_glimmerT_3301-T1
Valid prediction for snap_scaffold_2-snap.370-T1
Valid prediction for snap_scaffold_2-snap.366-T1
Valid prediction for CodingQuarry_transcript_28403-T1
Valid prediction for GlimmerHMM_glimmerT_3308-T1
Valid prediction for snap_scaffold_2-snap.402-T1
Valid prediction for GlimmerHMM_glimmerT_3318-T1
Valid prediction for snap_scaffold_2-snap.399-T1
Valid prediction for GlimmerHMM_glimmerT_3307-T1
Valid prediction for CodingQuarry_transcript_28404-T1
Valid prediction for Augustus_model.g2223.t1
Valid prediction for GeneMark_model.5329_t
Valid prediction for GeneMark_model.5322_t
Valid prediction for GlimmerHMM_glimmerT_3316-T1
Valid prediction for GlimmerHMM_glimmerT_3319-T1
Valid prediction for Augustus_model.g2225.t1
Valid prediction for Augustus_model.g2230.t1
Valid prediction for GeneMark_model.5345_t
Valid prediction for snap_scaffold_2-snap.364-T1
Valid prediction for Augustus_model.g2227.t1
Valid prediction for GlimmerHMM_glimmerT_3326-T1
Valid prediction for HiQ_model.g2219.t1
Valid prediction for CodingQuarry_transcript_28402-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: -)Couldn't classify 116921, 117066
Couldn't classify 117493, 117661
Sorry, prediction pasa_asmbl_23966.p3 fails validation.
(GGT)	 GG	116921-117066	GT	AAG
(GTT)	 AG	117493-117661	AA	CCA
Valid prediction for GeneMark_model.5349_t
Valid prediction for GeneMark_model.5328_t
Valid prediction for GlimmerHMM_glimmerT_3314-T1
Valid prediction for Augustus_model.g2218.t1
Valid prediction for GeneMark_model.5318_t
Valid prediction for snap_scaffold_2-snap.365-T1
Valid prediction for snap_scaffold_2-snap.359-T1
Valid prediction for GeneMark_model.5334_t
Valid prediction for snap_scaffold_2-snap.372-T1
Valid prediction for GlimmerHMM_glimmerT_3305-T1
Valid prediction for GeneMark_model.5357_t
Valid prediction for snap_scaffold_2-snap.369-T1
Valid prediction for snap_scaffold_2-snap.377-T1
Valid prediction for Augustus_model.g2226.t1
Valid prediction for GeneMark_model.5342_t
Valid prediction for GeneMark_model.5325_t
Valid prediction for snap_scaffold_2-snap.373-T1
Valid prediction for GeneMark_model.5330_t
Valid prediction for snap_scaffold_2-snap.395-T1
Valid prediction for snap_scaffold_2-snap.386-T1
Valid prediction for snap_scaffold_2-snap.394-T1
Couldn't classify 119585, 119914
Couldn't classify 125526, 125576
Sorry, prediction pasa_asmbl_22890.p1 fails validation.
(CGG)	 TC	119585-119914	GT	AGG
(GCA)	 AG	120094-120246	GT	AGG
(CTG)	 AG	120843-121018	GT	AGG
(GTT)	 AG	121276-121369	GT	GGG
(GTC)	 AG	122857-122934	GT	AGG
(GTG)	 AG	123177-123311	GT	AGG
(ATG)	 AG	123595-123707	GT	AGG
(GTT)	 AG	124281-124422	GT	AGG
(GTG)	 AG	124982-125272	GT	AGG
(ACC)	 AG	125526-125576	GC	AGG
-recovered pasa_asmbl_22890.p1, initial, 123595, 123707
-recovered pasa_asmbl_22890.p1, internal, 120094, 120246
-recovered pasa_asmbl_22890.p1, internal, 120843, 121018
-recovered pasa_asmbl_22890.p1, internal, 121276, 121369
-recovered pasa_asmbl_22890.p1, internal, 122857, 122934
-recovered pasa_asmbl_22890.p1, internal, 123177, 123311
-recovered pasa_asmbl_22890.p1, internal, 123595, 123707
-recovered pasa_asmbl_22890.p1, internal, 124281, 124422
-recovered pasa_asmbl_22890.p1, internal, 124982, 125272
-recovered pasa_asmbl_22890.p1, internal, 125526, 125576
Valid prediction for snap_scaffold_2-snap.361-T1
Valid prediction for GlimmerHMM_glimmerT_3312-T1
Valid prediction for GlimmerHMM_glimmerT_3300-T1
Valid prediction for GeneMark_model.5323_t
Valid prediction for HiQ_model.g2220.t1
Valid prediction for GeneMark_model.5347_t
Valid prediction for snap_scaffold_2-snap.401-T1
Valid prediction for GlimmerHMM_glimmerT_3310-T1
Valid prediction for snap_scaffold_2-snap.371-T1
Valid prediction for GlimmerHMM_glimmerT_3306-T1
Valid prediction for snap_scaffold_2-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_3317-T1
Couldn't classify 167176, 167667
Sorry, prediction pasa_asmbl_22881.p1 fails validation.
(ATG)	 AG	167176-167667	TT	GCT
Valid prediction for Augustus_model.g2221.t1
Valid prediction for GlimmerHMM_glimmerT_3304-T1
Valid prediction for GeneMark_model.5336_t
Valid prediction for snap_scaffold_2-snap.374-T1
Valid prediction for GeneMark_model.5353_t
Valid prediction for snap_scaffold_2-snap.387-T1
Valid prediction for GeneMark_model.5341_t
Valid prediction for snap_scaffold_2-snap.368-T1
Valid prediction for Augustus_model.g2222.t1
Valid prediction for GeneMark_model.5355_t
Valid prediction for snap_scaffold_2-snap.400-T1
Valid prediction for GlimmerHMM_glimmerT_3313-T1
Valid prediction for GlimmerHMM_glimmerT_3302-T1
Couldn't classify 151275, 152158
Couldn't classify 153533, 155581
Sorry, prediction pasa_asmbl_22885.p1 fails validation.
(AGC)	 AC	151275-152158	GT	AGG
(TCA)	 AG	152476-152528	GT	AGG
(GTG)	 AG	152616-152698	GT	GGG
(GTG)	 AG	153533-155581	GA	TGG
-recovered pasa_asmbl_22885.p1, internal, 152476, 152528
-recovered pasa_asmbl_22885.p1, internal, 152616, 152698
Valid prediction for GlimmerHMM_glimmerT_3327-T1
Couldn't classify 168268, 168312
Couldn't classify 169361, 169485
Sorry, prediction pasa_asmbl_22880.p1 fails validation.
(TTC)	 TC	168268-168312	GT	AGG
(TCT)	 AG	168411-168553	GT	AGG
(CCC)	 AG	168828-169102	GT	AGG
(GAG)	 AG	169361-169485	GG	GGG
-recovered pasa_asmbl_22880.p1, internal, 168411, 168553
-recovered pasa_asmbl_22880.p1, internal, 168828, 169102
Valid prediction for snap_scaffold_2-snap.393-T1
Valid prediction for GlimmerHMM_glimmerT_3325-T1
Valid prediction for snap_scaffold_2-snap.398-T1
Valid prediction for GeneMark_model.5350_t
Valid prediction for pasa_asmbl_22884.p1
Valid prediction for snap_scaffold_2-snap.380-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.403-T1
Valid prediction for GeneMark_model.5352_t
Valid prediction for snap_scaffold_2-snap.382-T1
Valid prediction for GeneMark_model.5340_t
Valid prediction for GeneMark_model.5338_t
Valid prediction for snap_scaffold_2-snap.378-T1
Valid prediction for snap_scaffold_2-snap.375-T1
Valid prediction for GlimmerHMM_glimmerT_3311-T1
Valid prediction for GeneMark_model.5332_t
Valid prediction for pasa_asmbl_22891.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9053, rend_intergenic: 3836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21990, rend_intergenic: 16029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27054, rend_intergenic: 25436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52214, rend_intergenic: 50019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69300, rend_intergenic: 67535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76290, rend_intergenic: 70247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89291, rend_intergenic: 85949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91872, rend_intergenic: 89413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92899, rend_intergenic: 91986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110721, rend_intergenic: 93579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143469, rend_intergenic: 141690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179689, rend_intergenic: 177234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192755, rend_intergenic: 180039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198687, rend_intergenic: 192853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214693
-exon list size: 641


building trellis

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99.2    
99.4    
99.5    
99.7    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 9053, rend_intergenic: 3836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21990, rend_intergenic: 16029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27054, rend_intergenic: 25436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52214, rend_intergenic: 50019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69300, rend_intergenic: 67535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76290, rend_intergenic: 70247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89291, rend_intergenic: 85949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91872, rend_intergenic: 89413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92899, rend_intergenic: 91986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110721, rend_intergenic: 93579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143469, rend_intergenic: 141690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179689, rend_intergenic: 177234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192755, rend_intergenic: 180039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198687, rend_intergenic: 192853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 20547
-exon list size: 59


building trellis

1.6    
3.3    
4.9    
6.6    
8.2    
9.8    
11.5    
13.1    
14.8    
16.4    
18.0    
19.7    
21.3    
23.0    
24.6    
26.2    
27.9    
29.5    
31.1    
32.8    
34.4    
36.1    
37.7    
39.3    
41.0    
42.6    
44.3    
45.9    
47.5    
49.2    
50.8    
52.5    
54.1    
55.7    
57.4    
59.0    
60.7    
62.3    
63.9    
65.6    
67.2    
68.9    
70.5    
72.1    
73.8    
75.4    
77.0    
78.7    
80.3    
82.0    
83.6    
85.2    
86.9    
88.5    
90.2    
91.8    
93.4    
95.1    
96.7    
98.4    
-found 3 predictions from path traversal

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