-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_3115757-3315939

-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.g21416.t1
Valid prediction for GeneMark_model.54930_t
Valid prediction for snap_scaffold_13-snap.576-T1
Valid prediction for GeneMark_model.54918_t
Valid prediction for snap_scaffold_13-snap.591-T1
Valid prediction for snap_scaffold_13-snap.578-T1
Valid prediction for GeneMark_model.54944_t
Valid prediction for Augustus_model.g21430.t1
Valid prediction for HiQ_model.g21420.t1
Valid prediction for GlimmerHMM_glimmerT_32048-T1
Valid prediction for snap_scaffold_13-snap.582-T1
Valid prediction for Augustus_model.g21419.t1
Valid prediction for snap_scaffold_13-snap.587-T1
Valid prediction for snap_scaffold_13-snap.601-T1
Valid prediction for snap_scaffold_13-snap.589-T1
Valid prediction for GeneMark_model.54923_t
Valid prediction for pasa_asmbl_10651.p1
Valid prediction for Augustus_model.g21409.t1
Valid prediction for GlimmerHMM_glimmerT_32044-T1
Valid prediction for Augustus_model.g21422.t1
Valid prediction for pasa_asmbl_10661.p1
Valid prediction for GeneMark_model.54940_t
Valid prediction for GlimmerHMM_glimmerT_32052-T1
Valid prediction for GlimmerHMM_glimmerT_32055-T1
Valid prediction for GlimmerHMM_glimmerT_32046-T1
Valid prediction for CodingQuarry_transcript_12893-T1
Valid prediction for GlimmerHMM_glimmerT_32053-T1
Valid prediction for GlimmerHMM_glimmerT_32033-T1
Valid prediction for GlimmerHMM_glimmerT_32038-T1
Valid prediction for snap_scaffold_13-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_32026-T1
Valid prediction for snap_scaffold_13-snap.594-T1
Valid prediction for Augustus_model.g21417.t1
Valid prediction for CodingQuarry_transcript_12889-T1
Valid prediction for GlimmerHMM_glimmerT_32039-T1
Valid prediction for Augustus_model.g21428.t1
Valid prediction for GlimmerHMM_glimmerT_32023-T1
Valid prediction for GlimmerHMM_glimmerT_32034-T1
Valid prediction for GlimmerHMM_glimmerT_32032-T1
Valid prediction for pasa_asmbl_10658.p1
Valid prediction for snap_scaffold_13-snap.596-T1
Valid prediction for snap_scaffold_13-snap.590-T1
Valid prediction for GeneMark_model.54929_t
Valid prediction for snap_scaffold_13-snap.581-T1
Valid prediction for snap_scaffold_13-snap.593-T1
Couldn't classify 76576, 76576
Sorry, prediction CodingQuarry_transcript_12891-T1 fails validation.
(AGT)	 TT	76576-76576	GT	TAG
(TGT)	 AG	76695-76763	GT	GGG
(GTG)	 AG	76857-77045	GT	AGG
(TTC)	 AG	77125-77199	GT	TGG
(GCT)	 AG	77293-77416	GT	CGG
(GAA)	 AG	77649-77776	GT	ATG
(CAA)	 AG	77908-78034	GT	GGG
(AAT)	 AG	78157-78296	GT	AGG
(CTG)	 AG	78398-78527	GT	GGG
(ATT)	 AG	78642-78775	GT	CGG
(TCG)	 AG	78963-79089	GT	GGG
(ATT)	 AG	79166-79374	GT	AGG
(ATA)	 AG	79519-79586	TC	GAT
-recovered CodingQuarry_transcript_12891-T1, terminal, 79519, 79586
-recovered CodingQuarry_transcript_12891-T1, internal, 76695, 76763
-recovered CodingQuarry_transcript_12891-T1, internal, 76857, 77045
-recovered CodingQuarry_transcript_12891-T1, internal, 77125, 77199
-recovered CodingQuarry_transcript_12891-T1, internal, 77293, 77416
-recovered CodingQuarry_transcript_12891-T1, internal, 77649, 77776
-recovered CodingQuarry_transcript_12891-T1, internal, 77908, 78034
-recovered CodingQuarry_transcript_12891-T1, internal, 78157, 78296
-recovered CodingQuarry_transcript_12891-T1, internal, 78398, 78527
-recovered CodingQuarry_transcript_12891-T1, internal, 78642, 78775
-recovered CodingQuarry_transcript_12891-T1, internal, 78963, 79089
-recovered CodingQuarry_transcript_12891-T1, internal, 79166, 79374
Valid prediction for GlimmerHMM_glimmerT_32050-T1
Valid prediction for GeneMark_model.54922_t
Valid prediction for pasa_asmbl_10649.p1
Valid prediction for HiQ_model.g21415.t1
Valid prediction for HiQ_model.g21408.t1
Valid prediction for GeneMark_model.54920_t
Valid prediction for GlimmerHMM_glimmerT_32031-T1
Valid prediction for GlimmerHMM_glimmerT_32041-T1
Valid prediction for GlimmerHMM_glimmerT_32022-T1
Valid prediction for GlimmerHMM_glimmerT_32056-T1
Valid prediction for GlimmerHMM_glimmerT_32025-T1
Valid prediction for GlimmerHMM_glimmerT_32036-T1
Valid prediction for snap_scaffold_13-snap.606-T1
Valid prediction for HiQ_model.g21424.t1
Valid prediction for HiQ_model.g21426.t1
Couldn't classify 127004, 127046
Sorry, prediction pasa_asmbl_10653.p1 fails validation.
(TCA)	 TC	127004-127046	GT	AGG
(ATT)	 AG	128619-128790	GT	AGG
(TGG)	 AG	128990-129211	GT	AGG
(GGG)	 AG	129312-130175	GT	AGG
(TCA)	 AG	130258-130385	GT	TGG
(AGA)	 AG	130505-130672	GT	AGG
(GTG)	 AG	130782-130912	GT	AGG
(GTG)	 AG	131002-131139	GT	ATG
(TGT)	 AG	131509-131646	GA	GAG
-recovered pasa_asmbl_10653.p1, terminal, 131509, 131646
-recovered pasa_asmbl_10653.p1, internal, 128619, 128790
-recovered pasa_asmbl_10653.p1, internal, 128990, 129211
-recovered pasa_asmbl_10653.p1, internal, 129312, 130175
-recovered pasa_asmbl_10653.p1, internal, 130258, 130385
-recovered pasa_asmbl_10653.p1, internal, 130505, 130672
-recovered pasa_asmbl_10653.p1, internal, 130782, 130912
-recovered pasa_asmbl_10653.p1, internal, 131002, 131139
Valid prediction for GeneMark_model.54932_t
Valid prediction for Augustus_model.g21407.t1
Valid prediction for snap_scaffold_13-snap.604-T1
Valid prediction for snap_scaffold_13-snap.600-T1
Valid prediction for GeneMark_model.54933_t
Valid prediction for GeneMark_model.54942_t
Valid prediction for Augustus_model.g21406.t1
Valid prediction for GeneMark_model.54938_t
Valid prediction for GeneMark_model.54935_t
Valid prediction for GlimmerHMM_glimmerT_32035-T1
Valid prediction for GlimmerHMM_glimmerT_32054-T1
Valid prediction for HiQ_model.g21411.t1
Couldn't classify 29258, 29313
Sorry, prediction pasa_asmbl_10647.p1 fails validation.
(TGT)	 GC	29258-29313	GT	AGG
(TGG)	 AG	29397-29466	GT	AGG
(AGC)	 AG	29550-29684	GT	AGG
(TGT)	 AG	29866-29987	GT	ACG
(TGG)	 AG	30425-30503	GT	AGG
(GCT)	 AG	30621-30695	GT	AGG
(CCA)	 AG	30897-30980	TC	GAT
-recovered pasa_asmbl_10647.p1, terminal, 30897, 30980
-recovered pasa_asmbl_10647.p1, internal, 29397, 29466
-recovered pasa_asmbl_10647.p1, internal, 29550, 29684
-recovered pasa_asmbl_10647.p1, internal, 29866, 29987
-recovered pasa_asmbl_10647.p1, internal, 30425, 30503
-recovered pasa_asmbl_10647.p1, internal, 30621, 30695
Valid prediction for GlimmerHMM_glimmerT_32024-T1
Valid prediction for snap_scaffold_13-snap.598-T1
Valid prediction for CodingQuarry_transcript_12895-T1
Valid prediction for snap_scaffold_13-snap.588-T1
Valid prediction for GlimmerHMM_glimmerT_32042-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_13-snap.608-T1
Valid prediction for GeneMark_model.54939_t
Valid prediction for snap_scaffold_13-snap.586-T1
Valid prediction for HiQ_model.g21421.t1
Valid prediction for GlimmerHMM_glimmerT_32045-T1
Valid prediction for GeneMark_model.54925_t
Valid prediction for CodingQuarry_transcript_12894-T1
Valid prediction for Augustus_model.g21412.t1
Valid prediction for CodingQuarry_transcript_12892-T1
Valid prediction for GeneMark_model.54927_t
Valid prediction for snap_scaffold_13-snap.595-T1
Valid prediction for GlimmerHMM_glimmerT_32040-T1
Valid prediction for snap_scaffold_13-snap.580-T1
Valid prediction for pasa_asmbl_9481.p1
Valid prediction for GlimmerHMM_glimmerT_32049-T1
Valid prediction for GeneMark_model.54945_t
Valid prediction for Augustus_model.g21413.t1
Valid prediction for GeneMark_model.54917_t
Valid prediction for snap_scaffold_13-snap.597-T1
Valid prediction for snap_scaffold_13-snap.607-T1
Valid prediction for GlimmerHMM_glimmerT_32057-T1
Valid prediction for GeneMark_model.54937_t
Valid prediction for GlimmerHMM_glimmerT_32029-T1
Valid prediction for Augustus_model.g21418.t1
Valid prediction for GlimmerHMM_glimmerT_32051-T1
Couldn't classify 48682, 48879
Sorry, prediction pasa_asmbl_9484.p1 fails validation.
(CAA)	 GC	48682-48879	GT	AGG
(TCA)	 AG	49119-49228	GT	CAG
(CTA)	 AG	49475-49635	GT	CGG
(ACA)	 AG	49807-49953	GT	AGG
(CTC)	 AG	50088-50242	TG	GAT
-recovered pasa_asmbl_9484.p1, terminal, 50088, 50242
-recovered pasa_asmbl_9484.p1, internal, 49119, 49228
-recovered pasa_asmbl_9484.p1, internal, 49475, 49635
-recovered pasa_asmbl_9484.p1, internal, 49807, 49953
Valid prediction for snap_scaffold_13-snap.605-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g21425.t1
Valid prediction for CodingQuarry_transcript_12890-T1
Valid prediction for snap_scaffold_13-snap.592-T1
Valid prediction for GeneMark_model.54936_t
Valid prediction for GeneMark_model.54941_t
Valid prediction for GlimmerHMM_glimmerT_32037-T1
Valid prediction for GeneMark_model.54919_t
Valid prediction for GeneMark_model.54921_t
Valid prediction for snap_scaffold_13-snap.583-T1
Valid prediction for Augustus_model.g21410.t1
Valid prediction for HiQ_model.g21414.t1
Valid prediction for GlimmerHMM_glimmerT_32027-T1
Valid prediction for GeneMark_model.54926_t
Valid prediction for GlimmerHMM_glimmerT_32028-T1
Valid prediction for GeneMark_model.54934_t
Valid prediction for HiQ_model.g21427.t1
Valid prediction for GlimmerHMM_glimmerT_32058-T1
Valid prediction for Augustus_model.g21431.t1
Valid prediction for GlimmerHMM_glimmerT_32043-T1
Valid prediction for GeneMark_model.54928_t
Valid prediction for snap_scaffold_13-snap.602-T1
Valid prediction for GeneMark_model.54943_t
Valid prediction for Augustus_model.g21423.t1
Valid prediction for snap_scaffold_13-snap.603-T1
Valid prediction for pasa_asmbl_9483.p1
Valid prediction for pasa_asmbl_9486.p2
Valid prediction for snap_scaffold_13-snap.599-T1
Couldn't classify 32960, 33331
Sorry, prediction pasa_asmbl_9488.p1 fails validation.
(ATG)	 AA	32960-33331	AC	CCA
Valid prediction for CodingQuarry_transcript_12896-T1
Valid prediction for snap_scaffold_13-snap.585-T1
Valid prediction for GlimmerHMM_glimmerT_32030-T1
Valid prediction for GlimmerHMM_glimmerT_32047-T1
Valid prediction for Augustus_model.g21429.t1
Valid prediction for snap_scaffold_13-snap.577-T1
Valid prediction for GeneMark_model.54924_t
Valid prediction for GeneMark_model.54931_t
Valid prediction for snap_scaffold_13-snap.584-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17903, rend_intergenic: 16519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28160, rend_intergenic: 26789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178241, rend_intergenic: 175058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181814, rend_intergenic: 178384  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200183
-exon list size: 639


building trellis

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95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 17903, rend_intergenic: 16519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28160, rend_intergenic: 26789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178241, rend_intergenic: 175058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181814, rend_intergenic: 178384  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 - 12923
-exon list size: 27


building trellis

3.4    
6.9    
10.3    
13.8    
17.2    
20.7    
24.1    
27.6    
31.0    
34.5    
37.9    
41.4    
44.8    
48.3    
51.7    
55.2    
58.6    
62.1    
65.5    
69.0    
72.4    
75.9    
79.3    
82.8    
86.2    
89.7    
93.1    
96.6    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 12036
-exon list size: 26


building trellis

3.6    
7.1    
10.7    
14.3    
17.9    
21.4    
25.0    
28.6    
32.1    
35.7    
39.3    
42.9    
46.4    
50.0    
53.6    
57.1    
60.7    
64.3    
67.9    
71.4    
75.0    
78.6    
82.1    
85.7    
89.3    
92.9    
96.4    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 1 - 10145
-exon list size: 21


building trellis

4.3    
8.7    
13.0    
17.4    
21.7    
26.1    
30.4    
34.8    
39.1    
43.5    
47.8    
52.2    
56.5    
60.9    
65.2    
69.6    
73.9    
78.3    
82.6    
87.0    
91.3    
95.7    
-found 1 predictions from path traversal

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