-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_13400124-13597728

-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.17433_t
Valid prediction for GeneMark_model.17445_t
Valid prediction for GlimmerHMM_glimmerT_10713-T1
Valid prediction for GeneMark_model.17457_t
Valid prediction for CodingQuarry_transcript_49088-T1
Valid prediction for snap_scaffold_4-snap.2786-T1
Valid prediction for GeneMark_model.17430_t
Valid prediction for HiQ_model.g7050.t1
Valid prediction for Augustus_model.g7054.t1
Valid prediction for GlimmerHMM_glimmerT_10726-T1
Valid prediction for snap_scaffold_4-snap.2802-T1
Valid prediction for GlimmerHMM_glimmerT_10721-T1
Valid prediction for GeneMark_model.17450_t
Valid prediction for pasa_asmbl_43136.p1
Valid prediction for pasa_asmbl_43121.p1
Valid prediction for pasa_asmbl_43129.p1
Valid prediction for HiQ_model.g7060.t1
Valid prediction for CodingQuarry_transcript_49086-T1
Valid prediction for GeneMark_model.17442_t
Valid prediction for snap_scaffold_4-snap.2796-T1
Valid prediction for snap_scaffold_4-snap.2783-T1
Valid prediction for snap_scaffold_4-snap.2795-T1
Valid prediction for GeneMark_model.17438_t
Valid prediction for pasa_asmbl_43126.p1
Valid prediction for HiQ_model.g7052.t1
Valid prediction for GlimmerHMM_glimmerT_10720-T1
Valid prediction for snap_scaffold_4-snap.2785-T1
Valid prediction for GlimmerHMM_glimmerT_10715-T1
Valid prediction for GeneMark_model.17432_t
Valid prediction for GlimmerHMM_glimmerT_10717-T1
Valid prediction for GeneMark_model.17458_t
Valid prediction for GlimmerHMM_glimmerT_10724-T1
Valid prediction for CodingQuarry_transcript_49093-T1
Valid prediction for GeneMark_model.17439_t
Valid prediction for GlimmerHMM_glimmerT_10719-T1
Valid prediction for CodingQuarry_transcript_49092-T1
Valid prediction for CodingQuarry_transcript_49089-T1
Valid prediction for snap_scaffold_4-snap.2788-T1
Couldn't classify 132742, 132919
Sorry, prediction pasa_asmbl_43132.p1 fails validation.
(ATG)	 AT	128851-128915	GT	AGG
(GGC)	 AG	129643-129741	GT	AAG
(GCT)	 AG	130133-130256	GT	AGG
(CAC)	 AG	130497-130653	GT	CGG
(GTC)	 AG	130901-130990	GT	AGG
(CGC)	 AG	131223-131312	GT	AGG
(GAA)	 AG	131678-131756	GT	TGG
(TAT)	 AG	132063-132188	GT	AGG
(GTC)	 AG	132471-132539	GC	AGG
(CCT)	 AG	132742-132919	GT	TGG
-recovered pasa_asmbl_43132.p1, initial, 128851, 128915
-recovered pasa_asmbl_43132.p1, terminal, 130901, 130990
-recovered pasa_asmbl_43132.p1, terminal, 131223, 131312
-recovered pasa_asmbl_43132.p1, internal, 129643, 129741
-recovered pasa_asmbl_43132.p1, internal, 130133, 130256
-recovered pasa_asmbl_43132.p1, internal, 130497, 130653
-recovered pasa_asmbl_43132.p1, internal, 130901, 130990
-recovered pasa_asmbl_43132.p1, internal, 131223, 131312
-recovered pasa_asmbl_43132.p1, internal, 131678, 131756
-recovered pasa_asmbl_43132.p1, internal, 132063, 132188
-recovered pasa_asmbl_43132.p1, internal, 132471, 132539
-recovered pasa_asmbl_43132.p1, internal, 132742, 132919
Valid prediction for GeneMark_model.17452_t
Valid prediction for HiQ_model.g7056.t1
Valid prediction for snap_scaffold_4-snap.2797-T1
Valid prediction for CodingQuarry_transcript_49087-T1
Valid prediction for GeneMark_model.17436_t
Valid prediction for CodingQuarry_transcript_49090-T1
Valid prediction for snap_scaffold_4-snap.2790-T1
Valid prediction for CodingQuarry_transcript_49085-T1
Valid prediction for Augustus_model.g7059.t1
Valid prediction for pasa_asmbl_43133.p1
Valid prediction for snap_scaffold_4-snap.2798-T1
Valid prediction for GeneMark_model.17453_t
Valid prediction for snap_scaffold_4-snap.2801-T1
Valid prediction for snap_scaffold_4-snap.2794-T1
Valid prediction for GeneMark_model.17447_t
Valid prediction for GlimmerHMM_glimmerT_10722-T1
Valid prediction for snap_scaffold_4-snap.2789-T1
Valid prediction for GlimmerHMM_glimmerT_10718-T1
Couldn't classify 144625, 144918
Sorry, prediction pasa_asmbl_43135.p1 fails validation.
(GTG)	 CA	144625-144918	GT	AGG
(GTT)	 AG	145303-145430	GT	TGG
(GTA)	 AG	145780-145985	GT	GGG
(GTT)	 AG	146634-146760	GT	AGG
(ATT)	 AG	147380-147476	GT	GAG
(TTG)	 AG	147741-147885	GT	TGG
(GTC)	 AG	148199-148464	AG	GAA
-recovered pasa_asmbl_43135.p1, terminal, 148199, 148464
-recovered pasa_asmbl_43135.p1, internal, 145303, 145430
-recovered pasa_asmbl_43135.p1, internal, 145780, 145985
-recovered pasa_asmbl_43135.p1, internal, 146634, 146760
-recovered pasa_asmbl_43135.p1, internal, 147380, 147476
-recovered pasa_asmbl_43135.p1, internal, 147741, 147885
Valid prediction for HiQ_model.g7057.t1
Valid prediction for Augustus_model.g7055.t1
Valid prediction for GeneMark_model.17456_t

-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_10727-T1
Valid prediction for snap_scaffold_4-snap.2787-T1
Couldn't classify 193927, 194064
Couldn't classify 194545, 194696
Sorry, prediction pasa_asmbl_41738.p1 fails validation.
(GAT)	 AG	193927-194064	GT	AGG
(CCC)	 AG	194287-194434	GT	CGG
(CTG)	 AG	194545-194696	CC	AGC
-recovered pasa_asmbl_41738.p1, internal, 193927, 194064
-recovered pasa_asmbl_41738.p1, internal, 194287, 194434
Valid prediction for GlimmerHMM_glimmerT_10714-T1
Valid prediction for GeneMark_model.17451_t
Valid prediction for HiQ_model.g7049.t1
Valid prediction for GeneMark_model.17448_t
Valid prediction for snap_scaffold_4-snap.2782-T1
Valid prediction for GlimmerHMM_glimmerT_10716-T1
Valid prediction for snap_scaffold_4-snap.2800-T1
Valid prediction for GeneMark_model.17434_t
Valid prediction for snap_scaffold_4-snap.2784-T1
Valid prediction for Augustus_model.g7051.t1
Valid prediction for CodingQuarry_transcript_49091-T1
Valid prediction for snap_scaffold_4-snap.2799-T1
Valid prediction for GeneMark_model.17431_t
Valid prediction for GeneMark_model.17441_t
Valid prediction for GeneMark_model.17440_t
Valid prediction for GeneMark_model.17437_t
Valid prediction for pasa_asmbl_42388.p1
Valid prediction for GeneMark_model.17446_t
Valid prediction for GlimmerHMM_glimmerT_10712-T1
Couldn't classify 189033, 189155
Sorry, prediction pasa_asmbl_41740.p1 fails validation.
(ATG)	 AA	185847-186158	GT	GGG
(CTT)	 AG	186442-186631	GT	TGG
(GTG)	 AG	186722-186836	GT	AGG
(TGC)	 AG	186984-187114	GT	AGG
(GGG)	 AG	187266-187471	GT	AGG
(GCA)	 AG	187631-187828	GT	GCG
(ATG)	 AG	188001-188129	GT	AGG
(GTT)	 AG	188221-188421	GT	AGG
(AAT)	 AG	188573-188746	GT	AGG
(ATC)	 AG	189033-189155	AA	ACA
-recovered pasa_asmbl_41740.p1, initial, 185847, 186158
-recovered pasa_asmbl_41740.p1, initial, 188001, 188129
-recovered pasa_asmbl_41740.p1, internal, 186442, 186631
-recovered pasa_asmbl_41740.p1, internal, 186722, 186836
-recovered pasa_asmbl_41740.p1, internal, 186984, 187114
-recovered pasa_asmbl_41740.p1, internal, 187266, 187471
-recovered pasa_asmbl_41740.p1, internal, 187631, 187828
-recovered pasa_asmbl_41740.p1, internal, 188001, 188129
-recovered pasa_asmbl_41740.p1, internal, 188221, 188421
-recovered pasa_asmbl_41740.p1, internal, 188573, 188746
Valid prediction for GeneMark_model.17455_t
Valid prediction for GlimmerHMM_glimmerT_10723-T1
Valid prediction for Augustus_model.g7058.t1
Valid prediction for snap_scaffold_4-snap.2792-T1
Valid prediction for GeneMark_model.17443_t
Valid prediction for GeneMark_model.17454_t
Valid prediction for HiQ_model.g7053.t1
Valid prediction for GeneMark_model.17435_t
Valid prediction for snap_scaffold_4-snap.2793-T1
Valid prediction for GeneMark_model.17429_t
Valid prediction for GeneMark_model.17444_t
Valid prediction for snap_scaffold_4-snap.2791-T1
Couldn't classify 189274, 189405
Sorry, prediction pasa_asmbl_41739.p1 fails validation.
(GGG)	 CG	189274-189405	GT	TGG
(GTG)	 AG	189539-189772	AC	AGA
-recovered pasa_asmbl_41739.p1, terminal, 189539, 189772
Couldn't classify 157830, 157904
Sorry, prediction pasa_asmbl_41742.p1 fails validation.
(TTG)	 TG	157830-157904	GT	TGG
(TCC)	 AG	158017-158183	GT	AGG
(ATT)	 AG	158323-158379	GT	AGG
(AGC)	 AG	158485-158678	GT	AGG
(ATA)	 AG	158970-159079	GT	CTG
(GAG)	 AG	159246-159461	GT	AGG
(GAG)	 AG	159911-160014	GT	AAG
(GGA)	 AG	160148-160232	GT	AGG
(GAG)	 AG	160903-160962	GT	GGG
(TCC)	 AG	161365-161451	GT	AGG
(AAT)	 AG	161573-161605	GT	GTG
(GAG)	 AG	161845-161966	GC	AGG
(TTA)	 AG	162085-162174	GT	GAG
(CTT)	 AG	162297-162390	GT	AGG
(CAT)	 AG	162682-162912	GT	TGG
(GTG)	 AG	163122-163236	GT	AGG
(AGT)	 AG	163336-163517	CA	GAC
-recovered pasa_asmbl_41742.p1, terminal, 163336, 163517
-recovered pasa_asmbl_41742.p1, internal, 158017, 158183
-recovered pasa_asmbl_41742.p1, internal, 158323, 158379
-recovered pasa_asmbl_41742.p1, internal, 158485, 158678
-recovered pasa_asmbl_41742.p1, internal, 158970, 159079
-recovered pasa_asmbl_41742.p1, internal, 159246, 159461
-recovered pasa_asmbl_41742.p1, internal, 159911, 160014
-recovered pasa_asmbl_41742.p1, internal, 160148, 160232
-recovered pasa_asmbl_41742.p1, internal, 160903, 160962
-recovered pasa_asmbl_41742.p1, internal, 161365, 161451
-recovered pasa_asmbl_41742.p1, internal, 161573, 161605
-recovered pasa_asmbl_41742.p1, internal, 161845, 161966
-recovered pasa_asmbl_41742.p1, internal, 162085, 162174
-recovered pasa_asmbl_41742.p1, internal, 162297, 162390
-recovered pasa_asmbl_41742.p1, internal, 162682, 162912
-recovered pasa_asmbl_41742.p1, internal, 163122, 163236
Valid prediction for GlimmerHMM_glimmerT_10725-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18664, rend_intergenic: 17566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 197605
-exon list size: 430


building trellis

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20.6    
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23.6    
23.8    
24.1    
24.3    
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25.0    
25.2    
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27.1    
27.3    
27.5    
27.8    
28.0    
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28.9    
29.2    
29.4    
29.6    
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30.3    
30.6    
30.8    
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31.9    
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33.1    
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33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
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35.6    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.4    
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38.9    
39.1    
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39.6    
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40.0    
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40.5    
40.7    
41.0    
41.2    
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42.1    
42.4    
42.6    
42.8    
43.1    
43.3    
43.5    
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44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.8    
46.1    
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47.9    
48.1    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
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50.0    
50.2    
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55.6    
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56.9    
57.2    
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57.6    
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58.6    
58.8    
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61.3    
61.6    
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62.0    
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63.4    
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63.9    
64.1    
64.4    
64.6    
64.8    
65.0    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.8    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.8    
71.1    
71.3    
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72.0    
72.2    
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73.4    
73.6    
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77.3    
77.5    
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78.9    
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82.6    
82.9    
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83.6    
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84.0    
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84.7    
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88.9    
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95.6    
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96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 18664, rend_intergenic: 17566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support