-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_5496534-5679023

-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 GlimmerHMM_glimmerT_25295-T1
Valid prediction for snap_scaffold_10-snap.1203-T1
Valid prediction for GlimmerHMM_glimmerT_25293-T1
Valid prediction for GeneMark_model.43216_t
Valid prediction for Augustus_model.g16958.t1
Valid prediction for GlimmerHMM_glimmerT_25290-T1
Valid prediction for GlimmerHMM_glimmerT_25283-T1
Valid prediction for CodingQuarry_transcript_5402-T1
Valid prediction for GeneMark_model.43219_t
Valid prediction for Augustus_model.g16955.t1
Valid prediction for GeneMark_model.43213_t
Valid prediction for pasa_asmbl_4461.p1
Valid prediction for Augustus_model.g16959.t1
Valid prediction for snap_scaffold_10-snap.1197-T1
Valid prediction for GeneMark_model.43224_t
Valid prediction for HiQ_model.g16953.t1
Valid prediction for GlimmerHMM_glimmerT_25279-T1
Valid prediction for GeneMark_model.43202_t
Valid prediction for pasa_asmbl_4460.p1
Valid prediction for snap_scaffold_10-snap.1202-T1
Valid prediction for HiQ_model.g16956.t1
Valid prediction for snap_scaffold_10-snap.1191-T1
Valid prediction for GeneMark_model.43232_t
Valid prediction for Augustus_model.g16960.t1
Valid prediction for GeneMark_model.43233_t
Valid prediction for GeneMark_model.43225_t
Couldn't classify 57983, 58080
Sorry, prediction pasa_asmbl_4467.p1 fails validation.
(AAT)	 AG	57983-58080	GT	AAG
(GTT)	 AG	58260-58358	GT	GGG
(TCC)	 AG	58476-58577	GT	CCG
(GCT)	 AG	58750-58953	GT	GAG
(GTT)	 AG	59154-59281	GT	AGG
(TTC)	 AG	59492-59709	GT	AGG
(GTT)	 AG	59950-60057	GT	AGG
(GTG)	 AG	60207-60321	GT	AGG
(GTG)	 AG	60565-60711	GT	AGG
(ATT)	 AG	60877-61001	GT	AGG
(GAG)	 AG	61090-61184	GT	GGG
(CAA)	 AG	61608-61752	TT	AAT
-recovered pasa_asmbl_4467.p1, terminal, 61608, 61752
-recovered pasa_asmbl_4467.p1, internal, 57983, 58080
-recovered pasa_asmbl_4467.p1, internal, 58260, 58358
-recovered pasa_asmbl_4467.p1, internal, 58476, 58577
-recovered pasa_asmbl_4467.p1, internal, 58750, 58953
-recovered pasa_asmbl_4467.p1, internal, 59154, 59281
-recovered pasa_asmbl_4467.p1, internal, 59492, 59709
-recovered pasa_asmbl_4467.p1, internal, 59950, 60057
-recovered pasa_asmbl_4467.p1, internal, 60207, 60321
-recovered pasa_asmbl_4467.p1, internal, 60565, 60711
-recovered pasa_asmbl_4467.p1, internal, 60877, 61001
-recovered pasa_asmbl_4467.p1, internal, 61090, 61184
Valid prediction for GlimmerHMM_glimmerT_25286-T1
Valid prediction for GeneMark_model.43209_t
Valid prediction for snap_scaffold_10-snap.1204-T1
Valid prediction for snap_scaffold_10-snap.1206-T1
Valid prediction for GlimmerHMM_glimmerT_25275-T1
Valid prediction for snap_scaffold_10-snap.1210-T1
Couldn't classify 46359, 46367
Couldn't classify 53268, 53399
Sorry, prediction pasa_asmbl_4465.p1 fails validation.
(CTC)	 AA	46359-46367	GT	AGG
(GTT)	 AG	46654-46698	GT	AGG
(GTC)	 AG	46979-47056	GT	AGG
(GTT)	 AG	47321-47389	GT	AGG
(GTG)	 AG	47727-47811	GT	AGG
(GAA)	 AG	48103-48224	GT	AAG
(AGC)	 AG	48354-48444	GT	TGG
(AAT)	 AG	48746-48855	GT	AGG
(AGC)	 AG	49054-49083	GT	AGG
(CAG)	 AG	49545-49667	GT	AGG
(GAC)	 AG	49846-49985	GT	CGG
(GCA)	 AG	50268-50312	GT	CGG
(GAT)	 AG	50470-50540	GT	AGG
(TGG)	 AG	50702-50801	GT	AGG
(CAT)	 AG	51029-51116	GT	AGG
(CAA)	 AG	51381-51455	GT	AGG
(ATC)	 AG	52274-52354	GT	AGG
(GAG)	 AG	52827-52922	GT	TGG
(GCA)	 AG	53041-53139	GT	AGG
(GAG)	 AG	53268-53399	GT	AGG
-recovered pasa_asmbl_4465.p1, internal, 46654, 46698
-recovered pasa_asmbl_4465.p1, internal, 46979, 47056
-recovered pasa_asmbl_4465.p1, internal, 47321, 47389
-recovered pasa_asmbl_4465.p1, internal, 47727, 47811
-recovered pasa_asmbl_4465.p1, internal, 48103, 48224
-recovered pasa_asmbl_4465.p1, internal, 48354, 48444
-recovered pasa_asmbl_4465.p1, internal, 48746, 48855
-recovered pasa_asmbl_4465.p1, internal, 49054, 49083
-recovered pasa_asmbl_4465.p1, internal, 49545, 49667
-recovered pasa_asmbl_4465.p1, internal, 49846, 49985
-recovered pasa_asmbl_4465.p1, internal, 50268, 50312
-recovered pasa_asmbl_4465.p1, internal, 50470, 50540
-recovered pasa_asmbl_4465.p1, internal, 50702, 50801
-recovered pasa_asmbl_4465.p1, internal, 51029, 51116
-recovered pasa_asmbl_4465.p1, internal, 51381, 51455
-recovered pasa_asmbl_4465.p1, internal, 52274, 52354
-recovered pasa_asmbl_4465.p1, internal, 52827, 52922
-recovered pasa_asmbl_4465.p1, internal, 53041, 53139
-recovered pasa_asmbl_4465.p1, internal, 53268, 53399
Valid prediction for snap_scaffold_10-snap.1205-T1
Valid prediction for GlimmerHMM_glimmerT_25282-T1
Valid prediction for snap_scaffold_10-snap.1190-T1
Valid prediction for GlimmerHMM_glimmerT_25284-T1
Valid prediction for GlimmerHMM_glimmerT_25289-T1
Valid prediction for GeneMark_model.43217_t
Valid prediction for snap_scaffold_10-snap.1199-T1
Valid prediction for GeneMark_model.43223_t
Valid prediction for GlimmerHMM_glimmerT_25280-T1
Valid prediction for HiQ_model.g16951.t1
Valid prediction for GeneMark_model.43210_t
Valid prediction for CodingQuarry_transcript_5401-T1
Valid prediction for GeneMark_model.43221_t
Valid prediction for snap_scaffold_10-snap.1193-T1
Valid prediction for GeneMark_model.43212_t
Valid prediction for GeneMark_model.43206_t
Valid prediction for GeneMark_model.43207_t
Valid prediction for snap_scaffold_10-snap.1208-T1
Valid prediction for snap_scaffold_10-snap.1195-T1
Valid prediction for GeneMark_model.43229_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 GeneMark_model.43220_t
Valid prediction for CodingQuarry_transcript_5403-T1
Valid prediction for GlimmerHMM_glimmerT_25278-T1
Valid prediction for GeneMark_model.43215_t
Valid prediction for GeneMark_model.43226_t
Valid prediction for GeneMark_model.43208_t
Valid prediction for GeneMark_model.43228_t
Valid prediction for GlimmerHMM_glimmerT_25291-T1
Valid prediction for GeneMark_model.43211_t
Valid prediction for snap_scaffold_10-snap.1192-T1
Valid prediction for GlimmerHMM_glimmerT_25296-T1
Valid prediction for snap_scaffold_10-snap.1194-T1
Valid prediction for snap_scaffold_10-snap.1198-T1
Valid prediction for snap_scaffold_10-snap.1196-T1
Valid prediction for HiQ_model.g16961.t1
Valid prediction for GlimmerHMM_glimmerT_25276-T1
Valid prediction for CodingQuarry_transcript_5406-T1
Valid prediction for GlimmerHMM_glimmerT_25277-T1
Valid prediction for pasa_asmbl_3289.p1
Valid prediction for snap_scaffold_10-snap.1207-T1
Couldn't classify 649, 691
Sorry, prediction pasa_asmbl_3293.p1 fails validation.
(ATA)	 TT	649-691	GT	AGG
(GAG)	 AG	1385-1497	GT	AGG
(GCA)	 AG	1755-1841	GT	AGG
(ACA)	 AG	2642-2767	GT	AGG
(GAG)	 AG	2913-3030	GT	AGG
(GTC)	 AG	3184-3283	GT	AGG
(GTA)	 AG	3448-3572	GT	AGG
(ATC)	 AG	4004-4104	GT	AGG
(ATG)	 AG	6026-6133	GT	AGG
(TGC)	 AG	8502-8576	TG	AAT
-recovered pasa_asmbl_3293.p1, initial, 6026, 6133
add_exon() Sorry, pasa_asmbl_3293.p1 3448-3572-terminal-2 is invalid.
-recovered pasa_asmbl_3293.p1, terminal, 3448, 3572
-recovered pasa_asmbl_3293.p1, terminal, 8502, 8576
-recovered pasa_asmbl_3293.p1, internal, 1385, 1497
-recovered pasa_asmbl_3293.p1, internal, 1755, 1841
-recovered pasa_asmbl_3293.p1, internal, 2642, 2767
-recovered pasa_asmbl_3293.p1, internal, 2913, 3030
-recovered pasa_asmbl_3293.p1, internal, 3184, 3283
-recovered pasa_asmbl_3293.p1, internal, 3448, 3572
-recovered pasa_asmbl_3293.p1, internal, 4004, 4104
-recovered pasa_asmbl_3293.p1, internal, 6026, 6133
Valid prediction for HiQ_model.g16954.t1
Valid prediction for GlimmerHMM_glimmerT_25292-T1
Valid prediction for snap_scaffold_10-snap.1201-T1
Valid prediction for GlimmerHMM_glimmerT_25287-T1
Valid prediction for snap_scaffold_10-snap.1200-T1
Valid prediction for CodingQuarry_transcript_5407-T1
Valid prediction for snap_scaffold_10-snap.1209-T1
Valid prediction for GeneMark_model.43230_t
Valid prediction for GeneMark_model.43218_t
Valid prediction for GlimmerHMM_glimmerT_25285-T1
Valid prediction for GlimmerHMM_glimmerT_25294-T1
Valid prediction for CodingQuarry_transcript_5404-T1
Valid prediction for GeneMark_model.43231_t
Valid prediction for Augustus_model.g16952.t1
Valid prediction for HiQ_model.g16957.t1
Valid prediction for GlimmerHMM_glimmerT_25281-T1
Valid prediction for GlimmerHMM_glimmerT_25288-T1
Valid prediction for GeneMark_model.43214_t
Valid prediction for GeneMark_model.43227_t
Valid prediction for pasa_asmbl_3291.p1
Valid prediction for GeneMark_model.43205_t
Valid prediction for GeneMark_model.43204_t
Valid prediction for GeneMark_model.43222_t
Valid prediction for GeneMark_model.43203_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 54318, rend_intergenic: 49518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181268, rend_intergenic: 175519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 182490
-exon list size: 326


building trellis

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11.6    
11.9    
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13.1    
13.4    
13.7    
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14.9    
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17.7    
18.0    
18.3    
18.6    
18.9    
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20.4    
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21.6    
22.0    
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22.9    
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25.6    
25.9    
26.2    
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27.1    
27.4    
27.7    
28.0    
28.4    
28.7    
29.0    
29.3    
29.6    
29.9    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.1    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
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38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.5    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.5    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.9    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.1    
70.4    
70.7    
71.0    
71.3    
71.6    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.4    
78.7    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.2    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.3    
89.6    
89.9    
90.2    
90.5    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.7    
93.0    
93.3    
93.6    
93.9    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 54318, rend_intergenic: 49518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181268, rend_intergenic: 175519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support