-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_13907001-14047310

-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 HiQ_model.g28387.t1
Valid prediction for Augustus_model.g28382.t1
Valid prediction for Augustus_model.g28389.t1
Valid prediction for Augustus_model.g28381.t1
Valid prediction for GeneMark_model.73284_t
Valid prediction for GeneMark_model.73303_t
Valid prediction for GlimmerHMM_glimmerT_42396-T1
Valid prediction for snap_scaffold_17-snap.2897-T1
Valid prediction for CodingQuarry_transcript_22204-T1
Valid prediction for snap_scaffold_17-snap.2900-T1
Valid prediction for GlimmerHMM_glimmerT_42393-T1
Valid prediction for GlimmerHMM_glimmerT_42389-T1
Valid prediction for GlimmerHMM_glimmerT_42385-T1
Valid prediction for snap_scaffold_17-snap.2902-T1
Valid prediction for snap_scaffold_17-snap.2910-T1
Valid prediction for GeneMark_model.73300_t
Valid prediction for GeneMark_model.73289_t
Valid prediction for GlimmerHMM_glimmerT_42378-T1
Valid prediction for snap_scaffold_17-snap.2912-T1
Valid prediction for Augustus_model.g28380.t1
Valid prediction for Augustus_model.g28390.t1
Valid prediction for GeneMark_model.73276_t
Valid prediction for GeneMark_model.73293_t
Valid prediction for GeneMark_model.73280_t
Valid prediction for pasa_asmbl_18489.p1
Valid prediction for GeneMark_model.73298_t
Valid prediction for GlimmerHMM_glimmerT_42380-T1
Valid prediction for GlimmerHMM_glimmerT_42383-T1
Valid prediction for snap_scaffold_17-snap.2918-T1
Valid prediction for snap_scaffold_17-snap.2893-T1
Couldn't classify 9945, 10005
Sorry, prediction pasa_asmbl_18479.p1 fails validation.
(GCC)	 GC	9945-10005	GT	AGG
(CTG)	 AG	10425-10684	CC	AGC
-recovered pasa_asmbl_18479.p1, terminal, 10425, 10684
Valid prediction for GeneMark_model.73295_t
Valid prediction for snap_scaffold_17-snap.2908-T1
Valid prediction for GeneMark_model.73281_t
Valid prediction for GeneMark_model.73278_t
Valid prediction for GlimmerHMM_glimmerT_42387-T1
Valid prediction for Augustus_model.g28378.t1
Valid prediction for snap_scaffold_17-snap.2913-T1
Valid prediction for GeneMark_model.73274_t
Valid prediction for GlimmerHMM_glimmerT_42382-T1
Valid prediction for pasa_asmbl_18488.p1
Valid prediction for GlimmerHMM_glimmerT_42384-T1
Valid prediction for GeneMark_model.73286_t
Valid prediction for snap_scaffold_17-snap.2905-T1
Valid prediction for snap_scaffold_17-snap.2895-T1
Valid prediction for snap_scaffold_17-snap.2914-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.73292_t
Valid prediction for HiQ_model.g28385.t1
Valid prediction for CodingQuarry_transcript_22206-T1
Couldn't classify 119164, 119301
Sorry, prediction pasa_asmbl_18492.p1 fails validation.
(AGC)	 AG	119164-119301	GT	GGG
(GAA)	 AG	121015-121107	GT	AGG
(TGT)	 AG	121899-121982	GT	AAG
(AGT)	 AG	122328-122498	GT	AGG
(ATC)	 AG	122705-122803	GT	CGG
(GTG)	 AG	123072-123161	GT	AGG
(GTG)	 AG	123810-123954	GT	AGG
(GTG)	 AG	124612-124676	GT	AGG
(GAA)	 AG	125016-125171	GT	AGG
(GCT)	 AG	125532-125596	GT	GGG
(CTA)	 AG	125885-125993	GT	AGG
(GGC)	 AG	126452-126509	GT	AGG
(GTG)	 AG	128370-128573	GT	CGG
(ATC)	 AG	129312-129448	GC	AAG
-recovered pasa_asmbl_18492.p1, terminal, 123810, 123954
-recovered pasa_asmbl_18492.p1, terminal, 129312, 129448
-recovered pasa_asmbl_18492.p1, internal, 119164, 119301
-recovered pasa_asmbl_18492.p1, internal, 121015, 121107
-recovered pasa_asmbl_18492.p1, internal, 121899, 121982
-recovered pasa_asmbl_18492.p1, internal, 122328, 122498
-recovered pasa_asmbl_18492.p1, internal, 122705, 122803
-recovered pasa_asmbl_18492.p1, internal, 123072, 123161
-recovered pasa_asmbl_18492.p1, internal, 123810, 123954
-recovered pasa_asmbl_18492.p1, internal, 124612, 124676
-recovered pasa_asmbl_18492.p1, internal, 125016, 125171
-recovered pasa_asmbl_18492.p1, internal, 125532, 125596
-recovered pasa_asmbl_18492.p1, internal, 125885, 125993
-recovered pasa_asmbl_18492.p1, internal, 126452, 126509
-recovered pasa_asmbl_18492.p1, internal, 128370, 128573
-recovered pasa_asmbl_18492.p1, internal, 129312, 129448
Valid prediction for Augustus_model.g28391.t1
Valid prediction for Augustus_model.g28384.t1
Valid prediction for GlimmerHMM_glimmerT_42377-T1
Valid prediction for snap_scaffold_17-snap.2891-T1
Valid prediction for GeneMark_model.73306_t
Valid prediction for GlimmerHMM_glimmerT_42392-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_42390-T1
Valid prediction for GeneMark_model.73304_t
Valid prediction for GlimmerHMM_glimmerT_42391-T1
Couldn't classify 90344, 90384
Sorry, prediction pasa_asmbl_19435.p1 fails validation.
(TTC)	 CC	90344-90384	GT	AGG
(TCA)	 AG	91303-91346	GT	AGG
(AGT)	 AG	91460-91575	GT	AGG
(GTG)	 AG	91822-91938	GT	AGG
(GCT)	 AG	92309-92465	GT	AGG
(GCC)	 AG	93031-93118	GT	GCG
(GAA)	 AG	93791-93849	GT	AGG
(TGG)	 AG	94076-94170	GT	CTG
(AGT)	 AG	94646-94774	GT	AGG
(ATT)	 AG	95218-95307	AG	GAA
-recovered pasa_asmbl_19435.p1, terminal, 95218, 95307
-recovered pasa_asmbl_19435.p1, internal, 91303, 91346
-recovered pasa_asmbl_19435.p1, internal, 91460, 91575
-recovered pasa_asmbl_19435.p1, internal, 91822, 91938
-recovered pasa_asmbl_19435.p1, internal, 92309, 92465
-recovered pasa_asmbl_19435.p1, internal, 93031, 93118
-recovered pasa_asmbl_19435.p1, internal, 93791, 93849
-recovered pasa_asmbl_19435.p1, internal, 94076, 94170
-recovered pasa_asmbl_19435.p1, internal, 94646, 94774
Valid prediction for GeneMark_model.73301_t
Valid prediction for snap_scaffold_17-snap.2894-T1
Valid prediction for snap_scaffold_17-snap.2899-T1
Valid prediction for HiQ_model.g28388.t1
Valid prediction for snap_scaffold_17-snap.2916-T1
Valid prediction for snap_scaffold_17-snap.2911-T1
Valid prediction for pasa_asmbl_19441.p1
Valid prediction for CodingQuarry_transcript_22202-T1
Valid prediction for GeneMark_model.73288_t
Valid prediction for CodingQuarry_transcript_22208-T1
Valid prediction for GeneMark_model.73296_t
Valid prediction for snap_scaffold_17-snap.2906-T1
Valid prediction for GlimmerHMM_glimmerT_42386-T1
Valid prediction for GeneMark_model.73297_t
Valid prediction for snap_scaffold_17-snap.2909-T1
Valid prediction for GeneMark_model.73283_t
Valid prediction for CodingQuarry_transcript_22207-T1
Valid prediction for GeneMark_model.73290_t
Valid prediction for HiQ_model.g28383.t1
Valid prediction for GlimmerHMM_glimmerT_42388-T1
Valid prediction for GlimmerHMM_glimmerT_42381-T1
Valid prediction for GeneMark_model.73287_t
Valid prediction for GlimmerHMM_glimmerT_42394-T1
Valid prediction for snap_scaffold_17-snap.2892-T1
Valid prediction for GeneMark_model.73291_t
Valid prediction for CodingQuarry_transcript_22203-T1
Valid prediction for CodingQuarry_transcript_22201-T1
Valid prediction for snap_scaffold_17-snap.2917-T1
Valid prediction for GeneMark_model.73273_t
Valid prediction for snap_scaffold_17-snap.2904-T1
Valid prediction for GeneMark_model.73285_t
Valid prediction for pasa_asmbl_19443.p1
Valid prediction for snap_scaffold_17-snap.2915-T1
Valid prediction for snap_scaffold_17-snap.2903-T1
Couldn't classify 127244, 127279
Sorry, prediction pasa_asmbl_19434.p1 fails validation.
(GCT)	 CA	127244-127279	GT	ATG
(TCA)	 AG	127373-127542	GT	AGG
(CTG)	 AG	128358-128440	GT	AGG
(CTT)	 AG	128681-128823	TG	AAT
-recovered pasa_asmbl_19434.p1, terminal, 128681, 128823
-recovered pasa_asmbl_19434.p1, internal, 127373, 127542
-recovered pasa_asmbl_19434.p1, internal, 128358, 128440
Valid prediction for GeneMark_model.73279_t
Valid prediction for Augustus_model.g28379.t1
Valid prediction for GeneMark_model.73302_t
Valid prediction for GeneMark_model.73305_t
Valid prediction for snap_scaffold_17-snap.2901-T1
Valid prediction for GeneMark_model.73277_t
Valid prediction for HiQ_model.g28386.t1
Valid prediction for snap_scaffold_17-snap.2898-T1
Valid prediction for CodingQuarry_transcript_22205-T1
Valid prediction for GlimmerHMM_glimmerT_42395-T1
Valid prediction for GeneMark_model.73294_t
Valid prediction for snap_scaffold_17-snap.2896-T1
Valid prediction for GeneMark_model.73282_t
Valid prediction for GlimmerHMM_glimmerT_42379-T1
Valid prediction for snap_scaffold_17-snap.2890-T1
Valid prediction for CodingQuarry_transcript_22209-T1
Valid prediction for snap_scaffold_17-snap.2907-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.73299_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6912, rend_intergenic: 4045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27635, rend_intergenic: 19890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37034, rend_intergenic: 33937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39780, rend_intergenic: 38258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75853, rend_intergenic: 75172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101317, rend_intergenic: 98841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111596, rend_intergenic: 110274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129448, rend_intergenic: 116683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 140310
-exon list size: 516


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.5    
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1.9    
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2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
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4.4    
4.6    
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5.8    
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8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
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10.8    
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11.4    
11.6    
11.8    
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12.2    
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12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.7    
13.9    
14.1    
14.3    
14.5    
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14.9    
15.1    
15.3    
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15.6    
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16.0    
16.2    
16.4    
16.6    
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17.0    
17.2    
17.4    
17.6    
17.8    
18.0    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.8    
21.0    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
28.8    
29.0    
29.2    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.0    
32.2    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.7    
36.9    
37.1    
37.3    
37.5    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.2    
43.4    
43.6    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.4    
56.6    
56.8    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.7    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.5    
62.7    
62.9    
63.1    
63.3    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 6912, rend_intergenic: 4045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27635, rend_intergenic: 19890  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37034, rend_intergenic: 33937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39780, rend_intergenic: 38258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75853, rend_intergenic: 75172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101317, rend_intergenic: 98841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111596, rend_intergenic: 110274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129448, rend_intergenic: 116683  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