-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_1374749-1552981

-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.42055_t
Valid prediction for snap_scaffold_10-snap.318-T1
Couldn't classify 103154, 103193
Sorry, prediction pasa_asmbl_4226.p1 fails validation.
(GAA)	 GG	103154-103193	GT	AGG
(GAT)	 AG	103482-103747	GT	AGG
(TCC)	 AG	103865-104040	GT	AGG
(TAA)	 AG	104187-104314	GT	AAG
(GTG)	 AG	104468-104712	AA	GAA
-recovered pasa_asmbl_4226.p1, terminal, 104468, 104712
-recovered pasa_asmbl_4226.p1, internal, 103482, 103747
-recovered pasa_asmbl_4226.p1, internal, 103865, 104040
-recovered pasa_asmbl_4226.p1, internal, 104187, 104314
Valid prediction for GeneMark_model.42047_t
Valid prediction for GeneMark_model.42066_t
Valid prediction for GlimmerHMM_glimmerT_24656-T1
Valid prediction for GeneMark_model.42071_t
Valid prediction for HiQ_model.g16525.t1
Valid prediction for GeneMark_model.42053_t
Valid prediction for GeneMark_model.42087_t
Valid prediction for GeneMark_model.42084_t
Valid prediction for Augustus_model.g16526.t1
Valid prediction for snap_scaffold_10-snap.301-T1
Valid prediction for snap_scaffold_10-snap.306-T1
Valid prediction for GeneMark_model.42090_t
Valid prediction for CodingQuarry_transcript_5276-T1
Valid prediction for GeneMark_model.42057_t
Valid prediction for Augustus_model.g16531.t1
Valid prediction for snap_scaffold_10-snap.327-T1
Valid prediction for snap_scaffold_10-snap.309-T1
Couldn't classify 64569, 64724
Sorry, prediction pasa_asmbl_4223.p1 fails validation.
(GAC)	 CT	64569-64724	GT	AGG
(ATC)	 AG	65274-65369	GT	AGG
(GTT)	 AG	66669-66741	GT	AGG
(GCA)	 AG	66864-67021	AC	GAA
-recovered pasa_asmbl_4223.p1, terminal, 66864, 67021
-recovered pasa_asmbl_4223.p1, internal, 65274, 65369
-recovered pasa_asmbl_4223.p1, internal, 66669, 66741
Valid prediction for GeneMark_model.42048_t
Valid prediction for GeneMark_model.42044_t
Valid prediction for snap_scaffold_10-snap.315-T1
Valid prediction for GlimmerHMM_glimmerT_24664-T1
Valid prediction for snap_scaffold_10-snap.314-T1
Valid prediction for GeneMark_model.42051_t
Couldn't classify 41091, 42947
Sorry, prediction pasa_asmbl_4209.p1 fails validation.
(GGT)	 GT	41091-42947	GT	AAG
Valid prediction for snap_scaffold_10-snap.300-T1
Valid prediction for Augustus_model.g16528.t1
Valid prediction for Augustus_model.g16524.t1
Valid prediction for GlimmerHMM_glimmerT_24647-T1
Valid prediction for GeneMark_model.42049_t
Valid prediction for snap_scaffold_10-snap.331-T1
Valid prediction for GlimmerHMM_glimmerT_24658-T1
Valid prediction for GeneMark_model.42085_t
Valid prediction for snap_scaffold_10-snap.320-T1
Valid prediction for GlimmerHMM_glimmerT_24644-T1
Valid prediction for GeneMark_model.42079_t
Valid prediction for HiQ_model.g16532.t1
Valid prediction for GlimmerHMM_glimmerT_24659-T1
Valid prediction for Augustus_model.g16534.t1
Couldn't classify 110093, 110196
Sorry, prediction pasa_asmbl_4228.p1 fails validation.
(ATG)	 AG	109096-109140	GT	TGG
(TGT)	 AG	109227-109305	GT	AGG
(ATG)	 AG	109425-109470	GC	AAG
(AAT)	 AG	109577-109674	GT	AGG
(ATG)	 AG	110093-110196	AT	GGA
-recovered pasa_asmbl_4228.p1, initial, 109096, 109140
-recovered pasa_asmbl_4228.p1, initial, 109425, 109470
-recovered pasa_asmbl_4228.p1, internal, 109096, 109140
-recovered pasa_asmbl_4228.p1, internal, 109227, 109305
-recovered pasa_asmbl_4228.p1, internal, 109425, 109470
-recovered pasa_asmbl_4228.p1, internal, 109577, 109674
Valid prediction for GlimmerHMM_glimmerT_24643-T1
Valid prediction for GlimmerHMM_glimmerT_24651-T1
Valid prediction for GeneMark_model.42089_t
Valid prediction for GeneMark_model.42082_t
Valid prediction for snap_scaffold_10-snap.313-T1
Valid prediction for snap_scaffold_10-snap.317-T1
Valid prediction for GlimmerHMM_glimmerT_24655-T1
Valid prediction for snap_scaffold_10-snap.323-T1
Couldn't classify 110618, 110643
Couldn't classify 114188, 114303
Sorry, prediction pasa_asmbl_4229.p1 fails validation.
(AAC)	 TG	110618-110643	GT	AGG
(TCT)	 AG	110772-110832	GT	AGG
(ATT)	 AG	110932-111117	GT	AGG
(GTT)	 AG	111317-111397	GT	AAG
(CTC)	 AG	111759-111907	GT	GTG
(GCG)	 AG	112058-112198	GT	ACG
(AGA)	 AG	112338-112437	GT	AGG
(ACG)	 AG	112668-112866	GT	AGG
(ATC)	 AG	113050-113126	GT	AGG
(ACT)	 AG	113448-113586	GT	AGG
(ACA)	 AG	113695-113880	GT	AGG
(GTC)	 AG	114188-114303	GT	AGG
-recovered pasa_asmbl_4229.p1, internal, 110772, 110832
-recovered pasa_asmbl_4229.p1, internal, 110932, 111117
-recovered pasa_asmbl_4229.p1, internal, 111317, 111397
-recovered pasa_asmbl_4229.p1, internal, 111759, 111907
-recovered pasa_asmbl_4229.p1, internal, 112058, 112198
-recovered pasa_asmbl_4229.p1, internal, 112338, 112437
-recovered pasa_asmbl_4229.p1, internal, 112668, 112866
-recovered pasa_asmbl_4229.p1, internal, 113050, 113126
-recovered pasa_asmbl_4229.p1, internal, 113448, 113586
-recovered pasa_asmbl_4229.p1, internal, 113695, 113880
-recovered pasa_asmbl_4229.p1, internal, 114188, 114303
Valid prediction for GeneMark_model.42068_t
Valid prediction for GeneMark_model.42072_t
Valid prediction for snap_scaffold_10-snap.305-T1
Valid prediction for pasa_asmbl_4212.p1
Couldn't classify 86325, 86390
Sorry, prediction Augustus_model.g16530.t1 fails validation.
(AAC)	 AG	86325-86390	GT	AGG
(CTG)	 AG	86855-87133	CC	AAC
-recovered Augustus_model.g16530.t1, terminal, 86855, 87133
-recovered Augustus_model.g16530.t1, internal, 86325, 86390
Valid prediction for GeneMark_model.42060_t
Valid prediction for GlimmerHMM_glimmerT_24650-T1
Valid prediction for GeneMark_model.42075_t
Valid prediction for GeneMark_model.42063_t
Valid prediction for Augustus_model.g16536.t1
Valid prediction for snap_scaffold_10-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_24653-T1
Valid prediction for GeneMark_model.42093_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 snap_scaffold_10-snap.308-T1
Valid prediction for GeneMark_model.42074_t
Valid prediction for snap_scaffold_10-snap.312-T1
Valid prediction for pasa_asmbl_2969.p1
Valid prediction for GeneMark_model.42061_t
Valid prediction for GeneMark_model.42083_t
Valid prediction for Augustus_model.g16538.t1
Valid prediction for CodingQuarry_transcript_5277-T1
Valid prediction for GeneMark_model.42056_t
Valid prediction for GeneMark_model.42073_t
Valid prediction for pasa_asmbl_2976.p1
Valid prediction for snap_scaffold_10-snap.302-T1
Valid prediction for GeneMark_model.42081_t
Valid prediction for snap_scaffold_10-snap.311-T1
Valid prediction for GlimmerHMM_glimmerT_24642-T1
Valid prediction for GlimmerHMM_glimmerT_24645-T1
Valid prediction for CodingQuarry_transcript_5279-T1
Valid prediction for GeneMark_model.42052_t
Valid prediction for pasa_asmbl_2967.p1
Valid prediction for GlimmerHMM_glimmerT_24654-T1
Valid prediction for GeneMark_model.42094_t
Valid prediction for snap_scaffold_10-snap.304-T1
Valid prediction for snap_scaffold_10-snap.307-T1
Valid prediction for GeneMark_model.42045_t
Valid prediction for snap_scaffold_10-snap.328-T1
Valid prediction for GeneMark_model.42076_t
Valid prediction for GeneMark_model.42078_t
Valid prediction for GeneMark_model.42086_t
Valid prediction for CodingQuarry_transcript_5274-T1
Valid prediction for GlimmerHMM_glimmerT_24652-T1
Valid prediction for GeneMark_model.42062_t
Valid prediction for snap_scaffold_10-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_24648-T1
Valid prediction for GeneMark_model.42064_t
Valid prediction for GeneMark_model.42069_t
Valid prediction for GeneMark_model.42059_t
Valid prediction for snap_scaffold_10-snap.326-T1
Valid prediction for snap_scaffold_10-snap.316-T1
Valid prediction for snap_scaffold_10-snap.325-T1
Valid prediction for GeneMark_model.42050_t
Valid prediction for CodingQuarry_transcript_5278-T1
Valid prediction for GeneMark_model.42058_t
Valid prediction for snap_scaffold_10-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_24646-T1
Valid prediction for GeneMark_model.42046_t
Valid prediction for snap_scaffold_10-snap.329-T1
Valid prediction for GlimmerHMM_glimmerT_24661-T1
Valid prediction for snap_scaffold_10-snap.324-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_24649-T1
Valid prediction for snap_scaffold_10-snap.322-T1
Valid prediction for GeneMark_model.42054_t
Valid prediction for GlimmerHMM_glimmerT_24657-T1
Valid prediction for GeneMark_model.42080_t
Valid prediction for HiQ_model.g16527.t1
Couldn't classify 69809, 69814
Couldn't classify 70411, 70595
Sorry, prediction CodingQuarry_transcript_5275-T1 fails validation.
(ATG)	 AA	69809-69814	GG	TTG
(CAG)	 GA	70411-70595	GT	ACG
(CAT)	 AG	70772-70922	GT	CTG
(GGG)	 AG	71129-71308	GT	TGG
(GGT)	 AG	71496-71688	GT	GGG
(GTA)	 AG	71819-71886	AA	AAA
-recovered CodingQuarry_transcript_5275-T1, terminal, 71819, 71886
-recovered CodingQuarry_transcript_5275-T1, internal, 70772, 70922
-recovered CodingQuarry_transcript_5275-T1, internal, 71129, 71308
-recovered CodingQuarry_transcript_5275-T1, internal, 71496, 71688
Valid prediction for GlimmerHMM_glimmerT_24662-T1
Valid prediction for snap_scaffold_10-snap.303-T1
Valid prediction for GeneMark_model.42091_t
Valid prediction for GlimmerHMM_glimmerT_24660-T1
Valid prediction for GlimmerHMM_glimmerT_24641-T1
Valid prediction for HiQ_model.g16533.t1
Valid prediction for GeneMark_model.42067_t
Valid prediction for snap_scaffold_10-snap.299-T1
Valid prediction for GeneMark_model.42070_t
Valid prediction for HiQ_model.g16529.t1
Valid prediction for Augustus_model.g16535.t1
Valid prediction for snap_scaffold_10-snap.321-T1
Valid prediction for snap_scaffold_10-snap.332-T1
Valid prediction for Augustus_model.g16537.t1
Valid prediction for GlimmerHMM_glimmerT_24665-T1
Valid prediction for GeneMark_model.42065_t
Valid prediction for GlimmerHMM_glimmerT_24663-T1
Valid prediction for GeneMark_model.42088_t
Valid prediction for GeneMark_model.42092_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15352, rend_intergenic: 12418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19458, rend_intergenic: 17813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92757, rend_intergenic: 83276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100395, rend_intergenic: 94757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142286, rend_intergenic: 139253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147631, rend_intergenic: 144339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162683, rend_intergenic: 153715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170791, rend_intergenic: 162858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178233
-exon list size: 563


building trellis

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98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 15352, rend_intergenic: 12418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19458, rend_intergenic: 17813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92757, rend_intergenic: 83276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100395, rend_intergenic: 94757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142286, rend_intergenic: 139253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147631, rend_intergenic: 144339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162683, rend_intergenic: 153715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170791, rend_intergenic: 162858  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 - 25335
-exon list size: 79


building trellis

1.2    
2.5    
3.7    
4.9    
6.2    
7.4    
8.6    
9.9    
11.1    
12.3    
13.6    
14.8    
16.0    
17.3    
18.5    
19.8    
21.0    
22.2    
23.5    
24.7    
25.9    
27.2    
28.4    
29.6    
30.9    
32.1    
33.3    
34.6    
35.8    
37.0    
38.3    
39.5    
40.7    
42.0    
43.2    
44.4    
45.7    
46.9    
48.1    
49.4    
50.6    
51.9    
53.1    
54.3    
55.6    
56.8    
58.0    
59.3    
60.5    
61.7    
63.0    
64.2    
65.4    
66.7    
67.9    
69.1    
70.4    
71.6    
72.8    
74.1    
75.3    
76.5    
77.8    
79.0    
80.2    
81.5    
82.7    
84.0    
85.2    
86.4    
87.7    
88.9    
90.1    
91.4    
92.6    
93.8    
95.1    
96.3    
97.5    
98.8    
-found 2 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 - 23918
-exon list size: 76


building trellis

1.3    
2.6    
3.8    
5.1    
6.4    
7.7    
9.0    
10.3    
11.5    
12.8    
14.1    
15.4    
16.7    
17.9    
19.2    
20.5    
21.8    
23.1    
24.4    
25.6    
26.9    
28.2    
29.5    
30.8    
32.1    
33.3    
34.6    
35.9    
37.2    
38.5    
39.7    
41.0    
42.3    
43.6    
44.9    
46.2    
47.4    
48.7    
50.0    
51.3    
52.6    
53.8    
55.1    
56.4    
57.7    
59.0    
60.3    
61.5    
62.8    
64.1    
65.4    
66.7    
67.9    
69.2    
70.5    
71.8    
73.1    
74.4    
75.6    
76.9    
78.2    
79.5    
80.8    
82.1    
83.3    
84.6    
85.9    
87.2    
88.5    
89.7    
91.0    
92.3    
93.6    
94.9    
96.2    
97.4    
98.7    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 21143
-exon list size: 69


building trellis

1.4    
2.8    
4.2    
5.6    
7.0    
8.5    
9.9    
11.3    
12.7    
14.1    
15.5    
16.9    
18.3    
19.7    
21.1    
22.5    
23.9    
25.4    
26.8    
28.2    
29.6    
31.0    
32.4    
33.8    
35.2    
36.6    
38.0    
39.4    
40.8    
42.3    
43.7    
45.1    
46.5    
47.9    
49.3    
50.7    
52.1    
53.5    
54.9    
56.3    
57.7    
59.2    
60.6    
62.0    
63.4    
64.8    
66.2    
67.6    
69.0    
70.4    
71.8    
73.2    
74.6    
76.1    
77.5    
78.9    
80.3    
81.7    
83.1    
84.5    
85.9    
87.3    
88.7    
90.1    
91.5    
93.0    
94.4    
95.8    
97.2    
98.6    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 18505
-exon list size: 57


building trellis

1.7    
3.4    
5.1    
6.8    
8.5    
10.2    
11.9    
13.6    
15.3    
16.9    
18.6    
20.3    
22.0    
23.7    
25.4    
27.1    
28.8    
30.5    
32.2    
33.9    
35.6    
37.3    
39.0    
40.7    
42.4    
44.1    
45.8    
47.5    
49.2    
50.8    
52.5    
54.2    
55.9    
57.6    
59.3    
61.0    
62.7    
64.4    
66.1    
67.8    
69.5    
71.2    
72.9    
74.6    
76.3    
78.0    
79.7    
81.4    
83.1    
84.7    
86.4    
88.1    
89.8    
91.5    
93.2    
94.9    
96.6    
98.3    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 12816
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 1 - 11562
-exon list size: 24


building trellis

3.8    
7.7    
11.5    
15.4    
19.2    
23.1    
26.9    
30.8    
34.6    
38.5    
42.3    
46.2    
50.0    
53.8    
57.7    
61.5    
65.4    
69.2    
73.1    
76.9    
80.8    
84.6    
88.5    
92.3    
96.2    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 163024 - 178233
-exon list size: 28


building trellis

3.3    
6.7    
10.0    
13.3    
16.7    
20.0    
23.3    
26.7    
30.0    
33.3    
36.7    
40.0    
43.3    
46.7    
50.0    
53.3    
56.7    
60.0    
63.3    
66.7    
70.0    
73.3    
76.7    
80.0    
83.3    
86.7    
90.0    
93.3    
96.7    
-found 1 predictions from path traversal

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