-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_12978167-13161704

-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.g12354.t1
Valid prediction for Augustus_model.g12367.t1
Couldn't classify 20985, 21902
Sorry, prediction pasa_asmbl_50305.p2 fails validation.
(GCC)	 CG	20985-21902	AG	AGA
Valid prediction for pasa_asmbl_50308.p1
Valid prediction for snap_scaffold_7-snap.2435-T1
Valid prediction for snap_scaffold_7-snap.2458-T1
Valid prediction for snap_scaffold_7-snap.2452-T1
Valid prediction for GlimmerHMM_glimmerT_18334-T1
Valid prediction for GlimmerHMM_glimmerT_18346-T1
Valid prediction for snap_scaffold_7-snap.2450-T1
Valid prediction for CodingQuarry_transcript_57685-T1
Valid prediction for snap_scaffold_7-snap.2434-T1
Valid prediction for pasa_asmbl_50312.p1
Valid prediction for GlimmerHMM_glimmerT_18345-T1
Valid prediction for snap_scaffold_7-snap.2460-T1
Valid prediction for HiQ_model.g12359.t1
Valid prediction for HiQ_model.g12363.t1
Valid prediction for GlimmerHMM_glimmerT_18349-T1
Valid prediction for snap_scaffold_7-snap.2464-T1
Valid prediction for snap_scaffold_7-snap.2449-T1
Valid prediction for Augustus_model.g12353.t1
Valid prediction for GlimmerHMM_glimmerT_18327-T1
Couldn't classify 111737, 111831
Sorry, prediction pasa_asmbl_50310.p1 fails validation.
(GTG)	 TG	111737-111831	GT	TGG
(GCC)	 AG	114368-114599	CA	AAC
-recovered pasa_asmbl_50310.p1, terminal, 114368, 114599
Valid prediction for Augustus_model.g12348.t1
Valid prediction for snap_scaffold_7-snap.2446-T1
Valid prediction for CodingQuarry_transcript_57686-T1
Valid prediction for snap_scaffold_7-snap.2441-T1
Valid prediction for pasa_asmbl_50309.p1
Valid prediction for GlimmerHMM_glimmerT_18336-T1
Valid prediction for Augustus_model.g12371.t1
Valid prediction for GlimmerHMM_glimmerT_18326-T1
Valid prediction for snap_scaffold_7-snap.2465-T1
Valid prediction for snap_scaffold_7-snap.2451-T1
Valid prediction for Augustus_model.g12366.t1
Valid prediction for snap_scaffold_7-snap.2468-T1
Valid prediction for GlimmerHMM_glimmerT_18342-T1
Valid prediction for snap_scaffold_7-snap.2442-T1
Valid prediction for Augustus_model.g12357.t1
Valid prediction for GlimmerHMM_glimmerT_18343-T1
Couldn't classify 119551, 119657
Couldn't classify 120161, 120215
Sorry, prediction pasa_asmbl_50598.p1 fails validation.
(CTA)	 CC	119551-119657	GT	TGG
(GGC)	 AG	119772-119857	GT	AGG
(GGT)	 AG	119950-120058	GT	AGG
(GAA)	 AG	120161-120215	CC	CTC
-recovered pasa_asmbl_50598.p1, internal, 119772, 119857
-recovered pasa_asmbl_50598.p1, internal, 119950, 120058
Valid prediction for GlimmerHMM_glimmerT_18325-T1
Valid prediction for Augustus_model.g12352.t1
Valid prediction for snap_scaffold_7-snap.2455-T1
Valid prediction for GlimmerHMM_glimmerT_18331-T1
Valid prediction for GlimmerHMM_glimmerT_18338-T1
Valid prediction for GlimmerHMM_glimmerT_18332-T1
Valid prediction for GlimmerHMM_glimmerT_18354-T1
Valid prediction for snap_scaffold_7-snap.2444-T1
Valid prediction for snap_scaffold_7-snap.2432-T1
Valid prediction for GlimmerHMM_glimmerT_18350-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_18348-T1
Valid prediction for pasa_asmbl_51290.p1
Valid prediction for Augustus_model.g12358.t1
Valid prediction for Augustus_model.g12351.t1
Valid prediction for snap_scaffold_7-snap.2463-T1
Valid prediction for Augustus_model.g12369.t1
Valid prediction for snap_scaffold_7-snap.2438-T1
Valid prediction for GlimmerHMM_glimmerT_18355-T1
Valid prediction for Augustus_model.g12347.t1
Valid prediction for Augustus_model.g12361.t1
Valid prediction for GlimmerHMM_glimmerT_18353-T1
Valid prediction for Augustus_model.g12364.t1
Valid prediction for GlimmerHMM_glimmerT_18337-T1
Valid prediction for snap_scaffold_7-snap.2459-T1
Couldn't classify 141367, 141472
Sorry, prediction pasa_asmbl_51278.p1 fails validation.
(CAG)	 TG	141367-141472	GT	CGG
(GTA)	 AG	141853-141921	GT	AAG
(GTC)	 AG	142014-142064	GT	CGG
(TGT)	 AG	142478-142544	GT	AAG
(CTT)	 AG	143945-144052	GT	AGG
(GTA)	 AG	144396-144477	GT	AGG
(GAC)	 AG	144716-144842	GT	TGG
(GGA)	 AG	145909-146063	GT	ATG
(GAA)	 AG	146254-146378	GT	GCG
(CTT)	 AG	146511-146608	GT	AGG
(CCA)	 AG	146716-146865	GT	AGG
(TGA)	 AG	147051-147103	CC	AAC
-recovered pasa_asmbl_51278.p1, terminal, 147051, 147103
-recovered pasa_asmbl_51278.p1, internal, 141853, 141921
-recovered pasa_asmbl_51278.p1, internal, 142014, 142064
-recovered pasa_asmbl_51278.p1, internal, 142478, 142544
-recovered pasa_asmbl_51278.p1, internal, 143945, 144052
-recovered pasa_asmbl_51278.p1, internal, 144396, 144477
-recovered pasa_asmbl_51278.p1, internal, 144716, 144842
-recovered pasa_asmbl_51278.p1, internal, 145909, 146063
-recovered pasa_asmbl_51278.p1, internal, 146254, 146378
-recovered pasa_asmbl_51278.p1, internal, 146511, 146608
-recovered pasa_asmbl_51278.p1, internal, 146716, 146865
Valid prediction for Augustus_model.g12355.t1
Valid prediction for snap_scaffold_7-snap.2439-T1
Valid prediction for GlimmerHMM_glimmerT_18351-T1
Valid prediction for Augustus_model.g12362.t1
Valid prediction for snap_scaffold_7-snap.2433-T1
Valid prediction for snap_scaffold_7-snap.2447-T1
Valid prediction for snap_scaffold_7-snap.2440-T1
Valid prediction for Augustus_model.g12368.t1
Valid prediction for snap_scaffold_7-snap.2431-T1
Valid prediction for snap_scaffold_7-snap.2466-T1
Valid prediction for snap_scaffold_7-snap.2437-T1
Valid prediction for snap_scaffold_7-snap.2461-T1
Valid prediction for GlimmerHMM_glimmerT_18352-T1
Valid prediction for snap_scaffold_7-snap.2462-T1
Valid prediction for snap_scaffold_7-snap.2454-T1
Valid prediction for GlimmerHMM_glimmerT_18329-T1
Valid prediction for GlimmerHMM_glimmerT_18339-T1
Couldn't classify 15540, 16972
Sorry, prediction pasa_asmbl_51289.p1 fails validation.
(AAT)	 TG	15540-16972	GT	AGG
(GAG)	 AG	18372-18498	GT	AGG
(GAG)	 AG	20717-20823	GT	GCG
(AAA)	 AG	20949-21031	GT	AGG
(AGC)	 AG	21123-21240	GT	ATG
(GCG)	 AG	21425-21531	GT	AGG
(AGT)	 AG	21637-21717	GT	CGG
(ACT)	 AG	21808-21902	GT	AGG
(GGG)	 AG	22012-22083	GT	ATG
(GTC)	 AG	22325-22453	GT	TGG
(ATG)	 AG	22625-22734	GT	TGG
(GAT)	 AG	22960-23218	GT	AGG
(GTC)	 AG	23334-23405	TG	AGT
-recovered pasa_asmbl_51289.p1, initial, 22625, 22734
-recovered pasa_asmbl_51289.p1, terminal, 23334, 23405
-recovered pasa_asmbl_51289.p1, internal, 18372, 18498
-recovered pasa_asmbl_51289.p1, internal, 20717, 20823
-recovered pasa_asmbl_51289.p1, internal, 20949, 21031
-recovered pasa_asmbl_51289.p1, internal, 21123, 21240
-recovered pasa_asmbl_51289.p1, internal, 21425, 21531
-recovered pasa_asmbl_51289.p1, internal, 21637, 21717
-recovered pasa_asmbl_51289.p1, internal, 21808, 21902
-recovered pasa_asmbl_51289.p1, internal, 22012, 22083
-recovered pasa_asmbl_51289.p1, internal, 22325, 22453
-recovered pasa_asmbl_51289.p1, internal, 22625, 22734
-recovered pasa_asmbl_51289.p1, internal, 22960, 23218
Valid prediction for Augustus_model.g12350.t1
Valid prediction for snap_scaffold_7-snap.2457-T1
Valid prediction for GlimmerHMM_glimmerT_18340-T1
Valid prediction for snap_scaffold_7-snap.2436-T1
Valid prediction for Augustus_model.g12365.t1
Valid prediction for GlimmerHMM_glimmerT_18330-T1
Valid prediction for snap_scaffold_7-snap.2453-T1
Valid prediction for GlimmerHMM_glimmerT_18333-T1
Valid prediction for Augustus_model.g12349.t1
Valid prediction for GlimmerHMM_glimmerT_18324-T1
Valid prediction for HiQ_model.g12370.t1
Valid prediction for Augustus_model.g12360.t1
Valid prediction for snap_scaffold_7-snap.2456-T1
Valid prediction for snap_scaffold_7-snap.2448-T1
Valid prediction for GlimmerHMM_glimmerT_18335-T1
Valid prediction for snap_scaffold_7-snap.2443-T1
Valid prediction for GlimmerHMM_glimmerT_18341-T1
Valid prediction for GlimmerHMM_glimmerT_18344-T1
Valid prediction for snap_scaffold_7-snap.2445-T1
Valid prediction for snap_scaffold_7-snap.2467-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g12346.t1
Couldn't classify 47192, 47248
Couldn't classify 49374, 49499
Sorry, prediction pasa_asmbl_51288.p1 fails validation.
(CTG)	 TC	47192-47248	GT	AAG
(ATC)	 AG	47469-47744	GT	AGG
(GGA)	 AG	48141-48296	GT	AGG
(GAG)	 AG	48475-48912	GT	ACG
(GGT)	 AG	49374-49499	AA	GCA
-recovered pasa_asmbl_51288.p1, internal, 47469, 47744
-recovered pasa_asmbl_51288.p1, internal, 48141, 48296
-recovered pasa_asmbl_51288.p1, internal, 48475, 48912
Valid prediction for GlimmerHMM_glimmerT_18328-T1
Valid prediction for GlimmerHMM_glimmerT_18347-T1
Valid prediction for Augustus_model.g12356.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 53467, rend_intergenic: 53464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7270, rend_intergenic: 4944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11992, rend_intergenic: 9657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13421, rend_intergenic: 12204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93563, rend_intergenic: 75535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125586, rend_intergenic: 122278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154469, rend_intergenic: 143722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181253, rend_intergenic: 175085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183538
-exon list size: 406


building trellis

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0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
2.9    
3.2    
3.4    
3.7    
3.9    
4.2    
4.4    
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4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.8    
8.1    
8.3    
8.6    
8.8    
9.1    
9.3    
9.6    
9.8    
10.0    
10.3    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.4    
15.7    
15.9    
16.2    
16.4    
16.7    
16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.0    
60.3    
60.5    
60.8    
61.0    
61.3    
61.5    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.6    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.4    
69.6    
69.9    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 53467, rend_intergenic: 53464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7270, rend_intergenic: 4944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11992, rend_intergenic: 9657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13421, rend_intergenic: 12204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93563, rend_intergenic: 75535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125586, rend_intergenic: 122278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154469, rend_intergenic: 143722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181253, rend_intergenic: 175085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support