-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_4127133-4363096

-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 snap_scaffold_2-snap.966-T1
Valid prediction for snap_scaffold_2-snap.962-T1
Valid prediction for snap_scaffold_2-snap.984-T1
Valid prediction for GlimmerHMM_glimmerT_3641-T1
Valid prediction for snap_scaffold_2-snap.969-T1
Valid prediction for snap_scaffold_2-snap.982-T1
Valid prediction for GlimmerHMM_glimmerT_3636-T1
Valid prediction for snap_scaffold_2-snap.993-T1
Valid prediction for snap_scaffold_2-snap.960-T1
Valid prediction for Augustus_model.g2448.t1
Valid prediction for CodingQuarry_transcript_28527-T1
Valid prediction for GlimmerHMM_glimmerT_3633-T1
Valid prediction for snap_scaffold_2-snap.979-T1
Valid prediction for Augustus_model.g2434.t1
Valid prediction for GlimmerHMM_glimmerT_3635-T1
Valid prediction for snap_scaffold_2-snap.964-T1
Valid prediction for snap_scaffold_2-snap.1004-T1
Valid prediction for snap_scaffold_2-snap.1002-T1
Valid prediction for GlimmerHMM_glimmerT_3629-T1
Valid prediction for snap_scaffold_2-snap.967-T1
Valid prediction for pasa_asmbl_24337.p1
Valid prediction for snap_scaffold_2-snap.995-T1
Valid prediction for Augustus_model.g2433.t1
Valid prediction for GlimmerHMM_glimmerT_3652-T1
Couldn't classify 38488, 38715
Sorry, prediction pasa_asmbl_24342.p2 fails validation.
(GCA)	 AG	38488-38715	GT	GGG
(CTG)	 AG	40771-42036	GT	AGG
(GCT)	 AG	43958-43975	TC	AGT
-recovered pasa_asmbl_24342.p2, terminal, 43958, 43975
-recovered pasa_asmbl_24342.p2, internal, 38488, 38715
-recovered pasa_asmbl_24342.p2, internal, 40771, 42036
Valid prediction for snap_scaffold_2-snap.975-T1
Valid prediction for snap_scaffold_2-snap.980-T1
Valid prediction for snap_scaffold_2-snap.1003-T1
Valid prediction for snap_scaffold_2-snap.996-T1
Valid prediction for CodingQuarry_transcript_28526-T1
Valid prediction for snap_scaffold_2-snap.988-T1
Valid prediction for snap_scaffold_2-snap.999-T1
Valid prediction for GlimmerHMM_glimmerT_3630-T1
Valid prediction for GlimmerHMM_glimmerT_3644-T1
Valid prediction for GlimmerHMM_glimmerT_3634-T1
Valid prediction for snap_scaffold_2-snap.977-T1
Valid prediction for Augustus_model.g2437.t1
Valid prediction for snap_scaffold_2-snap.992-T1
Valid prediction for pasa_asmbl_24344.p1
Valid prediction for snap_scaffold_2-snap.968-T1
Valid prediction for snap_scaffold_2-snap.976-T1
Valid prediction for snap_scaffold_2-snap.970-T1
Valid prediction for HiQ_model.g2435.t1
Valid prediction for GlimmerHMM_glimmerT_3631-T1
Valid prediction for GlimmerHMM_glimmerT_3642-T1
Valid prediction for Augustus_model.g2438.t1
Valid prediction for Augustus_model.g2439.t1
Valid prediction for GlimmerHMM_glimmerT_3639-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 Augustus_model.g2450.t1
Valid prediction for snap_scaffold_2-snap.974-T1
Valid prediction for GlimmerHMM_glimmerT_3654-T1
Valid prediction for snap_scaffold_2-snap.991-T1
Valid prediction for snap_scaffold_2-snap.1005-T1
Valid prediction for HiQ_model.g2440.t1
Valid prediction for snap_scaffold_2-snap.985-T1
Valid prediction for Augustus_model.g2436.t1
Valid prediction for GlimmerHMM_glimmerT_3651-T1
Valid prediction for GlimmerHMM_glimmerT_3650-T1
Valid prediction for snap_scaffold_2-snap.998-T1
Valid prediction for GlimmerHMM_glimmerT_3637-T1
Valid prediction for CodingQuarry_transcript_28529-T1
Valid prediction for GlimmerHMM_glimmerT_3647-T1
Valid prediction for snap_scaffold_2-snap.994-T1
Valid prediction for snap_scaffold_2-snap.965-T1
Valid prediction for snap_scaffold_2-snap.1001-T1
Couldn't classify 94721, 94787
Sorry, prediction pasa_asmbl_23058.p1 fails validation.
(CAG)	 CG	94721-94787	GT	CGG
(ATG)	 AG	96712-96763	GT	CAG
(TGC)	 AG	96948-97011	GT	AGG
(GTG)	 AG	97892-98098	GT	CTG
(ATT)	 AG	98335-98414	GT	TGG
(GAA)	 AG	98913-98991	GT	AGG
(GTT)	 AG	99383-99454	GT	CTG
(AAT)	 AG	99937-99999	GT	AGG
(ACT)	 AG	100291-100431	AA	AAA
-recovered pasa_asmbl_23058.p1, initial, 96712, 96763
-recovered pasa_asmbl_23058.p1, terminal, 100291, 100431
-recovered pasa_asmbl_23058.p1, internal, 96712, 96763
-recovered pasa_asmbl_23058.p1, internal, 96948, 97011
-recovered pasa_asmbl_23058.p1, internal, 97892, 98098
-recovered pasa_asmbl_23058.p1, internal, 98335, 98414
-recovered pasa_asmbl_23058.p1, internal, 98913, 98991
-recovered pasa_asmbl_23058.p1, internal, 99383, 99454
-recovered pasa_asmbl_23058.p1, internal, 99937, 99999
Valid prediction for snap_scaffold_2-snap.989-T1
Valid prediction for CodingQuarry_transcript_28528-T1
Couldn't classify 4472, 4576
Couldn't classify 5295, 5798
Sorry, prediction pasa_asmbl_23071.p1 fails validation.
(CCG)	 TG	4472-4576	GT	TGG
(GCG)	 AG	5295-5798	GG	GGG
Valid prediction for snap_scaffold_2-snap.971-T1
Couldn't classify 35457, 35603
Sorry, prediction pasa_asmbl_23064.p1 fails validation.
(GCC)	 AA	35457-35603	GT	AGG
(GAA)	 AG	36366-36533	GT	AGG
(GTG)	 AG	39290-39631	TG	AGT
-recovered pasa_asmbl_23064.p1, terminal, 39290, 39631
-recovered pasa_asmbl_23064.p1, internal, 36366, 36533
Valid prediction for snap_scaffold_2-snap.990-T1
Valid prediction for GlimmerHMM_glimmerT_3649-T1
Valid prediction for Augustus_model.g2449.t1
Valid prediction for snap_scaffold_2-snap.973-T1
Valid prediction for GlimmerHMM_glimmerT_3648-T1
Valid prediction for Augustus_model.g2442.t1
Valid prediction for snap_scaffold_2-snap.983-T1
Valid prediction for snap_scaffold_2-snap.986-T1
Valid prediction for Augustus_model.g2445.t1
Valid prediction for snap_scaffold_2-snap.997-T1
Valid prediction for snap_scaffold_2-snap.1000-T1
Valid prediction for GlimmerHMM_glimmerT_3632-T1
Valid prediction for GlimmerHMM_glimmerT_3643-T1
Valid prediction for HiQ_model.g2446.t1
Valid prediction for snap_scaffold_2-snap.959-T1
Valid prediction for snap_scaffold_2-snap.981-T1
Valid prediction for Augustus_model.g2443.t1
Valid prediction for GlimmerHMM_glimmerT_3646-T1
Valid prediction for HiQ_model.g2447.t1
Valid prediction for Augustus_model.g2441.t1
Valid prediction for Augustus_model.g2444.t1
Valid prediction for GlimmerHMM_glimmerT_3645-T1
Couldn't classify 6236, 6316
Sorry, prediction pasa_asmbl_23070.p1 fails validation.
(GGC)	 TG	6236-6316	GT	TTG
(TCC)	 AG	7308-7523	GT	AGG
(CTC)	 AG	7656-7814	GT	TGG
(AAG)	 AG	7929-8120	GC	AAG
-recovered pasa_asmbl_23070.p1, terminal, 7929, 8120
-recovered pasa_asmbl_23070.p1, internal, 7308, 7523
-recovered pasa_asmbl_23070.p1, internal, 7656, 7814
-recovered pasa_asmbl_23070.p1, internal, 7929, 8120
Valid prediction for pasa_asmbl_23068.p1
Valid prediction for snap_scaffold_2-snap.963-T1
Valid prediction for GlimmerHMM_glimmerT_3638-T1
Valid prediction for snap_scaffold_2-snap.978-T1
Valid prediction for snap_scaffold_2-snap.961-T1
Valid prediction for GlimmerHMM_glimmerT_3653-T1
Valid prediction for GlimmerHMM_glimmerT_3655-T1
Valid prediction for snap_scaffold_2-snap.972-T1
Couldn't classify 117303, 117383
Sorry, prediction pasa_asmbl_23055.p1 fails validation.
(AGC)	 TA	117303-117383	GT	TGG
(ATA)	 AG	117716-117875	GT	AGG
(AAT)	 AG	118959-119013	GT	CGG
(GTA)	 AG	119521-119636	GT	TAG
(TCA)	 AG	119899-119974	GT	GAG
(CTG)	 AG	120177-120331	GT	CAG
(GAA)	 AG	120722-120819	GT	ACG
(TTA)	 AG	121130-121244	GT	TGG
(ATA)	 AG	121610-121682	GT	AAG
(GTT)	 AG	122310-122412	GT	AAG
(TAC)	 AG	124275-124425	GT	CAG
(CTT)	 AG	124651-124743	GT	AAG
(TGT)	 AG	125111-125250	GT	CTG
(TTC)	 AG	127736-127831	TT	GAT
-recovered pasa_asmbl_23055.p1, terminal, 127736, 127831
-recovered pasa_asmbl_23055.p1, internal, 117716, 117875
-recovered pasa_asmbl_23055.p1, internal, 118959, 119013
-recovered pasa_asmbl_23055.p1, internal, 119521, 119636
-recovered pasa_asmbl_23055.p1, internal, 119899, 119974
-recovered pasa_asmbl_23055.p1, internal, 120177, 120331
-recovered pasa_asmbl_23055.p1, internal, 120722, 120819
-recovered pasa_asmbl_23055.p1, internal, 121130, 121244
-recovered pasa_asmbl_23055.p1, internal, 121610, 121682
-recovered pasa_asmbl_23055.p1, internal, 122310, 122412
-recovered pasa_asmbl_23055.p1, internal, 124275, 124425
-recovered pasa_asmbl_23055.p1, internal, 124651, 124743
-recovered pasa_asmbl_23055.p1, internal, 125111, 125250
Valid prediction for snap_scaffold_2-snap.987-T1
Valid prediction for GlimmerHMM_glimmerT_3640-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17621, rend_intergenic: 16034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21968, rend_intergenic: 21109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59715, rend_intergenic: 57876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80398, rend_intergenic: 73508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105784, rend_intergenic: 103617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111678, rend_intergenic: 109941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132640, rend_intergenic: 128414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163484, rend_intergenic: 158895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170076, rend_intergenic: 167595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235964
-exon list size: 379


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.6    
1.8    
2.1    
2.4    
2.6    
2.9    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.8    
6.0    
6.3    
6.6    
6.8    
7.1    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
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9.7    
10.0    
10.2    
10.5    
10.8    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.3    
17.6    
17.8    
18.1    
18.4    
18.6    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.3    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.8    
27.0    
27.3    
27.6    
27.8    
28.1    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.2    
57.5    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.0    
64.3    
64.6    
64.8    
65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
71.9    
72.2    
72.4    
72.7    
73.0    
73.2    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.7    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.4    
81.6    
81.9    
82.2    
82.4    
82.7    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
92.9    
93.2    
93.4    
93.7    
94.0    
94.2    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.1    
97.4    
97.6    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 17621, rend_intergenic: 16034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21968, rend_intergenic: 21109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59715, rend_intergenic: 57876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80398, rend_intergenic: 73508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105784, rend_intergenic: 103617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111678, rend_intergenic: 109941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132640, rend_intergenic: 128414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163484, rend_intergenic: 158895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170076, rend_intergenic: 167595  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