-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_7737863-7910156

-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_21-snap.1655-T1
Valid prediction for Augustus_model.g32127.t1
Valid prediction for snap_scaffold_21-snap.1658-T1
Valid prediction for GlimmerHMM_glimmerT_48106-T1
Valid prediction for snap_scaffold_21-snap.1644-T1
Valid prediction for snap_scaffold_21-snap.1663-T1
Valid prediction for GlimmerHMM_glimmerT_48118-T1
Valid prediction for GlimmerHMM_glimmerT_48123-T1
Valid prediction for snap_scaffold_21-snap.1636-T1
Valid prediction for Augustus_model.g32122.t1
Valid prediction for snap_scaffold_21-snap.1649-T1
Valid prediction for snap_scaffold_21-snap.1630-T1
Valid prediction for snap_scaffold_21-snap.1640-T1
Valid prediction for snap_scaffold_21-snap.1633-T1
Valid prediction for snap_scaffold_21-snap.1629-T1
Valid prediction for snap_scaffold_21-snap.1642-T1
Valid prediction for snap_scaffold_21-snap.1631-T1
Valid prediction for GlimmerHMM_glimmerT_48108-T1
Valid prediction for GlimmerHMM_glimmerT_48113-T1
Valid prediction for snap_scaffold_21-snap.1634-T1
Valid prediction for snap_scaffold_21-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_48122-T1
Valid prediction for Augustus_model.g32126.t1
Valid prediction for GlimmerHMM_glimmerT_48114-T1
Valid prediction for snap_scaffold_21-snap.1660-T1
Valid prediction for snap_scaffold_21-snap.1643-T1
Valid prediction for snap_scaffold_21-snap.1639-T1
Valid prediction for snap_scaffold_21-snap.1651-T1
Valid prediction for snap_scaffold_21-snap.1637-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: -)Couldn't classify 22451, 22639
Sorry, prediction pasa_asmbl_28178.p1 fails validation.
(ATG)	 TC	16675-16768	GT	CGG
(CAA)	 AG	16923-16994	GT	AGG
(CCT)	 AG	17143-17210	GT	AGG
(GTG)	 AG	17534-17684	GT	GGG
(ACT)	 AG	17906-18021	GT	AGG
(CTG)	 AG	18145-18252	GT	AGG
(AAA)	 AG	18445-18525	GT	AGG
(TCT)	 AG	18788-18891	GT	AAG
(GCG)	 AG	20135-20285	GT	AGG
(GGT)	 AG	20487-20648	GT	AGG
(GGT)	 AG	20813-20938	GT	AGG
(GAC)	 AG	21305-21438	GT	AGG
(AAT)	 AG	21687-21780	GT	AGG
(TAC)	 AG	22090-22260	GT	AGG
(AAT)	 AG	22451-22639	CT	TCC
-recovered pasa_asmbl_28178.p1, initial, 16675, 16768
-recovered pasa_asmbl_28178.p1, internal, 16923, 16994
-recovered pasa_asmbl_28178.p1, internal, 17143, 17210
-recovered pasa_asmbl_28178.p1, internal, 17534, 17684
-recovered pasa_asmbl_28178.p1, internal, 17906, 18021
-recovered pasa_asmbl_28178.p1, internal, 18145, 18252
-recovered pasa_asmbl_28178.p1, internal, 18445, 18525
-recovered pasa_asmbl_28178.p1, internal, 18788, 18891
-recovered pasa_asmbl_28178.p1, internal, 20135, 20285
-recovered pasa_asmbl_28178.p1, internal, 20487, 20648
-recovered pasa_asmbl_28178.p1, internal, 20813, 20938
-recovered pasa_asmbl_28178.p1, internal, 21305, 21438
-recovered pasa_asmbl_28178.p1, internal, 21687, 21780
-recovered pasa_asmbl_28178.p1, internal, 22090, 22260
Valid prediction for snap_scaffold_21-snap.1650-T1
Valid prediction for GlimmerHMM_glimmerT_48112-T1
Valid prediction for GlimmerHMM_glimmerT_48119-T1
Valid prediction for GlimmerHMM_glimmerT_48107-T1
Valid prediction for Augustus_model.g32125.t1
Valid prediction for snap_scaffold_21-snap.1648-T1
Valid prediction for snap_scaffold_21-snap.1668-T1
Valid prediction for GlimmerHMM_glimmerT_48115-T1
Valid prediction for snap_scaffold_21-snap.1665-T1
Valid prediction for snap_scaffold_21-snap.1647-T1
Valid prediction for pasa_asmbl_27860.p1
Valid prediction for GlimmerHMM_glimmerT_48116-T1
Valid prediction for GlimmerHMM_glimmerT_48109-T1
Valid prediction for snap_scaffold_21-snap.1632-T1
Valid prediction for GlimmerHMM_glimmerT_48117-T1
Valid prediction for snap_scaffold_21-snap.1661-T1
Valid prediction for CodingQuarry_transcript_32638-T1
Valid prediction for GlimmerHMM_glimmerT_48110-T1
Valid prediction for snap_scaffold_21-snap.1654-T1
Couldn't classify 93556, 93638
Sorry, prediction pasa_asmbl_27858.p1 fails validation.
(CTC)	 AT	93556-93638	GT	AGG
(GTT)	 AG	93731-93872	GT	AGG
(GTG)	 AG	94151-94330	AT	AGA
-recovered pasa_asmbl_27858.p1, terminal, 94151, 94330
-recovered pasa_asmbl_27858.p1, internal, 93731, 93872
Valid prediction for Augustus_model.g32120.t1
Valid prediction for GlimmerHMM_glimmerT_48111-T1
Valid prediction for Augustus_model.g32132.t1
Valid prediction for snap_scaffold_21-snap.1669-T1
Valid prediction for Augustus_model.g32123.t1
Valid prediction for GlimmerHMM_glimmerT_48127-T1
Valid prediction for GlimmerHMM_glimmerT_48105-T1
Valid prediction for snap_scaffold_21-snap.1657-T1
Valid prediction for GlimmerHMM_glimmerT_48121-T1
Couldn't classify 94943, 94969
Couldn't classify 96957, 96989
Sorry, prediction pasa_asmbl_27857.p1 fails validation.
(CAG)	 CA	94943-94969	GT	CGG
(GTT)	 AG	95080-95146	GT	GCG
(CCT)	 AG	95570-95638	GT	CTG
(TTA)	 AG	95785-96047	GT	AGG
(AGG)	 AG	96629-96697	GT	CGG
(AAG)	 AG	96957-96989	CA	CGC
-recovered pasa_asmbl_27857.p1, internal, 95080, 95146
-recovered pasa_asmbl_27857.p1, internal, 95570, 95638
-recovered pasa_asmbl_27857.p1, internal, 95785, 96047
-recovered pasa_asmbl_27857.p1, internal, 96629, 96697
Valid prediction for GlimmerHMM_glimmerT_48126-T1
Valid prediction for snap_scaffold_21-snap.1635-T1
Valid prediction for snap_scaffold_21-snap.1645-T1
Valid prediction for snap_scaffold_21-snap.1638-T1
Valid prediction for snap_scaffold_21-snap.1656-T1
Couldn't classify 137994, 138030
Couldn't classify 141308, 141386
Sorry, prediction pasa_asmbl_27850.p1 fails validation.
(TCC)	 AC	137994-138030	GT	GAG
(TCC)	 AG	139899-139997	GT	GGG
(ACC)	 AG	140823-140913	GT	AGG
(TGA)	 AG	141308-141386	GT	AGG
-recovered pasa_asmbl_27850.p1, internal, 139899, 139997
-recovered pasa_asmbl_27850.p1, internal, 140823, 140913
-recovered pasa_asmbl_27850.p1, internal, 141308, 141386
Valid prediction for snap_scaffold_21-snap.1653-T1
Valid prediction for snap_scaffold_21-snap.1628-T1
Valid prediction for Augustus_model.g32133.t1
Valid prediction for snap_scaffold_21-snap.1646-T1
Valid prediction for snap_scaffold_21-snap.1667-T1
Valid prediction for CodingQuarry_transcript_32639-T1
Valid prediction for Augustus_model.g32135.t1
Valid prediction for HiQ_model.g32130.t1
Valid prediction for HiQ_model.g32128.t1
Valid prediction for snap_scaffold_21-snap.1641-T1
Valid prediction for Augustus_model.g32121.t1
Valid prediction for snap_scaffold_21-snap.1659-T1
Couldn't classify 97272, 97310
Sorry, prediction pasa_asmbl_27855.p1 fails validation.
(GGC)	 CG	97272-97310	GT	AGG
(GAC)	 AG	98468-98716	GT	TGG
(ACG)	 AG	98841-98930	GT	AAG
(ACC)	 AG	99117-99257	GT	AGG
(GAG)	 AG	99405-99498	GT	CAG
(GTT)	 AG	99586-99745	GT	AAG
(TGA)	 AG	100109-100190	GT	AGG
(GGC)	 AG	100529-100663	AG	AGA
-recovered pasa_asmbl_27855.p1, terminal, 100529, 100663
-recovered pasa_asmbl_27855.p1, internal, 98468, 98716
-recovered pasa_asmbl_27855.p1, internal, 98841, 98930
-recovered pasa_asmbl_27855.p1, internal, 99117, 99257
-recovered pasa_asmbl_27855.p1, internal, 99405, 99498
-recovered pasa_asmbl_27855.p1, internal, 99586, 99745
-recovered pasa_asmbl_27855.p1, internal, 100109, 100190
Valid prediction for GlimmerHMM_glimmerT_48125-T1
Valid prediction for Augustus_model.g32131.t1
Valid prediction for Augustus_model.g32124.t1
Valid prediction for snap_scaffold_21-snap.1652-T1
Valid prediction for CodingQuarry_transcript_32640-T1
Valid prediction for GlimmerHMM_glimmerT_48124-T1
Valid prediction for snap_scaffold_21-snap.1662-T1
Valid prediction for Augustus_model.g32129.t1
Valid prediction for Augustus_model.g32134.t1
Valid prediction for snap_scaffold_21-snap.1664-T1
Valid prediction for GlimmerHMM_glimmerT_48120-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13241, rend_intergenic: 1987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20990, rend_intergenic: 14711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34412, rend_intergenic: 26529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40539, rend_intergenic: 34449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41046, rend_intergenic: 40710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42632, rend_intergenic: 41310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55780, rend_intergenic: 49825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70502, rend_intergenic: 70057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117187, rend_intergenic: 104232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121101, rend_intergenic: 117353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124220, rend_intergenic: 122636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129774, rend_intergenic: 127440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136165, rend_intergenic: 130559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139547, rend_intergenic: 137235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146046, rend_intergenic: 144684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155620, rend_intergenic: 153035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172294
-exon list size: 389


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.6    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.9    
5.1    
5.4    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.0    
12.3    
12.5    
12.8    
13.0    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.6    
16.9    
17.1    
17.4    
17.6    
17.9    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.2    
20.5    
20.7    
21.0    
21.2    
21.5    
21.7    
22.0    
22.3    
22.5    
22.8    
23.0    
23.3    
23.5    
23.8    
24.0    
24.3    
24.6    
24.8    
25.1    
25.3    
25.6    
25.8    
26.1    
26.3    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.2    
43.5    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.8    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.2    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.5    
53.7    
54.0    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.5    
56.8    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.8    
59.1    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.1    
61.4    
61.6    
61.9    
62.1    
62.4    
62.7    
62.9    
63.2    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.4    
73.7    
73.9    
74.2    
74.4    
74.7    
74.9    
75.2    
75.4    
75.7    
76.0    
76.2    
76.5    
76.7    
77.0    
77.2    
77.5    
77.7    
78.0    
78.3    
78.5    
78.8    
79.0    
79.3    
79.5    
79.8    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.1    
82.4    
82.6    
82.9    
83.1    
83.4    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
87.0    
87.2    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.4    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 13241, rend_intergenic: 1987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20990, rend_intergenic: 14711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34412, rend_intergenic: 26529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40539, rend_intergenic: 34449  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41046, rend_intergenic: 40710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42632, rend_intergenic: 41310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55780, rend_intergenic: 49825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70502, rend_intergenic: 70057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117187, rend_intergenic: 104232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121101, rend_intergenic: 117353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124220, rend_intergenic: 122636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129774, rend_intergenic: 127440  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136165, rend_intergenic: 130559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139547, rend_intergenic: 137235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146046, rend_intergenic: 144684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155620, rend_intergenic: 153035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support