-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_7642885-7799959

-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_20-snap.1663-T1
Valid prediction for pasa_asmbl_26728.p1
Couldn't classify 100958, 101308
Sorry, prediction pasa_asmbl_26726.p4 fails validation.
(TGG)	 GG	100958-101308	TA	GCT
Valid prediction for HiQ_model.g30768.t1
Couldn't classify 131243, 131374
Couldn't classify 132157, 132219
Sorry, prediction pasa_asmbl_26727.p2 fails validation.
(TAC)	 CC	131243-131374	GT	GGG
(GCT)	 AG	131703-131824	GT	AGG
(ATA)	 AG	131954-132023	GT	TGG
(ATC)	 AG	132157-132219	AC	GGA
-recovered pasa_asmbl_26727.p2, internal, 131703, 131824
-recovered pasa_asmbl_26727.p2, internal, 131954, 132023
Valid prediction for Augustus_model.g30769.t1
Valid prediction for snap_scaffold_20-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_46354-T1
Valid prediction for snap_scaffold_20-snap.1686-T1
Valid prediction for snap_scaffold_20-snap.1687-T1
Valid prediction for snap_scaffold_20-snap.1665-T1
Valid prediction for Augustus_model.g30771.t1
Valid prediction for CodingQuarry_transcript_30556-T1
Valid prediction for GlimmerHMM_glimmerT_46331-T1
Valid prediction for GlimmerHMM_glimmerT_46342-T1
Valid prediction for GlimmerHMM_glimmerT_46352-T1
Valid prediction for GlimmerHMM_glimmerT_46341-T1
Valid prediction for snap_scaffold_20-snap.1666-T1
Valid prediction for Augustus_model.g30776.t1
Valid prediction for snap_scaffold_20-snap.1675-T1
Valid prediction for snap_scaffold_20-snap.1679-T1
Valid prediction for snap_scaffold_20-snap.1676-T1
Valid prediction for Augustus_model.g30770.t1
Valid prediction for Augustus_model.g30775.t1
Valid prediction for Augustus_model.g30772.t1
Valid prediction for snap_scaffold_20-snap.1685-T1
Valid prediction for pasa_asmbl_26724.p1
Couldn't classify 69317, 69337
Sorry, prediction pasa_asmbl_27205.p1 fails validation.
(ATG)	 GC	67015-67027	GT	GGG
(GCT)	 AG	68025-68126	GT	AGG
(GAA)	 AG	68630-68721	GT	GGG
(GCC)	 AG	68838-68906	GT	AGG
(TCT)	 AG	69317-69337	CT	ACC
-recovered pasa_asmbl_27205.p1, initial, 67015, 67027
-recovered pasa_asmbl_27205.p1, internal, 68025, 68126
-recovered pasa_asmbl_27205.p1, internal, 68630, 68721
-recovered pasa_asmbl_27205.p1, internal, 68838, 68906
Valid prediction for GlimmerHMM_glimmerT_46355-T1
Valid prediction for snap_scaffold_20-snap.1698-T1
Valid prediction for snap_scaffold_20-snap.1678-T1
Valid prediction for snap_scaffold_20-snap.1683-T1
Couldn't classify 72316, 72422
Sorry, prediction pasa_asmbl_27153.p1 fails validation.
(ATG)	 AC	71426-71513	GT	AGG
(AGC)	 AG	71934-72020	GT	CTG
(GGC)	 AG	72316-72422	AT	AGA
-recovered pasa_asmbl_27153.p1, initial, 71426, 71513
-recovered pasa_asmbl_27153.p1, internal, 71934, 72020
Valid prediction for GlimmerHMM_glimmerT_46345-T1
Valid prediction for Augustus_model.g30773.t1
Valid prediction for GlimmerHMM_glimmerT_46332-T1
Valid prediction for GlimmerHMM_glimmerT_46338-T1
Valid prediction for snap_scaffold_20-snap.1692-T1
Valid prediction for GlimmerHMM_glimmerT_46336-T1
Valid prediction for snap_scaffold_20-snap.1696-T1
Valid prediction for GlimmerHMM_glimmerT_46349-T1
Couldn't classify 72744, 72781
Sorry, prediction pasa_asmbl_26725.p1 fails validation.
(GTG)	 GA	72744-72781	GT	AGG
(GAA)	 AG	73143-73242	GT	GAG
(GAA)	 AG	73833-73955	GT	TGG
(TCA)	 AG	74443-74550	GT	AGG
(ATG)	 AG	74846-74945	GT	AGG
(ACG)	 AG	75098-75168	GT	AGG
(GTG)	 AG	75361-75451	GT	AGG
(ATC)	 AG	75600-75652	GT	CGG
(GAC)	 AG	75763-75869	GT	AGG
(CAT)	 AG	76257-76413	CA	GAC
-recovered pasa_asmbl_26725.p1, initial, 74846, 74945
-recovered pasa_asmbl_26725.p1, terminal, 76257, 76413
-recovered pasa_asmbl_26725.p1, internal, 73143, 73242
-recovered pasa_asmbl_26725.p1, internal, 73833, 73955
-recovered pasa_asmbl_26725.p1, internal, 74443, 74550
-recovered pasa_asmbl_26725.p1, internal, 74846, 74945
-recovered pasa_asmbl_26725.p1, internal, 75098, 75168
-recovered pasa_asmbl_26725.p1, internal, 75361, 75451
-recovered pasa_asmbl_26725.p1, internal, 75600, 75652
-recovered pasa_asmbl_26725.p1, internal, 75763, 75869
Valid prediction for snap_scaffold_20-snap.1669-T1
Valid prediction for snap_scaffold_20-snap.1661-T1
Valid prediction for GlimmerHMM_glimmerT_46335-T1
Valid prediction for Augustus_model.g30764.t1
Valid prediction for snap_scaffold_20-snap.1684-T1
Valid prediction for snap_scaffold_20-snap.1700-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_30555-T1
Valid prediction for GlimmerHMM_glimmerT_46347-T1
Valid prediction for GlimmerHMM_glimmerT_46353-T1
Valid prediction for snap_scaffold_20-snap.1690-T1
Valid prediction for snap_scaffold_20-snap.1689-T1
Valid prediction for Augustus_model.g30765.t1
Valid prediction for GlimmerHMM_glimmerT_46343-T1
Valid prediction for snap_scaffold_20-snap.1681-T1
Valid prediction for GlimmerHMM_glimmerT_46339-T1
Valid prediction for snap_scaffold_20-snap.1694-T1
Valid prediction for GlimmerHMM_glimmerT_46351-T1
Valid prediction for GlimmerHMM_glimmerT_46337-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 snap_scaffold_20-snap.1672-T1
Valid prediction for snap_scaffold_20-snap.1660-T1
Couldn't classify 1466, 1552
Couldn't classify 3613, 3820
Sorry, prediction pasa_asmbl_25918.p1 fails validation.
(GTC)	 CT	1466-1552	GT	ATG
(GGG)	 AG	1709-1810	GT	CCG
(TAT)	 AG	2270-2398	GT	GGG
(AAA)	 AG	2746-2849	GT	GGG
(AGT)	 AG	3613-3820	CA	TGC
-recovered pasa_asmbl_25918.p1, internal, 1709, 1810
-recovered pasa_asmbl_25918.p1, internal, 2270, 2398
-recovered pasa_asmbl_25918.p1, internal, 2746, 2849
Valid prediction for snap_scaffold_20-snap.1699-T1
Valid prediction for snap_scaffold_20-snap.1682-T1
Valid prediction for GlimmerHMM_glimmerT_46340-T1
Valid prediction for Augustus_model.g30763.t1
Valid prediction for snap_scaffold_20-snap.1673-T1
Valid prediction for snap_scaffold_20-snap.1667-T1
Valid prediction for GlimmerHMM_glimmerT_46348-T1
Valid prediction for snap_scaffold_20-snap.1674-T1
Valid prediction for snap_scaffold_20-snap.1697-T1
Valid prediction for Augustus_model.g30767.t1
Valid prediction for snap_scaffold_20-snap.1695-T1
Valid prediction for snap_scaffold_20-snap.1693-T1
Valid prediction for GlimmerHMM_glimmerT_46344-T1
Valid prediction for Augustus_model.g30774.t1
Valid prediction for GlimmerHMM_glimmerT_46350-T1
Valid prediction for snap_scaffold_20-snap.1670-T1
Valid prediction for snap_scaffold_20-snap.1671-T1
Valid prediction for snap_scaffold_20-snap.1662-T1
Valid prediction for snap_scaffold_20-snap.1677-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g30766.t1
Valid prediction for GlimmerHMM_glimmerT_46346-T1
Valid prediction for snap_scaffold_20-snap.1664-T1
Valid prediction for Augustus_model.g30777.t1
Valid prediction for GlimmerHMM_glimmerT_46333-T1
Valid prediction for snap_scaffold_20-snap.1688-T1
Valid prediction for snap_scaffold_20-snap.1668-T1
Valid prediction for snap_scaffold_20-snap.1680-T1
Valid prediction for GlimmerHMM_glimmerT_46334-T1
Valid prediction for CodingQuarry_transcript_30557-T1
Valid prediction for GlimmerHMM_glimmerT_46356-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8615, rend_intergenic: 2784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15382, rend_intergenic: 12854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22522, rend_intergenic: 19473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29759, rend_intergenic: 23771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45918, rend_intergenic: 41976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54917, rend_intergenic: 52216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69499, rend_intergenic: 67015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128630, rend_intergenic: 124828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135366, rend_intergenic: 131140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144620, rend_intergenic: 137345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156779, rend_intergenic: 149391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 109714, rend_intergenic: 109711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157075
-exon list size: 366


building trellis

0.3    
0.5    
0.8    
1.1    
1.4    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.3    
3.5    
3.8    
4.1    
4.3    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.2    
6.5    
6.8    
7.1    
7.3    
7.6    
7.9    
8.2    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
13.3    
13.6    
13.9    
14.1    
14.4    
14.7    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.8    
17.1    
17.4    
17.7    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.7    
20.9    
21.2    
21.5    
21.7    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.3    
29.6    
29.9    
30.2    
30.4    
30.7    
31.0    
31.2    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.1    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
64.9    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.8    
69.0    
69.3    
69.6    
69.8    
70.1    
70.4    
70.7    
70.9    
71.2    
71.5    
71.7    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.3    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.3    
82.6    
82.9    
83.2    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.3    
85.6    
85.9    
86.1    
86.4    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.8    
92.1    
92.4    
92.7    
92.9    
93.2    
93.5    
93.8    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
95.9    
96.2    
96.5    
96.7    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 8615, rend_intergenic: 2784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15382, rend_intergenic: 12854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22522, rend_intergenic: 19473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29759, rend_intergenic: 23771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45918, rend_intergenic: 41976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54917, rend_intergenic: 52216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69499, rend_intergenic: 67015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128630, rend_intergenic: 124828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135366, rend_intergenic: 131140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144620, rend_intergenic: 137345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156779, rend_intergenic: 149391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 109714, rend_intergenic: 109711  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