-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_8893201-9085894

-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_24-snap.1848-T1
Valid prediction for GlimmerHMM_glimmerT_54370-T1
Valid prediction for GlimmerHMM_glimmerT_54366-T1
Valid prediction for GeneMark_model.94761_t
Valid prediction for GeneMark_model.94737_t
Valid prediction for snap_scaffold_24-snap.1850-T1
Valid prediction for snap_scaffold_24-snap.1859-T1
Valid prediction for GeneMark_model.94758_t
Valid prediction for GlimmerHMM_glimmerT_54354-T1
Valid prediction for GlimmerHMM_glimmerT_54364-T1
Valid prediction for GlimmerHMM_glimmerT_54376-T1
Couldn't classify 69885, 70022
Sorry, prediction pasa_asmbl_32473.p1 fails validation.
(GTG)	 AG	69885-70022	GT	AGG
(GTG)	 AG	70346-70471	GT	TGG
(ATG)	 AG	70732-70977	GT	AGG
(GCA)	 AG	71200-71436	GT	AGG
-recovered pasa_asmbl_32473.p1, initial, 70732, 70977
-recovered pasa_asmbl_32473.p1, terminal, 71200, 71436
-recovered pasa_asmbl_32473.p1, internal, 69885, 70022
-recovered pasa_asmbl_32473.p1, internal, 70346, 70471
-recovered pasa_asmbl_32473.p1, internal, 70732, 70977
-recovered pasa_asmbl_32473.p1, internal, 71200, 71436
Valid prediction for snap_scaffold_24-snap.1855-T1
Couldn't classify 169179, 169200
Sorry, prediction pasa_asmbl_32490.p1 fails validation.
(TCA)	 AT	169179-169200	GT	TGG
(CTC)	 AG	169770-169806	GT	AGG
(ACC)	 AG	170002-170070	GT	AGG
(TCT)	 AG	170181-170301	GT	GGG
(AGC)	 AG	170402-170581	GT	AGG
(GTG)	 AG	170824-170870	GT	AGG
(CTG)	 AG	171182-171270	GT	AGG
(GTT)	 AG	171377-171474	AA	GAA
-recovered pasa_asmbl_32490.p1, terminal, 171377, 171474
-recovered pasa_asmbl_32490.p1, internal, 169770, 169806
-recovered pasa_asmbl_32490.p1, internal, 170002, 170070
-recovered pasa_asmbl_32490.p1, internal, 170181, 170301
-recovered pasa_asmbl_32490.p1, internal, 170402, 170581
-recovered pasa_asmbl_32490.p1, internal, 170824, 170870
-recovered pasa_asmbl_32490.p1, internal, 171182, 171270
Valid prediction for Augustus_model.g36402.t1
Valid prediction for GeneMark_model.94745_t
Valid prediction for snap_scaffold_24-snap.1853-T1
Valid prediction for GlimmerHMM_glimmerT_54363-T1
Valid prediction for GeneMark_model.94743_t
Valid prediction for HiQ_model.g36391.t1
Valid prediction for GeneMark_model.94756_t
Valid prediction for GlimmerHMM_glimmerT_54353-T1
Valid prediction for GeneMark_model.94744_t
Valid prediction for GlimmerHMM_glimmerT_54360-T1
Valid prediction for snap_scaffold_24-snap.1863-T1
Valid prediction for HiQ_model.g36403.t1
Valid prediction for GeneMark_model.94734_t
Valid prediction for GeneMark_model.94746_t
Couldn't classify 94260, 94664
Couldn't classify 95100, 95155
Sorry, prediction pasa_asmbl_32479.p1 fails validation.
(CTG)	 CG	94260-94664	GT	AGG
(AGG)	 AG	94804-94834	GT	TGG
(TGC)	 AG	95100-95155	TA	ACT
-recovered pasa_asmbl_32479.p1, internal, 94804, 94834
Valid prediction for CodingQuarry_transcript_37327-T1
Couldn't classify 137959, 138179
Couldn't classify 138380, 138662
Sorry, prediction pasa_asmbl_32484.p1 fails validation.
(GGA)	 TG	137959-138179	GT	ATG
(CAA)	 AG	138380-138662	GT	AGG
-recovered pasa_asmbl_32484.p1, internal, 138380, 138662
Valid prediction for GeneMark_model.94753_t
Valid prediction for snap_scaffold_24-snap.1844-T1
Valid prediction for snap_scaffold_24-snap.1865-T1
Valid prediction for Augustus_model.g36394.t1
Valid prediction for HiQ_model.g36406.t1
Valid prediction for snap_scaffold_24-snap.1849-T1
Valid prediction for Augustus_model.g36388.t1
Couldn't classify 163831, 163916
Sorry, prediction pasa_asmbl_32489.p1 fails validation.
(CTC)	 TT	163831-163916	GT	AGG
(GCT)	 AG	164025-164283	GG	GAG
-recovered pasa_asmbl_32489.p1, terminal, 164025, 164283
Couldn't classify 147633, 147696
Sorry, prediction pasa_asmbl_32485.p1 fails validation.
(CTG)	 AA	147633-147696	GT	AGG
(GAA)	 AG	149081-149264	GT	CAG
(GTA)	 AG	149550-149797	GT	AGG
(AAG)	 AG	150115-150405	GT	AGG
(ATG)	 AG	151415-151504	GT	TGG
(GTG)	 AG	151718-151863	CA	AAC
add_exon() Sorry, pasa_asmbl_32485.p1 151415-151504-initial-1 is invalid.
-recovered pasa_asmbl_32485.p1, initial, 151415, 151504
-recovered pasa_asmbl_32485.p1, terminal, 151718, 151863
-recovered pasa_asmbl_32485.p1, internal, 149081, 149264
-recovered pasa_asmbl_32485.p1, internal, 149550, 149797
-recovered pasa_asmbl_32485.p1, internal, 150115, 150405
-recovered pasa_asmbl_32485.p1, internal, 151415, 151504
Valid prediction for GlimmerHMM_glimmerT_54362-T1
Valid prediction for Augustus_model.g36408.t1
Valid prediction for Augustus_model.g36396.t1
Valid prediction for GlimmerHMM_glimmerT_54361-T1
Valid prediction for snap_scaffold_24-snap.1854-T1
Valid prediction for CodingQuarry_transcript_37322-T1
Valid prediction for GlimmerHMM_glimmerT_54356-T1
Valid prediction for Augustus_model.g36401.t1
Valid prediction for GeneMark_model.94739_t
Valid prediction for GeneMark_model.94752_t
Valid prediction for snap_scaffold_24-snap.1868-T1
Valid prediction for Augustus_model.g36400.t1
Valid prediction for snap_scaffold_24-snap.1851-T1
Valid prediction for GlimmerHMM_glimmerT_54372-T1
Valid prediction for Augustus_model.g36397.t1
Valid prediction for Augustus_model.g36387.t1
Valid prediction for CodingQuarry_transcript_37321-T1
Valid prediction for snap_scaffold_24-snap.1841-T1
Valid prediction for pasa_asmbl_32495.p1
Couldn't classify 91181, 91228
Sorry, prediction pasa_asmbl_32476.p2 fails validation.
(ATG)	 AC	90562-90624	GT	TGG
(ATA)	 AG	90811-90999	GT	AGG
(GAA)	 AG	91181-91228	GA	CTG
-recovered pasa_asmbl_32476.p2, initial, 90562, 90624
-recovered pasa_asmbl_32476.p2, internal, 90811, 90999
Valid prediction for Augustus_model.g36393.t1
Valid prediction for GeneMark_model.94747_t
Valid prediction for snap_scaffold_24-snap.1852-T1
Valid prediction for GlimmerHMM_glimmerT_54367-T1
Valid prediction for GeneMark_model.94742_t
Valid prediction for GlimmerHMM_glimmerT_54355-T1
Valid prediction for pasa_asmbl_32469.p1
Valid prediction for snap_scaffold_24-snap.1866-T1
Valid prediction for GeneMark_model.94757_t
Valid prediction for Augustus_model.g36404.t1
Valid prediction for snap_scaffold_24-snap.1872-T1
Valid prediction for pasa_asmbl_32478.p2
Valid prediction for snap_scaffold_24-snap.1867-T1
Valid prediction for CodingQuarry_transcript_37326-T1
Valid prediction for snap_scaffold_24-snap.1858-T1
Valid prediction for snap_scaffold_24-snap.1870-T1
Valid prediction for GlimmerHMM_glimmerT_54378-T1
Valid prediction for Augustus_model.g36398.t1
Valid prediction for GeneMark_model.94760_t
Valid prediction for pasa_asmbl_32488.p1
Valid prediction for HiQ_model.g36392.t1
Valid prediction for Augustus_model.g36395.t1
Valid prediction for GlimmerHMM_glimmerT_54365-T1
Valid prediction for GeneMark_model.94751_t
Valid prediction for snap_scaffold_24-snap.1845-T1
Couldn't classify 97339, 97515
Sorry, prediction pasa_asmbl_32480.p1 fails validation.
(CAG)	 CC	97339-97515	GT	AGG
(GTA)	 AG	97637-97849	GT	GAG
(GAC)	 AG	98278-98397	GT	TTG
(ATA)	 AG	98611-98751	GT	AGG
(ATC)	 AG	98843-98914	GG	GAG
-recovered pasa_asmbl_32480.p1, terminal, 98843, 98914
-recovered pasa_asmbl_32480.p1, internal, 97637, 97849
-recovered pasa_asmbl_32480.p1, internal, 98278, 98397
-recovered pasa_asmbl_32480.p1, internal, 98611, 98751
Couldn't classify 127234, 127317
Sorry, prediction pasa_asmbl_32482.p1 fails validation.
(ATG)	 AA	124825-124865	GT	ATG
(CCT)	 AG	125584-125741	GT	CAG
(CTC)	 AG	125902-126026	GT	AGG
(CCC)	 AG	126671-126785	GT	GGG
(TAA)	 AG	127058-127143	GT	TTG
(GGG)	 AG	127234-127317	AG	GCA
-recovered pasa_asmbl_32482.p1, initial, 124825, 124865
-recovered pasa_asmbl_32482.p1, internal, 125584, 125741
-recovered pasa_asmbl_32482.p1, internal, 125902, 126026
-recovered pasa_asmbl_32482.p1, internal, 126671, 126785
-recovered pasa_asmbl_32482.p1, internal, 127058, 127143
Valid prediction for CodingQuarry_transcript_37320-T1
Valid prediction for GlimmerHMM_glimmerT_54373-T1
Valid prediction for snap_scaffold_24-snap.1861-T1
Valid prediction for snap_scaffold_24-snap.1856-T1
Valid prediction for GlimmerHMM_glimmerT_54374-T1
Valid prediction for snap_scaffold_24-snap.1862-T1
Valid prediction for GeneMark_model.94749_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 pasa_asmbl_33120.p1
Valid prediction for GlimmerHMM_glimmerT_54357-T1
Valid prediction for HiQ_model.g36407.t1
Valid prediction for snap_scaffold_24-snap.1842-T1
Couldn't classify 19948, 20055
Couldn't classify 20221, 20337
Sorry, prediction CodingQuarry_transcript_37324-T1 fails validation.
(ATG)	 TT	18149-18206	GT	AGG
(GTG)	 AG	19150-19295	GT	AAG
(ATT)	 AG	19463-19526	GT	TGG
(GTA)	 AG	19647-19714	GT	AGG
(GGT)	 AG	19948-20055	CA	TCC
(AGG)	 TC	20221-20337	TC	GAT
-recovered CodingQuarry_transcript_37324-T1, initial, 18149, 18206
-recovered CodingQuarry_transcript_37324-T1, internal, 19150, 19295
-recovered CodingQuarry_transcript_37324-T1, internal, 19463, 19526
-recovered CodingQuarry_transcript_37324-T1, internal, 19647, 19714
Valid prediction for snap_scaffold_24-snap.1860-T1
Valid prediction for CodingQuarry_transcript_37325-T1
Valid prediction for Augustus_model.g36386.t1
Valid prediction for pasa_asmbl_33114.p1
Valid prediction for GlimmerHMM_glimmerT_54351-T1
Valid prediction for GlimmerHMM_glimmerT_54371-T1
Valid prediction for GeneMark_model.94750_t
Valid prediction for GeneMark_model.94732_t
Valid prediction for GlimmerHMM_glimmerT_54368-T1
Valid prediction for snap_scaffold_24-snap.1847-T1
Valid prediction for HiQ_model.g36390.t1
Valid prediction for Augustus_model.g36405.t1
Valid prediction for snap_scaffold_24-snap.1843-T1
Valid prediction for GeneMark_model.94740_t
Valid prediction for GeneMark_model.94748_t
Valid prediction for GlimmerHMM_glimmerT_54359-T1
Valid prediction for GeneMark_model.94741_t
Valid prediction for CodingQuarry_transcript_37319-T1
Valid prediction for GeneMark_model.94733_t
Valid prediction for GeneMark_model.94755_t
Valid prediction for GlimmerHMM_glimmerT_54352-T1
Valid prediction for GlimmerHMM_glimmerT_54369-T1
Valid prediction for snap_scaffold_24-snap.1846-T1
Valid prediction for Augustus_model.g36399.t1
Valid prediction for snap_scaffold_24-snap.1869-T1
Valid prediction for CodingQuarry_transcript_37318-T1
Valid prediction for GeneMark_model.94754_t
Valid prediction for snap_scaffold_24-snap.1840-T1
Valid prediction for snap_scaffold_24-snap.1871-T1
Valid prediction for HiQ_model.g36389.t1
Valid prediction for snap_scaffold_24-snap.1857-T1
Valid prediction for GeneMark_model.94735_t
Valid prediction for GlimmerHMM_glimmerT_54377-T1
Valid prediction for snap_scaffold_24-snap.1864-T1
Valid prediction for pasa_asmbl_33117.p1
Valid prediction for GeneMark_model.94759_t
Valid prediction for GlimmerHMM_glimmerT_54358-T1
Valid prediction for GlimmerHMM_glimmerT_54375-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 107107, rend_intergenic: 104279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192694
-exon list size: 490


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.2    
2.4    
2.6    
2.8    
3.0    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.9    
6.1    
6.3    
6.5    
6.7    
6.9    
7.1    
7.3    
7.5    
7.7    
7.9    
8.1    
8.3    
8.5    
8.7    
8.9    
9.1    
9.3    
9.6    
9.8    
10.0    
10.2    
10.4    
10.6    
10.8    
11.0    
11.2    
11.4    
11.6    
11.8    
12.0    
12.2    
12.4    
12.6    
12.8    
13.0    
13.2    
13.4    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.2    
15.4    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.3    
21.5    
21.7    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
29.9    
30.1    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.2    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.8    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
90.4    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 107107, rend_intergenic: 104279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13089
-exon list size: 38


building trellis

2.5    
5.0    
7.5    
10.0    
12.5    
15.0    
17.5    
20.0    
22.5    
25.0    
27.5    
30.0    
32.5    
35.0    
37.5    
40.0    
42.5    
45.0    
47.5    
50.0    
52.5    
55.0    
57.5    
60.0    
62.5    
65.0    
67.5    
70.0    
72.5    
75.0    
77.5    
80.0    
82.5    
85.0    
87.5    
90.0    
92.5    
95.0    
97.5    
-found 2 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support