-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_6393328-6656389

-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_4-snap.1403-T1
Valid prediction for GlimmerHMM_glimmerT_9740-T1
Valid prediction for GeneMark_model.15810_t
Valid prediction for GlimmerHMM_glimmerT_9737-T1
Valid prediction for pasa_asmbl_42744.p1
Valid prediction for Augustus_model.g6373.t1
Valid prediction for GlimmerHMM_glimmerT_9735-T1
Valid prediction for snap_scaffold_4-snap.1367-T1
Valid prediction for GlimmerHMM_glimmerT_9732-T1
Valid prediction for GeneMark_model.15813_t
Valid prediction for snap_scaffold_4-snap.1372-T1
Couldn't classify 174732, 174875
Sorry, prediction pasa_asmbl_42739.p1 fails validation.
(ATG)	 AG	171073-171211	GT	AGG
(GGG)	 AG	171323-171520	GT	AGG
(GGG)	 AG	171667-171801	GT	CAG
(TCC)	 AG	172119-172238	GT	TGG
(ATG)	 AG	172387-172956	GT	GGG
(AAA)	 AG	173212-173267	GT	TGG
(TTC)	 AG	173414-173488	GT	AGG
(AGT)	 AG	173772-173957	GT	TGG
(GGG)	 AG	174194-174385	GT	AGG
(CTT)	 AG	174732-174875	CC	CTC
-recovered pasa_asmbl_42739.p1, initial, 171073, 171211
add_exon() Sorry, pasa_asmbl_42739.p1 172387-172956-initial-1 is invalid.
-recovered pasa_asmbl_42739.p1, initial, 172387, 172956
-recovered pasa_asmbl_42739.p1, internal, 171073, 171211
-recovered pasa_asmbl_42739.p1, internal, 171323, 171520
-recovered pasa_asmbl_42739.p1, internal, 171667, 171801
-recovered pasa_asmbl_42739.p1, internal, 172119, 172238
-recovered pasa_asmbl_42739.p1, internal, 172387, 172956
-recovered pasa_asmbl_42739.p1, internal, 173212, 173267
-recovered pasa_asmbl_42739.p1, internal, 173414, 173488
-recovered pasa_asmbl_42739.p1, internal, 173772, 173957
-recovered pasa_asmbl_42739.p1, internal, 174194, 174385
Valid prediction for snap_scaffold_4-snap.1394-T1
Valid prediction for snap_scaffold_4-snap.1399-T1
Valid prediction for Augustus_model.g6365.t1
Valid prediction for GeneMark_model.15815_t
Valid prediction for snap_scaffold_4-snap.1400-T1
Valid prediction for Augustus_model.g6366.t1
Valid prediction for snap_scaffold_4-snap.1380-T1
Valid prediction for GlimmerHMM_glimmerT_9720-T1
Valid prediction for GlimmerHMM_glimmerT_9728-T1
Valid prediction for GlimmerHMM_glimmerT_9731-T1
Valid prediction for pasa_asmbl_42751.p1
Valid prediction for GlimmerHMM_glimmerT_9742-T1
Valid prediction for snap_scaffold_4-snap.1392-T1
Valid prediction for HiQ_model.g6371.t1
Valid prediction for GeneMark_model.15837_t
Valid prediction for snap_scaffold_4-snap.1381-T1
Valid prediction for GeneMark_model.15824_t
Valid prediction for snap_scaffold_4-snap.1368-T1
Valid prediction for snap_scaffold_4-snap.1378-T1
Valid prediction for Augustus_model.g6368.t1
Valid prediction for GlimmerHMM_glimmerT_9733-T1
Valid prediction for GlimmerHMM_glimmerT_9726-T1
Valid prediction for snap_scaffold_4-snap.1382-T1
Valid prediction for GlimmerHMM_glimmerT_9721-T1
Valid prediction for GlimmerHMM_glimmerT_9717-T1
Valid prediction for Augustus_model.g6360.t1
Valid prediction for GeneMark_model.15831_t
Valid prediction for snap_scaffold_4-snap.1384-T1
Valid prediction for snap_scaffold_4-snap.1371-T1
Valid prediction for GeneMark_model.15833_t
Valid prediction for GeneMark_model.15825_t
Valid prediction for GeneMark_model.15812_t
Valid prediction for GeneMark_model.15835_t
Valid prediction for GeneMark_model.15820_t
Valid prediction for snap_scaffold_4-snap.1388-T1
Valid prediction for GlimmerHMM_glimmerT_9738-T1
Valid prediction for snap_scaffold_4-snap.1387-T1
Valid prediction for snap_scaffold_4-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_9725-T1
Valid prediction for snap_scaffold_4-snap.1379-T1
Valid prediction for snap_scaffold_4-snap.1386-T1
Valid prediction for Augustus_model.g6364.t1
Valid prediction for GeneMark_model.15819_t
Valid prediction for Augustus_model.g6357.t1
Valid prediction for snap_scaffold_4-snap.1396-T1
Valid prediction for snap_scaffold_4-snap.1383-T1
Valid prediction for CodingQuarry_transcript_48921-T1
Valid prediction for GeneMark_model.15821_t
Valid prediction for snap_scaffold_4-snap.1385-T1
Valid prediction for GlimmerHMM_glimmerT_9741-T1
Valid prediction for HiQ_model.g6374.t1
Valid prediction for Augustus_model.g6363.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_4-snap.1402-T1
Valid prediction for Augustus_model.g6370.t1
Valid prediction for HiQ_model.g6361.t1
Valid prediction for GlimmerHMM_glimmerT_9716-T1
Valid prediction for snap_scaffold_4-snap.1376-T1
Valid prediction for snap_scaffold_4-snap.1369-T1
Valid prediction for snap_scaffold_4-snap.1375-T1
Valid prediction for GeneMark_model.15823_t
Valid prediction for HiQ_model.g6367.t1
Valid prediction for GeneMark_model.15829_t
Valid prediction for snap_scaffold_4-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_9718-T1
Couldn't classify 75002, 75604
Sorry, prediction pasa_asmbl_41427.p1 fails validation.
(ACC)	 GC	75002-75604	GG	GGG
Valid prediction for GeneMark_model.15834_t
Valid prediction for snap_scaffold_4-snap.1370-T1
Valid prediction for snap_scaffold_4-snap.1389-T1
Couldn't classify 43224, 43245
Couldn't classify 47099, 47475
Sorry, prediction pasa_asmbl_41430.p1 fails validation.
(GGA)	 CT	43224-43245	GT	GGG
(GCA)	 AG	45378-45593	GC	AGG
(ACG)	 AG	46342-46566	GT	AGG
(GTG)	 AG	47099-47475	CC	AGC
-recovered pasa_asmbl_41430.p1, internal, 45378, 45593
-recovered pasa_asmbl_41430.p1, internal, 46342, 46566
Couldn't classify 93372, 93412
Sorry, prediction pasa_asmbl_41425.p1 fails validation.
(GGT)	 CA	93372-93412	GT	GGG
(ACC)	 AG	94715-94795	GT	AGG
(GTC)	 AG	95207-95292	GT	GTG
(GCA)	 AG	95398-95770	GT	AGG
(GGT)	 AG	96184-96338	GT	CGG
(GTC)	 AG	97130-97241	GT	AGG
(TGG)	 AG	97879-98065	GT	TGG
(TCC)	 AG	98174-98263	AA	GAA
-recovered pasa_asmbl_41425.p1, terminal, 98174, 98263
-recovered pasa_asmbl_41425.p1, internal, 94715, 94795
-recovered pasa_asmbl_41425.p1, internal, 95207, 95292
-recovered pasa_asmbl_41425.p1, internal, 95398, 95770
-recovered pasa_asmbl_41425.p1, internal, 96184, 96338
-recovered pasa_asmbl_41425.p1, internal, 97130, 97241
-recovered pasa_asmbl_41425.p1, internal, 97879, 98065
Valid prediction for GlimmerHMM_glimmerT_9739-T1
Valid prediction for HiQ_model.g6369.t1
Valid prediction for GeneMark_model.15822_t
Valid prediction for GlimmerHMM_glimmerT_9723-T1
Valid prediction for GlimmerHMM_glimmerT_9736-T1
Valid prediction for Augustus_model.g6362.t1
Valid prediction for snap_scaffold_4-snap.1398-T1
Couldn't classify 71119, 71297
Couldn't classify 74899, 75001
Sorry, prediction pasa_asmbl_41428.p1 fails validation.
(CGT)	 AG	71119-71297	GT	GAG
(AGC)	 AG	72771-72905	GT	AGG
(GCA)	 AG	74899-75001	AC	GCA
-recovered pasa_asmbl_41428.p1, internal, 71119, 71297
-recovered pasa_asmbl_41428.p1, internal, 72771, 72905
Couldn't classify 163068, 163130
Couldn't classify 168004, 168124
Sorry, prediction pasa_asmbl_41421.p1 fails validation.
(AGT)	 AT	163068-163130	GT	CGG
(GAA)	 AG	163316-163381	GT	AGG
(TCT)	 AG	163486-163559	GT	AAG
(GTC)	 AG	163750-163831	GT	TGG
(TCA)	 AG	163934-164026	GT	ATG
(GCA)	 AG	164148-164282	GT	GGG
(ATT)	 AG	164626-164782	GC	AGG
(GAA)	 AG	164873-164953	GT	AGG
(GCA)	 AG	165065-165229	GT	CCG
(CCC)	 AG	165433-165505	GT	TCG
(CTG)	 AG	165989-166123	GT	GAG
(TTA)	 AG	168004-168124	GT	AGG
add_exon() Sorry, pasa_asmbl_41421.p1 164873-164953-terminal-1 is invalid.
-recovered pasa_asmbl_41421.p1, terminal, 164873, 164953
-recovered pasa_asmbl_41421.p1, internal, 163316, 163381
-recovered pasa_asmbl_41421.p1, internal, 163486, 163559
-recovered pasa_asmbl_41421.p1, internal, 163750, 163831
-recovered pasa_asmbl_41421.p1, internal, 163934, 164026
-recovered pasa_asmbl_41421.p1, internal, 164148, 164282
-recovered pasa_asmbl_41421.p1, internal, 164626, 164782
-recovered pasa_asmbl_41421.p1, internal, 164873, 164953
-recovered pasa_asmbl_41421.p1, internal, 165065, 165229
-recovered pasa_asmbl_41421.p1, internal, 165433, 165505
-recovered pasa_asmbl_41421.p1, internal, 165989, 166123
-recovered pasa_asmbl_41421.p1, internal, 168004, 168124
Valid prediction for GlimmerHMM_glimmerT_9724-T1
Valid prediction for GeneMark_model.15832_t
Valid prediction for snap_scaffold_4-snap.1373-T1
Valid prediction for snap_scaffold_4-snap.1395-T1
Valid prediction for snap_scaffold_4-snap.1393-T1
Valid prediction for GeneMark_model.15826_t
Valid prediction for GlimmerHMM_glimmerT_9734-T1
Valid prediction for GeneMark_model.15808_t
Valid prediction for GlimmerHMM_glimmerT_9727-T1
Valid prediction for GlimmerHMM_glimmerT_9722-T1
Valid prediction for Augustus_model.g6356.t1
Valid prediction for GeneMark_model.15807_t
Valid prediction for GeneMark_model.15828_t
Valid prediction for GlimmerHMM_glimmerT_9719-T1
Valid prediction for GeneMark_model.15809_t
Valid prediction for GeneMark_model.15817_t
Valid prediction for snap_scaffold_4-snap.1390-T1
Valid prediction for Augustus_model.g6372.t1
Valid prediction for GeneMark_model.15806_t
Valid prediction for GeneMark_model.15816_t
Valid prediction for HiQ_model.g6359.t1
Valid prediction for snap_scaffold_4-snap.1401-T1
Valid prediction for snap_scaffold_4-snap.1397-T1
Valid prediction for snap_scaffold_4-snap.1374-T1
Valid prediction for snap_scaffold_4-snap.1377-T1
Valid prediction for GeneMark_model.15811_t
Valid prediction for GlimmerHMM_glimmerT_9730-T1
Valid prediction for GlimmerHMM_glimmerT_9729-T1
Valid prediction for GeneMark_model.15836_t
Couldn't classify 63381, 64052
Sorry, prediction pasa_asmbl_41429.p1 fails validation.
(ATG)	 AC	63381-64052	GG	TGG
Valid prediction for Augustus_model.g6358.t1
Couldn't classify 157197, 157244
Sorry, prediction pasa_asmbl_41423.p1 fails validation.
(ACA)	 CG	157197-157244	GT	ATG
(GGC)	 AG	157603-157720	GT	GGG
(TAG)	 AG	158028-158097	GT	AGG
(ATT)	 AG	158684-158810	GT	CAG
(GCA)	 AG	159039-159086	GT	AAG
-recovered pasa_asmbl_41423.p1, terminal, 159039, 159086
-recovered pasa_asmbl_41423.p1, internal, 157603, 157720
-recovered pasa_asmbl_41423.p1, internal, 158028, 158097
-recovered pasa_asmbl_41423.p1, internal, 158684, 158810
-recovered pasa_asmbl_41423.p1, internal, 159039, 159086

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 108371, rend_intergenic: 108368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78668, rend_intergenic: 76149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167860, rend_intergenic: 161236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191965, rend_intergenic: 188857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263062
-exon list size: 410


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
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1.9    
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2.9    
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3.6    
3.9    
4.1    
4.4    
4.6    
4.9    
5.1    
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5.6    
5.8    
6.1    
6.3    
6.6    
6.8    
7.0    
7.3    
7.5    
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8.0    
8.3    
8.5    
8.7    
9.0    
9.2    
9.5    
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10.0    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
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    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
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    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
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    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 108371, rend_intergenic: 108368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78668, rend_intergenic: 76149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167860, rend_intergenic: 161236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191965, rend_intergenic: 188857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12365
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12155
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support