-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_7503421-7659819

-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 GeneMark_model.25845_t
Valid prediction for GeneMark_model.25853_t
Valid prediction for Augustus_model.g10204.t1
Valid prediction for GeneMark_model.25838_t
Valid prediction for GeneMark_model.25866_t
Valid prediction for GeneMark_model.25842_t
Valid prediction for GeneMark_model.25843_t
Valid prediction for GeneMark_model.25862_t
Valid prediction for GlimmerHMM_glimmerT_15322-T1
Valid prediction for GlimmerHMM_glimmerT_15319-T1
Valid prediction for GeneMark_model.25858_t
Couldn't classify 143827, 143909
Sorry, prediction pasa_asmbl_47019.p1 fails validation.
(CCC)	 CC	143827-143909	GT	AGG
(TGA)	 AG	144499-144583	GT	AGG
(GAG)	 AG	144690-144811	GT	TGG
(GAC)	 AG	145520-145669	GT	TGG
(GTA)	 AG	146372-149795	GT	AGG
(GAG)	 AG	149929-150100	GT	GAG
(GTG)	 AG	150264-150470	GT	AGG
(GAA)	 AG	150598-150623	CT	GAC
-recovered pasa_asmbl_47019.p1, terminal, 150598, 150623
-recovered pasa_asmbl_47019.p1, internal, 144499, 144583
-recovered pasa_asmbl_47019.p1, internal, 144690, 144811
-recovered pasa_asmbl_47019.p1, internal, 145520, 145669
-recovered pasa_asmbl_47019.p1, internal, 146372, 149795
-recovered pasa_asmbl_47019.p1, internal, 149929, 150100
-recovered pasa_asmbl_47019.p1, internal, 150264, 150470
Valid prediction for snap_scaffold_6-snap.1682-T1
Valid prediction for GlimmerHMM_glimmerT_15300-T1
Valid prediction for snap_scaffold_6-snap.1701-T1
Valid prediction for GeneMark_model.25849_t
Valid prediction for Augustus_model.g10206.t1
Valid prediction for GlimmerHMM_glimmerT_15308-T1
Valid prediction for snap_scaffold_6-snap.1692-T1
Valid prediction for Augustus_model.g10197.t1
Valid prediction for snap_scaffold_6-snap.1705-T1
Valid prediction for snap_scaffold_6-snap.1685-T1
Valid prediction for snap_scaffold_6-snap.1677-T1
Valid prediction for Augustus_model.g10190.t1
Valid prediction for GlimmerHMM_glimmerT_15312-T1
Valid prediction for GlimmerHMM_glimmerT_15306-T1
Valid prediction for snap_scaffold_6-snap.1674-T1
Valid prediction for GlimmerHMM_glimmerT_15320-T1
Valid prediction for snap_scaffold_6-snap.1686-T1
Valid prediction for snap_scaffold_6-snap.1679-T1
Valid prediction for HiQ_model.g10196.t1
Valid prediction for CodingQuarry_transcript_54957-T1
Valid prediction for GlimmerHMM_glimmerT_15302-T1
Valid prediction for GlimmerHMM_glimmerT_15325-T1
Valid prediction for Augustus_model.g10200.t1
Valid prediction for CodingQuarry_transcript_54962-T1
Valid prediction for GeneMark_model.25840_t
Valid prediction for GlimmerHMM_glimmerT_15324-T1
Couldn't classify 40394, 40426
Sorry, prediction pasa_asmbl_47014.p1 fails validation.
(CGC)	 TC	40394-40426	GT	AGG
(GAT)	 AG	40717-40787	GT	AAG
(GTA)	 AG	40890-41034	GT	AGG
(AAC)	 AG	41194-41283	GT	AGG
(GCA)	 AG	41423-41548	GT	TGG
(GCA)	 AG	41696-41824	GT	AGG
(GCA)	 AG	41988-42014	AG	AGA
add_exon() Sorry, pasa_asmbl_47014.p1 40717-40787-terminal-2 is invalid.
-recovered pasa_asmbl_47014.p1, terminal, 40717, 40787
-recovered pasa_asmbl_47014.p1, terminal, 41988, 42014
-recovered pasa_asmbl_47014.p1, internal, 40717, 40787
-recovered pasa_asmbl_47014.p1, internal, 40890, 41034
-recovered pasa_asmbl_47014.p1, internal, 41194, 41283
-recovered pasa_asmbl_47014.p1, internal, 41423, 41548
-recovered pasa_asmbl_47014.p1, internal, 41696, 41824
Valid prediction for GeneMark_model.25860_t
Valid prediction for GeneMark_model.25856_t
Valid prediction for Augustus_model.g10199.t1
Valid prediction for GeneMark_model.25864_t
Valid prediction for GlimmerHMM_glimmerT_15305-T1
Valid prediction for snap_scaffold_6-snap.1681-T1
Valid prediction for GlimmerHMM_glimmerT_15310-T1
Valid prediction for Augustus_model.g10212.t1
Valid prediction for Augustus_model.g10193.t1
Valid prediction for pasa_asmbl_47017.p1
Valid prediction for snap_scaffold_6-snap.1704-T1
Valid prediction for GeneMark_model.25868_t
Valid prediction for GlimmerHMM_glimmerT_15315-T1
Valid prediction for Augustus_model.g10208.t1
Valid prediction for snap_scaffold_6-snap.1680-T1
Valid prediction for CodingQuarry_transcript_54958-T1
Couldn't classify 32415, 33026
Sorry, prediction pasa_asmbl_47012.p1 fails validation.
(CTC)	 CT	32415-33026	AT	GCA
Valid prediction for GlimmerHMM_glimmerT_15299-T1
Valid prediction for snap_scaffold_6-snap.1688-T1
Valid prediction for snap_scaffold_6-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_15311-T1
Couldn't classify 35444, 35608
Couldn't classify 36293, 36373
Sorry, prediction pasa_asmbl_47872.p1 fails validation.
(GTG)	 TG	35444-35608	GT	AGG
(ATA)	 AG	36043-36138	GT	AGG
(AGT)	 AG	36293-36373	GT	GAG
-recovered pasa_asmbl_47872.p1, internal, 36043, 36138
-recovered pasa_asmbl_47872.p1, internal, 36293, 36373
Valid prediction for snap_scaffold_6-snap.1700-T1
Valid prediction for GlimmerHMM_glimmerT_15317-T1
Valid prediction for Augustus_model.g10194.t1
Valid prediction for Augustus_model.g10211.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 GlimmerHMM_glimmerT_15323-T1
Valid prediction for Augustus_model.g10192.t1
Valid prediction for snap_scaffold_6-snap.1697-T1
Valid prediction for snap_scaffold_6-snap.1687-T1
Valid prediction for CodingQuarry_transcript_54961-T1
Valid prediction for GlimmerHMM_glimmerT_15321-T1
Valid prediction for snap_scaffold_6-snap.1696-T1
Valid prediction for Augustus_model.g10203.t1
Valid prediction for snap_scaffold_6-snap.1694-T1
Valid prediction for GeneMark_model.25855_t
Valid prediction for snap_scaffold_6-snap.1673-T1
Valid prediction for GeneMark_model.25863_t
Valid prediction for GlimmerHMM_glimmerT_15307-T1
Valid prediction for Augustus_model.g10202.t1
Valid prediction for GlimmerHMM_glimmerT_15309-T1
Valid prediction for GlimmerHMM_glimmerT_15318-T1
Valid prediction for HiQ_model.g10189.t1
Valid prediction for snap_scaffold_6-snap.1698-T1
Valid prediction for pasa_asmbl_48438.p1
Valid prediction for GeneMark_model.25865_t
Valid prediction for Augustus_model.g10207.t1
Valid prediction for GlimmerHMM_glimmerT_15303-T1
Valid prediction for GeneMark_model.25848_t
Valid prediction for GlimmerHMM_glimmerT_15316-T1
Valid prediction for snap_scaffold_6-snap.1684-T1
Valid prediction for Augustus_model.g10195.t1
Valid prediction for HiQ_model.g10205.t1
Valid prediction for GeneMark_model.25859_t
Valid prediction for GeneMark_model.25857_t
Valid prediction for snap_scaffold_6-snap.1690-T1
Valid prediction for snap_scaffold_6-snap.1672-T1
Valid prediction for Augustus_model.g10191.t1
Valid prediction for GeneMark_model.25850_t
Valid prediction for GeneMark_model.25841_t
Valid prediction for GlimmerHMM_glimmerT_15313-T1
Valid prediction for GeneMark_model.25851_t
Valid prediction for snap_scaffold_6-snap.1676-T1
Valid prediction for GeneMark_model.25854_t
Valid prediction for snap_scaffold_6-snap.1693-T1
Valid prediction for Augustus_model.g10209.t1
Valid prediction for HiQ_model.g10201.t1
Valid prediction for pasa_asmbl_48440.p1
Valid prediction for CodingQuarry_transcript_54960-T1
Valid prediction for CodingQuarry_transcript_54956-T1
Valid prediction for GeneMark_model.25837_t
Valid prediction for GlimmerHMM_glimmerT_15314-T1
Valid prediction for GeneMark_model.25839_t
Valid prediction for snap_scaffold_6-snap.1675-T1
Valid prediction for snap_scaffold_6-snap.1703-T1
Valid prediction for snap_scaffold_6-snap.1678-T1
Valid prediction for Augustus_model.g10210.t1
Valid prediction for GlimmerHMM_glimmerT_15301-T1
Valid prediction for GlimmerHMM_glimmerT_15304-T1
Valid prediction for GeneMark_model.25861_t
Valid prediction for pasa_asmbl_48436.p1
Valid prediction for snap_scaffold_6-snap.1702-T1
Valid prediction for snap_scaffold_6-snap.1683-T1
Valid prediction for GeneMark_model.25867_t
Valid prediction for snap_scaffold_6-snap.1691-T1
Valid prediction for Augustus_model.g10198.t1
Valid prediction for snap_scaffold_6-snap.1689-T1
Valid prediction for GeneMark_model.25852_t
Valid prediction for snap_scaffold_6-snap.1699-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 39838, rend_intergenic: 35144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74230, rend_intergenic: 71261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132610, rend_intergenic: 124240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141773, rend_intergenic: 133845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142260, rend_intergenic: 141999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156399
-exon list size: 425


building trellis

0.2    
0.5    
0.7    
0.9    
1.2    
1.4    
1.6    
1.9    
2.1    
2.3    
2.6    
2.8    
3.0    
3.3    
3.5    
3.7    
4.0    
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4.9    
5.2    
5.4    
5.6    
5.9    
6.1    
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6.6    
6.8    
7.0    
7.3    
7.5    
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8.0    
8.2    
8.4    
8.7    
8.9    
9.1    
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9.8    
10.1    
10.3    
10.5    
10.8    
11.0    
11.2    
11.5    
11.7    
11.9    
12.2    
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12.6    
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13.1    
13.3    
13.6    
13.8    
14.1    
14.3    
14.5    
14.8    
15.0    
15.2    
15.5    
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15.9    
16.2    
16.4    
16.6    
16.9    
17.1    
17.3    
17.6    
17.8    
18.0    
18.3    
18.5    
18.7    
19.0    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.8    
21.1    
21.3    
21.5    
21.8    
22.0    
22.2    
22.5    
22.7    
23.0    
23.2    
23.4    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.1    
25.3    
25.5    
25.8    
26.0    
26.2    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.4    
34.7    
34.9    
35.1    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.5    
37.7    
37.9    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.1    
46.4    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.5    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.5    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.2    
53.4    
53.6    
53.9    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.1    
62.3    
62.5    
62.8    
63.0    
63.2    
63.5    
63.7    
63.9    
64.2    
64.4    
64.6    
64.9    
65.1    
65.3    
65.6    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.4    
67.7    
67.9    
68.1    
68.4    
68.6    
68.9    
69.1    
69.3    
69.6    
69.8    
70.0    
70.3    
70.5    
70.7    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.3    
77.5    
77.8    
78.0    
78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.0    
81.3    
81.5    
81.7    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.8    
88.1    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.7    
93.9    
94.1    
94.4    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.0    
96.3    
96.5    
96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 39838, rend_intergenic: 35144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74230, rend_intergenic: 71261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132610, rend_intergenic: 124240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141773, rend_intergenic: 133845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142260, rend_intergenic: 141999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support