-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_7047849-7233635

-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_27-snap.1669-T1
Valid prediction for snap_scaffold_27-snap.1657-T1
Valid prediction for snap_scaffold_27-snap.1673-T1
Valid prediction for snap_scaffold_27-snap.1689-T1
Valid prediction for snap_scaffold_27-snap.1664-T1
Valid prediction for Augustus_model.g38147.t1
Valid prediction for snap_scaffold_27-snap.1674-T1
Valid prediction for snap_scaffold_27-snap.1661-T1
Valid prediction for GlimmerHMM_glimmerT_57566-T1
Valid prediction for GlimmerHMM_glimmerT_57579-T1
Valid prediction for snap_scaffold_27-snap.1685-T1
Valid prediction for GlimmerHMM_glimmerT_57561-T1
Valid prediction for Augustus_model.g38150.t1
Valid prediction for GlimmerHMM_glimmerT_57572-T1
Valid prediction for GlimmerHMM_glimmerT_57582-T1
Valid prediction for GlimmerHMM_glimmerT_57569-T1
Valid prediction for snap_scaffold_27-snap.1682-T1
Couldn't classify 183362, 183426
Sorry, prediction pasa_asmbl_36436.p1 fails validation.
(CCA)	 CC	183362-183426	GT	AGG
(AGA)	 AG	183690-183807	GT	CGG
(CTC)	 AG	183892-184044	GT	AGG
(CCA)	 AG	184374-184475	GT	AGG
(TGC)	 AG	184638-184700	AA	GAA
-recovered pasa_asmbl_36436.p1, terminal, 184638, 184700
-recovered pasa_asmbl_36436.p1, internal, 183690, 183807
-recovered pasa_asmbl_36436.p1, internal, 183892, 184044
-recovered pasa_asmbl_36436.p1, internal, 184374, 184475
Valid prediction for GlimmerHMM_glimmerT_57560-T1
Valid prediction for Augustus_model.g38155.t1
Valid prediction for snap_scaffold_27-snap.1666-T1
Valid prediction for GlimmerHMM_glimmerT_57567-T1
Valid prediction for GlimmerHMM_glimmerT_57583-T1
Valid prediction for GlimmerHMM_glimmerT_57584-T1
Valid prediction for Augustus_model.g38152.t1
Valid prediction for CodingQuarry_transcript_41937-T1
Valid prediction for snap_scaffold_27-snap.1687-T1
Valid prediction for snap_scaffold_27-snap.1667-T1
Valid prediction for snap_scaffold_27-snap.1679-T1
Valid prediction for snap_scaffold_27-snap.1676-T1
Valid prediction for HiQ_model.g38156.t1
Valid prediction for GlimmerHMM_glimmerT_57559-T1
Valid prediction for snap_scaffold_27-snap.1677-T1
Valid prediction for GlimmerHMM_glimmerT_57576-T1
Valid prediction for snap_scaffold_27-snap.1690-T1
Valid prediction for snap_scaffold_27-snap.1696-T1
Valid prediction for Augustus_model.g38154.t1
Valid prediction for snap_scaffold_27-snap.1656-T1
Couldn't classify 183101, 183166
Sorry, prediction pasa_asmbl_36433.p1 fails validation.
(ATG)	 AC	180599-180645	GT	AAG
(TGC)	 AG	180741-180909	GT	AGG
(ACA)	 AG	180999-181058	GT	AGG
(GCT)	 AG	181254-181397	GT	AGG
(GCC)	 AG	181544-181677	GT	AGG
(ACT)	 AG	181865-181933	GT	AAG
(GCA)	 AG	182054-182150	GT	AGG
(ATA)	 AG	182311-182399	GT	GGG
(GAT)	 AG	182518-182599	GT	AGG
(AAC)	 AG	182769-182864	GT	CGG
(GTG)	 AG	183101-183166	CC	GAC
-recovered pasa_asmbl_36433.p1, initial, 180599, 180645
-recovered pasa_asmbl_36433.p1, internal, 180741, 180909
-recovered pasa_asmbl_36433.p1, internal, 180999, 181058
-recovered pasa_asmbl_36433.p1, internal, 181254, 181397
-recovered pasa_asmbl_36433.p1, internal, 181544, 181677
-recovered pasa_asmbl_36433.p1, internal, 181865, 181933
-recovered pasa_asmbl_36433.p1, internal, 182054, 182150
-recovered pasa_asmbl_36433.p1, internal, 182311, 182399
-recovered pasa_asmbl_36433.p1, internal, 182518, 182599
-recovered pasa_asmbl_36433.p1, internal, 182769, 182864
Valid prediction for snap_scaffold_27-snap.1670-T1
Valid prediction for snap_scaffold_27-snap.1662-T1
Valid prediction for GlimmerHMM_glimmerT_57568-T1
Couldn't classify 167379, 167492
Couldn't classify 168408, 168444
Sorry, prediction pasa_asmbl_36429.p1 fails validation.
(TTC)	 AC	167379-167492	GT	TGG
(GTG)	 AG	167587-167743	GT	TGG
(CGG)	 AG	168149-168263	GT	AGG
(GCC)	 AG	168408-168444	GT	AGG
-recovered pasa_asmbl_36429.p1, internal, 167587, 167743
-recovered pasa_asmbl_36429.p1, internal, 168149, 168263
-recovered pasa_asmbl_36429.p1, internal, 168408, 168444
Valid prediction for snap_scaffold_27-snap.1683-T1
Valid prediction for GlimmerHMM_glimmerT_57578-T1
Valid prediction for GlimmerHMM_glimmerT_57562-T1
Valid prediction for snap_scaffold_27-snap.1694-T1
Valid prediction for Augustus_model.g38145.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_27-snap.1672-T1
Valid prediction for snap_scaffold_27-snap.1671-T1
Valid prediction for snap_scaffold_27-snap.1691-T1
Valid prediction for GlimmerHMM_glimmerT_57558-T1
Valid prediction for pasa_asmbl_37094.p1
Valid prediction for GlimmerHMM_glimmerT_57580-T1
Valid prediction for snap_scaffold_27-snap.1692-T1
Valid prediction for snap_scaffold_27-snap.1695-T1
Valid prediction for GlimmerHMM_glimmerT_57563-T1
Valid prediction for Augustus_model.g38142.t1
Valid prediction for snap_scaffold_27-snap.1658-T1
Valid prediction for HiQ_model.g38153.t1
Valid prediction for snap_scaffold_27-snap.1678-T1
Valid prediction for GlimmerHMM_glimmerT_57570-T1
Valid prediction for snap_scaffold_27-snap.1659-T1
Valid prediction for snap_scaffold_27-snap.1655-T1
Valid prediction for GlimmerHMM_glimmerT_57577-T1
Valid prediction for Augustus_model.g38140.t1
Valid prediction for Augustus_model.g38141.t1
Valid prediction for Augustus_model.g38149.t1
Valid prediction for GlimmerHMM_glimmerT_57581-T1
Valid prediction for GlimmerHMM_glimmerT_57574-T1
Valid prediction for Augustus_model.g38148.t1
Valid prediction for GlimmerHMM_glimmerT_57565-T1
Valid prediction for snap_scaffold_27-snap.1654-T1
Valid prediction for Augustus_model.g38151.t1
Valid prediction for GlimmerHMM_glimmerT_57564-T1
Valid prediction for Augustus_model.g38146.t1
Valid prediction for snap_scaffold_27-snap.1668-T1
Valid prediction for Augustus_model.g38144.t1
Valid prediction for snap_scaffold_27-snap.1693-T1
Valid prediction for snap_scaffold_27-snap.1681-T1
Valid prediction for GlimmerHMM_glimmerT_57571-T1
Valid prediction for snap_scaffold_27-snap.1686-T1
Valid prediction for GlimmerHMM_glimmerT_57573-T1
Valid prediction for snap_scaffold_27-snap.1665-T1
Valid prediction for snap_scaffold_27-snap.1675-T1
Valid prediction for CodingQuarry_transcript_41935-T1
Valid prediction for snap_scaffold_27-snap.1680-T1
Valid prediction for snap_scaffold_27-snap.1688-T1
Valid prediction for snap_scaffold_27-snap.1663-T1
Valid prediction for CodingQuarry_transcript_41934-T1
Valid prediction for CodingQuarry_transcript_41933-T1
Valid prediction for snap_scaffold_27-snap.1653-T1
Valid prediction for snap_scaffold_27-snap.1660-T1
Valid prediction for GlimmerHMM_glimmerT_57575-T1
Valid prediction for Augustus_model.g38143.t1
Valid prediction for snap_scaffold_27-snap.1684-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14534, rend_intergenic: 10028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49185, rend_intergenic: 35463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49591, rend_intergenic: 49292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68280, rend_intergenic: 50498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73020, rend_intergenic: 68927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88892, rend_intergenic: 73229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97914, rend_intergenic: 89625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112194, rend_intergenic: 102029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112703, rend_intergenic: 112586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115702, rend_intergenic: 113281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121138, rend_intergenic: 119619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125025, rend_intergenic: 122780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131110, rend_intergenic: 126051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137183, rend_intergenic: 131857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141865, rend_intergenic: 138019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145949, rend_intergenic: 144182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176406, rend_intergenic: 156763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183459, rend_intergenic: 181547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185787
-exon list size: 444


building trellis

0.2    
0.4    
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0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.5    
2.7    
2.9    
3.1    
3.4    
3.6    
3.8    
4.0    
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4.5    
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4.9    
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5.8    
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7.0    
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8.7    
9.0    
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11.0    
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11.9    
12.1    
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12.6    
12.8    
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13.5    
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13.9    
14.1    
14.3    
14.6    
14.8    
15.0    
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15.5    
15.7    
15.9    
16.1    
16.4    
16.6    
16.8    
17.0    
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17.5    
17.7    
17.9    
18.2    
18.4    
18.6    
18.8    
19.1    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.9    
21.1    
21.3    
21.5    
21.7    
22.0    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.5    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.5    
26.7    
26.9    
27.1    
27.4    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.5    
34.8    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.2    
39.5    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.0    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.6    
46.9    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.4    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.6    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.1    
53.4    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.8    
56.1    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.7    
59.0    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.5    
60.8    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.5    
63.7    
63.9    
64.1    
64.3    
64.6    
64.8    
65.0    
65.2    
65.5    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
67.9    
68.2    
68.4    
68.6    
68.8    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.7    
83.0    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 14534, rend_intergenic: 10028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49185, rend_intergenic: 35463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49591, rend_intergenic: 49292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68280, rend_intergenic: 50498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73020, rend_intergenic: 68927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88892, rend_intergenic: 73229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97914, rend_intergenic: 89625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112194, rend_intergenic: 102029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112703, rend_intergenic: 112586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115702, rend_intergenic: 113281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121138, rend_intergenic: 119619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125025, rend_intergenic: 122780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131110, rend_intergenic: 126051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137183, rend_intergenic: 131857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141865, rend_intergenic: 138019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145949, rend_intergenic: 144182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176406, rend_intergenic: 156763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183459, rend_intergenic: 181547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support