-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_3044192-3237356

-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 GlimmerHMM_glimmerT_21822-T1
Valid prediction for GlimmerHMM_glimmerT_21814-T1
Valid prediction for Augustus_model.g14521.t1
Valid prediction for GlimmerHMM_glimmerT_21817-T1
Valid prediction for snap_scaffold_9-snap.648-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21834-T1
Couldn't classify 88123, 88880
Couldn't classify 89125, 89215
Sorry, prediction pasa_asmbl_53877.p1 fails validation.
(GAG)	 CG	88123-88880	GT	AGG
(CAG)	 AG	89125-89215	GT	AGG
-recovered pasa_asmbl_53877.p1, internal, 89125, 89215
Valid prediction for GlimmerHMM_glimmerT_21824-T1
Valid prediction for snap_scaffold_9-snap.640-T1
Valid prediction for CodingQuarry_transcript_62130-T1
Valid prediction for snap_scaffold_9-snap.643-T1
Valid prediction for snap_scaffold_9-snap.661-T1
Valid prediction for Augustus_model.g14509.t1
Valid prediction for Augustus_model.g14510.t1
Valid prediction for snap_scaffold_9-snap.651-T1
Valid prediction for snap_scaffold_9-snap.660-T1
Valid prediction for snap_scaffold_9-snap.670-T1
Valid prediction for GlimmerHMM_glimmerT_21833-T1
Valid prediction for GlimmerHMM_glimmerT_21816-T1
Valid prediction for snap_scaffold_9-snap.645-T1
Valid prediction for snap_scaffold_9-snap.653-T1
Valid prediction for GlimmerHMM_glimmerT_21828-T1
Valid prediction for snap_scaffold_9-snap.637-T1
Valid prediction for snap_scaffold_9-snap.674-T1
Valid prediction for HiQ_model.g14511.t1
Valid prediction for GlimmerHMM_glimmerT_21811-T1
Valid prediction for CodingQuarry_transcript_62129-T1
Valid prediction for GlimmerHMM_glimmerT_21809-T1
Valid prediction for snap_scaffold_9-snap.664-T1
Valid prediction for GlimmerHMM_glimmerT_21815-T1
Valid prediction for Augustus_model.g14518.t1
Couldn't classify 84073, 84102
Sorry, prediction pasa_asmbl_53876.p1 fails validation.
(ATG)	 CC	81454-81472	GT	CGG
(AGG)	 AG	81798-82011	GT	AGG
(CCT)	 AG	82150-82297	GT	AGG
(GTG)	 AG	84073-84102	CA	GGC
-recovered pasa_asmbl_53876.p1, initial, 81454, 81472
-recovered pasa_asmbl_53876.p1, internal, 81798, 82011
-recovered pasa_asmbl_53876.p1, internal, 82150, 82297
Valid prediction for snap_scaffold_9-snap.629-T1
Valid prediction for GlimmerHMM_glimmerT_21826-T1
Valid prediction for snap_scaffold_9-snap.662-T1
Valid prediction for Augustus_model.g14512.t1
Couldn't classify 105039, 105298
Sorry, prediction pasa_asmbl_53879.p1 fails validation.
(GGT)	 GT	105039-105298	GT	AGG
(CAG)	 AG	105451-105631	GT	AGG
(GCC)	 AG	105984-106118	TA	GAT
-recovered pasa_asmbl_53879.p1, terminal, 105984, 106118
-recovered pasa_asmbl_53879.p1, internal, 105451, 105631
Valid prediction for snap_scaffold_9-snap.647-T1
Valid prediction for snap_scaffold_9-snap.634-T1
Valid prediction for snap_scaffold_9-snap.656-T1
Valid prediction for pasa_asmbl_53882.p1
Valid prediction for GlimmerHMM_glimmerT_21810-T1
Valid prediction for Augustus_model.g14506.t1
Valid prediction for snap_scaffold_9-snap.636-T1
Valid prediction for GlimmerHMM_glimmerT_21808-T1
Valid prediction for snap_scaffold_9-snap.658-T1
Valid prediction for snap_scaffold_9-snap.667-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_21830-T1
Valid prediction for snap_scaffold_9-snap.663-T1
Valid prediction for snap_scaffold_9-snap.641-T1
Valid prediction for snap_scaffold_9-snap.671-T1
Valid prediction for GlimmerHMM_glimmerT_21820-T1
Valid prediction for snap_scaffold_9-snap.649-T1
Valid prediction for snap_scaffold_9-snap.644-T1
Valid prediction for snap_scaffold_9-snap.642-T1
Valid prediction for snap_scaffold_9-snap.673-T1
Valid prediction for Augustus_model.g14508.t1
Valid prediction for snap_scaffold_9-snap.672-T1
Valid prediction for GlimmerHMM_glimmerT_21831-T1
Valid prediction for GlimmerHMM_glimmerT_21818-T1
Valid prediction for GlimmerHMM_glimmerT_21813-T1
Valid prediction for snap_scaffold_9-snap.666-T1
Valid prediction for snap_scaffold_9-snap.665-T1
Valid prediction for GlimmerHMM_glimmerT_21827-T1
Valid prediction for Augustus_model.g14515.t1
Valid prediction for GlimmerHMM_glimmerT_21832-T1
Valid prediction for snap_scaffold_9-snap.654-T1
Valid prediction for Augustus_model.g14504.t1
Valid prediction for snap_scaffold_9-snap.655-T1
Valid prediction for Augustus_model.g14519.t1
Valid prediction for snap_scaffold_9-snap.646-T1
Valid prediction for Augustus_model.g14505.t1
Valid prediction for Augustus_model.g14514.t1
Valid prediction for snap_scaffold_9-snap.638-T1
Valid prediction for Augustus_model.g14520.t1
Valid prediction for snap_scaffold_9-snap.652-T1
Valid prediction for snap_scaffold_9-snap.631-T1
Valid prediction for Augustus_model.g14517.t1
Valid prediction for Augustus_model.g14507.t1
Valid prediction for GlimmerHMM_glimmerT_21812-T1
Valid prediction for GlimmerHMM_glimmerT_21829-T1
Valid prediction for snap_scaffold_9-snap.639-T1
Valid prediction for GlimmerHMM_glimmerT_21821-T1
Valid prediction for Augustus_model.g14516.t1
Valid prediction for snap_scaffold_9-snap.669-T1
Valid prediction for GlimmerHMM_glimmerT_21819-T1
Valid prediction for Augustus_model.g14513.t1
Valid prediction for snap_scaffold_9-snap.659-T1
Valid prediction for snap_scaffold_9-snap.632-T1
Valid prediction for snap_scaffold_9-snap.633-T1
Valid prediction for snap_scaffold_9-snap.635-T1
Valid prediction for snap_scaffold_9-snap.657-T1
Couldn't classify 73845, 73953
Couldn't classify 74812, 74912
Sorry, prediction pasa_asmbl_55795.p1 fails validation.
(GGC)	 AT	73845-73953	GT	AGG
(CTT)	 AG	74429-74557	GT	CCG
(AGT)	 AG	74812-74912	GG	CTG
-recovered pasa_asmbl_55795.p1, internal, 74429, 74557
Valid prediction for snap_scaffold_9-snap.668-T1
Valid prediction for GlimmerHMM_glimmerT_21825-T1
Valid prediction for GlimmerHMM_glimmerT_21836-T1
Valid prediction for snap_scaffold_9-snap.650-T1
Valid prediction for GlimmerHMM_glimmerT_21835-T1
Valid prediction for snap_scaffold_9-snap.630-T1
Valid prediction for GlimmerHMM_glimmerT_21823-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10548, rend_intergenic: 4247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14924, rend_intergenic: 11783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23989, rend_intergenic: 15362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37601, rend_intergenic: 24335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41722, rend_intergenic: 38048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57127, rend_intergenic: 41905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58682, rend_intergenic: 57224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67684, rend_intergenic: 59862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77302, rend_intergenic: 77094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82107, rend_intergenic: 78718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89794, rend_intergenic: 82125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97641, rend_intergenic: 90783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97993, rend_intergenic: 97641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103516, rend_intergenic: 98216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122655, rend_intergenic: 107761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123044, rend_intergenic: 122956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127140, rend_intergenic: 124542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134436, rend_intergenic: 129339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139161, rend_intergenic: 134464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164049, rend_intergenic: 161962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174326, rend_intergenic: 164806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189397, rend_intergenic: 175577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191348, rend_intergenic: 190065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193165
-exon list size: 432


building trellis

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18.9    
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20.7    
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22.6    
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23.0    
23.3    
23.5    
23.7    
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24.9    
25.1    
25.3    
25.6    
25.8    
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26.3    
26.5    
26.7    
27.0    
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    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.6    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.2    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.5    
44.7    
44.9    
45.2    
45.4    
45.6    
45.9    
46.1    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.8    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.2    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
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53.0    
53.2    
53.5    
53.7    
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54.1    
54.4    
54.6    
54.8    
55.1    
55.3    
55.5    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
57.1    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.8    
59.0    
59.2    
59.4    
59.7    
59.9    
60.1    
60.4    
60.6    
60.8    
61.1    
61.3    
61.5    
61.8    
62.0    
62.2    
62.4    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.1    
64.3    
64.5    
64.7    
65.0    
65.2    
65.4    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.1    
69.4    
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    
73.0    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
77.0    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.9    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.7    
82.9    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
85.7    
85.9    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.2    
89.4    
89.6    
89.9    
90.1    
90.3    
90.6    
90.8    
91.0    
91.2    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 10548, rend_intergenic: 4247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14924, rend_intergenic: 11783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23989, rend_intergenic: 15362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37601, rend_intergenic: 24335  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41722, rend_intergenic: 38048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57127, rend_intergenic: 41905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58682, rend_intergenic: 57224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67684, rend_intergenic: 59862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77302, rend_intergenic: 77094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82107, rend_intergenic: 78718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89794, rend_intergenic: 82125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97641, rend_intergenic: 90783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97993, rend_intergenic: 97641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103516, rend_intergenic: 98216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122655, rend_intergenic: 107761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123044, rend_intergenic: 122956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127140, rend_intergenic: 124542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134436, rend_intergenic: 129339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139161, rend_intergenic: 134464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164049, rend_intergenic: 161962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174326, rend_intergenic: 164806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189397, rend_intergenic: 175577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191348, rend_intergenic: 190065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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