-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_10762847-10970281

-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_10-snap.2128-T1
Valid prediction for snap_scaffold_10-snap.2107-T1
Valid prediction for Augustus_model.g16875.t1
Valid prediction for snap_scaffold_10-snap.2124-T1
Valid prediction for snap_scaffold_10-snap.2127-T1
Valid prediction for GlimmerHMM_glimmerT_25401-T1
Valid prediction for snap_scaffold_10-snap.2150-T1
Valid prediction for Augustus_model.g16887.t1
Valid prediction for HiQ_model.g16877.t1
Valid prediction for pasa_asmbl_3442.p1
Valid prediction for CodingQuarry_transcript_5563-T1
Valid prediction for GlimmerHMM_glimmerT_25394-T1
Valid prediction for snap_scaffold_10-snap.2108-T1
Valid prediction for GlimmerHMM_glimmerT_25400-T1
Valid prediction for GlimmerHMM_glimmerT_25402-T1
Valid prediction for CodingQuarry_transcript_5562-T1
Valid prediction for HiQ_model.g16888.t1
Valid prediction for Augustus_model.g16881.t1
Valid prediction for GlimmerHMM_glimmerT_25398-T1
Valid prediction for HiQ_model.g16878.t1
Valid prediction for snap_scaffold_10-snap.2104-T1
Valid prediction for snap_scaffold_10-snap.2137-T1
Valid prediction for snap_scaffold_10-snap.2132-T1
Valid prediction for GlimmerHMM_glimmerT_25387-T1
Valid prediction for GlimmerHMM_glimmerT_25383-T1
Valid prediction for snap_scaffold_10-snap.2110-T1
Valid prediction for snap_scaffold_10-snap.2119-T1
Valid prediction for snap_scaffold_10-snap.2130-T1
Valid prediction for GlimmerHMM_glimmerT_25391-T1
Valid prediction for Augustus_model.g16883.t1
Valid prediction for snap_scaffold_10-snap.2103-T1
Valid prediction for GlimmerHMM_glimmerT_25389-T1
Valid prediction for snap_scaffold_10-snap.2101-T1
Valid prediction for snap_scaffold_10-snap.2122-T1
Valid prediction for snap_scaffold_10-snap.2139-T1
Valid prediction for HiQ_model.g16876.t1
Valid prediction for snap_scaffold_10-snap.2123-T1
Valid prediction for GlimmerHMM_glimmerT_25388-T1
Valid prediction for GlimmerHMM_glimmerT_25375-T1
Valid prediction for snap_scaffold_10-snap.2116-T1
Valid prediction for snap_scaffold_10-snap.2105-T1
Valid prediction for snap_scaffold_10-snap.2145-T1
Valid prediction for GlimmerHMM_glimmerT_25371-T1
Valid prediction for snap_scaffold_10-snap.2135-T1
Couldn't classify 38012, 38318
Sorry, prediction pasa_asmbl_3438.p1 fails validation.
(ATC)	 CA	38012-38318	GT	AGG
(AGA)	 AG	38533-38649	GT	AGG
(ATG)	 AG	40441-40662	GT	AGG
(GCG)	 AG	41037-41293	GT	AGG
(GGC)	 AG	41521-41664	AC	AAA
-recovered pasa_asmbl_3438.p1, initial, 40441, 40662
-recovered pasa_asmbl_3438.p1, terminal, 41521, 41664
-recovered pasa_asmbl_3438.p1, internal, 38533, 38649
-recovered pasa_asmbl_3438.p1, internal, 40441, 40662
-recovered pasa_asmbl_3438.p1, internal, 41037, 41293
Valid prediction for GlimmerHMM_glimmerT_25379-T1
Valid prediction for snap_scaffold_10-snap.2152-T1
Valid prediction for Augustus_model.g16891.t1
Valid prediction for GlimmerHMM_glimmerT_25376-T1
Valid prediction for snap_scaffold_10-snap.2120-T1
Valid prediction for snap_scaffold_10-snap.2142-T1
Valid prediction for GlimmerHMM_glimmerT_25397-T1
Valid prediction for CodingQuarry_transcript_5559-T1
Valid prediction for GlimmerHMM_glimmerT_25372-T1
Valid prediction for GlimmerHMM_glimmerT_25393-T1
Valid prediction for GlimmerHMM_glimmerT_25399-T1
Valid prediction for snap_scaffold_10-snap.2112-T1
Valid prediction for snap_scaffold_10-snap.2148-T1
Valid prediction for snap_scaffold_10-snap.2121-T1
Valid prediction for snap_scaffold_10-snap.2144-T1
Valid prediction for GlimmerHMM_glimmerT_25396-T1
Valid prediction for GlimmerHMM_glimmerT_25377-T1
Valid prediction for pasa_asmbl_3434.p1
Valid prediction for CodingQuarry_transcript_5560-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_10-snap.2151-T1
Valid prediction for Augustus_model.g16885.t1
Valid prediction for snap_scaffold_10-snap.2117-T1
Couldn't classify 142177, 142497
Sorry, prediction pasa_asmbl_4761.p1 fails validation.
(AGC)	 GG	142177-142497	TC	CCT
Valid prediction for snap_scaffold_10-snap.2109-T1
Valid prediction for snap_scaffold_10-snap.2131-T1
Valid prediction for snap_scaffold_10-snap.2102-T1
Valid prediction for snap_scaffold_10-snap.2111-T1
Valid prediction for snap_scaffold_10-snap.2114-T1
Valid prediction for Augustus_model.g16880.t1
Valid prediction for Augustus_model.g16879.t1
Valid prediction for snap_scaffold_10-snap.2143-T1
Valid prediction for snap_scaffold_10-snap.2138-T1
Valid prediction for snap_scaffold_10-snap.2118-T1
Valid prediction for Augustus_model.g16890.t1
Valid prediction for snap_scaffold_10-snap.2115-T1
Valid prediction for Augustus_model.g16889.t1
Valid prediction for snap_scaffold_10-snap.2125-T1
Valid prediction for Augustus_model.g16886.t1
Valid prediction for snap_scaffold_10-snap.2141-T1
Valid prediction for snap_scaffold_10-snap.2147-T1
Valid prediction for snap_scaffold_10-snap.2149-T1
Valid prediction for Augustus_model.g16882.t1
Valid prediction for snap_scaffold_10-snap.2129-T1
Valid prediction for GlimmerHMM_glimmerT_25386-T1
Valid prediction for GlimmerHMM_glimmerT_25382-T1
Valid prediction for GlimmerHMM_glimmerT_25385-T1
Valid prediction for GlimmerHMM_glimmerT_25373-T1
Valid prediction for GlimmerHMM_glimmerT_25384-T1
Valid prediction for GlimmerHMM_glimmerT_25395-T1
Valid prediction for snap_scaffold_10-snap.2136-T1
Valid prediction for snap_scaffold_10-snap.2113-T1
Valid prediction for GlimmerHMM_glimmerT_25381-T1
Valid prediction for GlimmerHMM_glimmerT_25380-T1
Couldn't classify 108815, 108836
Couldn't classify 112255, 112410
Sorry, prediction pasa_asmbl_5214.p1 fails validation.
(TCC)	 GA	108815-108836	GT	AGG
(GTT)	 AG	111559-111731	GT	AGG
(GTT)	 AG	112255-112410	GG	AGG
-recovered pasa_asmbl_5214.p1, internal, 111559, 111731
Valid prediction for GlimmerHMM_glimmerT_25403-T1
Valid prediction for GlimmerHMM_glimmerT_25390-T1
Valid prediction for Augustus_model.g16892.t1
Valid prediction for snap_scaffold_10-snap.2134-T1
Valid prediction for snap_scaffold_10-snap.2140-T1
Valid prediction for GlimmerHMM_glimmerT_25374-T1
Couldn't classify 138088, 138295
Sorry, prediction pasa_asmbl_4762.p1 fails validation.
(CTA)	 GT	138088-138295	GC	AGG
(GCT)	 AG	138693-138870	GT	AAG
(GGT)	 AG	141046-141094	AT	AAA
-recovered pasa_asmbl_4762.p1, terminal, 141046, 141094
-recovered pasa_asmbl_4762.p1, internal, 138693, 138870
Valid prediction for Augustus_model.g16884.t1
Valid prediction for GlimmerHMM_glimmerT_25392-T1
Valid prediction for snap_scaffold_10-snap.2106-T1
Valid prediction for snap_scaffold_10-snap.2126-T1
Valid prediction for snap_scaffold_10-snap.2146-T1
Valid prediction for GlimmerHMM_glimmerT_25378-T1
Valid prediction for snap_scaffold_10-snap.2133-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15053, rend_intergenic: 13692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26137, rend_intergenic: 23353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41664, rend_intergenic: 33370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48602, rend_intergenic: 47005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50956, rend_intergenic: 48852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54552, rend_intergenic: 52517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66467, rend_intergenic: 64994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92266, rend_intergenic: 72777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99384, rend_intergenic: 97349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105303, rend_intergenic: 102289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108417, rend_intergenic: 105904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113491, rend_intergenic: 108728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127282, rend_intergenic: 119089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147431, rend_intergenic: 145042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155551, rend_intergenic: 150909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177394, rend_intergenic: 170979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183840, rend_intergenic: 182245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196315, rend_intergenic: 194358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204222, rend_intergenic: 199403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207435
-exon list size: 382


building trellis

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3.6    
3.9    
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7.0    
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7.8    
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9.6    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.8    
13.0    
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13.5    
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14.6    
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15.4    
15.6    
15.9    
16.1    
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16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
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19.5    
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20.6    
20.8    
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21.4    
21.6    
21.9    
22.1    
22.4    
22.7    
22.9    
23.2    
23.4    
23.7    
24.0    
24.2    
24.5    
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25.0    
25.3    
25.5    
25.8    
26.0    
26.3    
26.6    
26.8    
27.1    
27.3    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.8    
32.0    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.6    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.1    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.6    
51.8    
52.1    
52.3    
52.6    
52.9    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.2    
62.5    
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63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
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65.1    
65.4    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.4    
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68.0    
68.2    
68.5    
68.8    
69.0    
69.3    
69.5    
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70.1    
70.3    
70.6    
70.8    
71.1    
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71.6    
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72.1    
72.4    
72.7    
72.9    
73.2    
73.4    
73.7    
74.0    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.0    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.2    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.4    
92.7    
93.0    
93.2    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.4    
96.6    
96.9    
97.1    
97.4    
97.7    
97.9    
98.2    
98.4    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 15053, rend_intergenic: 13692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26137, rend_intergenic: 23353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41664, rend_intergenic: 33370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48602, rend_intergenic: 47005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50956, rend_intergenic: 48852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54552, rend_intergenic: 52517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66467, rend_intergenic: 64994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92266, rend_intergenic: 72777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99384, rend_intergenic: 97349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105303, rend_intergenic: 102289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108417, rend_intergenic: 105904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113491, rend_intergenic: 108728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127282, rend_intergenic: 119089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147431, rend_intergenic: 145042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155551, rend_intergenic: 150909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177394, rend_intergenic: 170979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183840, rend_intergenic: 182245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196315, rend_intergenic: 194358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204222, rend_intergenic: 199403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support