-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_11000608-11240178

-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.52952_t
Valid prediction for snap_scaffold_12-snap.2092-T1
Valid prediction for snap_scaffold_12-snap.2106-T1
Valid prediction for snap_scaffold_12-snap.2111-T1
Valid prediction for GeneMark_model.52958_t
Valid prediction for GlimmerHMM_glimmerT_30681-T1
Valid prediction for snap_scaffold_12-snap.2102-T1
Valid prediction for GlimmerHMM_glimmerT_30693-T1
Valid prediction for GeneMark_model.52990_t
Valid prediction for snap_scaffold_12-snap.2083-T1
Valid prediction for GeneMark_model.52970_t
Valid prediction for GeneMark_model.52972_t
Valid prediction for GeneMark_model.52989_t
Valid prediction for snap_scaffold_12-snap.2089-T1
Valid prediction for GeneMark_model.52956_t
Valid prediction for GeneMark_model.52980_t
Valid prediction for snap_scaffold_12-snap.2105-T1
Valid prediction for GeneMark_model.52973_t
Valid prediction for GeneMark_model.52961_t
Valid prediction for GlimmerHMM_glimmerT_30695-T1
Valid prediction for GeneMark_model.52969_t
Valid prediction for Augustus_model.g20456.t1
Valid prediction for GlimmerHMM_glimmerT_30691-T1
Valid prediction for GeneMark_model.52984_t
Valid prediction for GeneMark_model.52963_t
Valid prediction for GlimmerHMM_glimmerT_30678-T1
Valid prediction for GeneMark_model.52968_t
Valid prediction for GeneMark_model.52965_t
Valid prediction for GlimmerHMM_glimmerT_30684-T1
Valid prediction for GlimmerHMM_glimmerT_30680-T1
Valid prediction for GeneMark_model.52979_t
Valid prediction for Augustus_model.g20461.t1
Valid prediction for snap_scaffold_12-snap.2087-T1
Valid prediction for GeneMark_model.52959_t
Valid prediction for snap_scaffold_12-snap.2090-T1
Valid prediction for GlimmerHMM_glimmerT_30692-T1
Valid prediction for GeneMark_model.52982_t
Valid prediction for snap_scaffold_12-snap.2116-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g20457.t1
Valid prediction for GlimmerHMM_glimmerT_30676-T1
Valid prediction for GlimmerHMM_glimmerT_30683-T1
Valid prediction for GeneMark_model.52988_t
Valid prediction for Augustus_model.g20460.t1
Valid prediction for GeneMark_model.52966_t
Valid prediction for GlimmerHMM_glimmerT_30690-T1
Valid prediction for snap_scaffold_12-snap.2094-T1
Valid prediction for GeneMark_model.52964_t
Valid prediction for GeneMark_model.52962_t
Valid prediction for GeneMark_model.52986_t

-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 Augustus_model.g20466.t1
Valid prediction for GeneMark_model.52983_t
Valid prediction for snap_scaffold_12-snap.2108-T1
Valid prediction for snap_scaffold_12-snap.2095-T1
Valid prediction for CodingQuarry_transcript_10356-T1
Valid prediction for snap_scaffold_12-snap.2101-T1
Valid prediction for GlimmerHMM_glimmerT_30677-T1
Valid prediction for snap_scaffold_12-snap.2110-T1
Valid prediction for snap_scaffold_12-snap.2081-T1
Valid prediction for GlimmerHMM_glimmerT_30688-T1
Valid prediction for GlimmerHMM_glimmerT_30679-T1
Valid prediction for Augustus_model.g20459.t1
Valid prediction for snap_scaffold_12-snap.2100-T1
Valid prediction for snap_scaffold_12-snap.2107-T1
Valid prediction for GeneMark_model.52971_t
Valid prediction for GeneMark_model.52977_t
Valid prediction for snap_scaffold_12-snap.2091-T1
Valid prediction for GlimmerHMM_glimmerT_30682-T1
Valid prediction for snap_scaffold_12-snap.2104-T1
Valid prediction for Augustus_model.g20463.t1
Valid prediction for Augustus_model.g20464.t1
Valid prediction for snap_scaffold_12-snap.2103-T1
Valid prediction for Augustus_model.g20469.t1
Valid prediction for snap_scaffold_12-snap.2109-T1
Valid prediction for Augustus_model.g20458.t1
Valid prediction for snap_scaffold_12-snap.2088-T1
Valid prediction for GeneMark_model.52957_t
Valid prediction for snap_scaffold_12-snap.2084-T1
Valid prediction for GeneMark_model.52987_t
Valid prediction for GlimmerHMM_glimmerT_30694-T1
Valid prediction for GlimmerHMM_glimmerT_30686-T1
Valid prediction for snap_scaffold_12-snap.2113-T1
Valid prediction for GeneMark_model.52954_t
Valid prediction for Augustus_model.g20468.t1
Valid prediction for snap_scaffold_12-snap.2085-T1
Valid prediction for snap_scaffold_12-snap.2114-T1
Valid prediction for CodingQuarry_transcript_10355-T1
Valid prediction for snap_scaffold_12-snap.2086-T1
Valid prediction for GeneMark_model.52953_t
Valid prediction for GlimmerHMM_glimmerT_30687-T1
Valid prediction for GeneMark_model.52974_t
Couldn't classify 125999, 126119
Sorry, prediction pasa_asmbl_7915.p1 fails validation.
(AGG)	 CT	125999-126119	GT	CGG
(ATC)	 AG	127150-127214	GT	AGG
(TTC)	 AG	128020-128124	GT	AGG
(GCT)	 AG	128279-128389	TT	AAT
-recovered pasa_asmbl_7915.p1, terminal, 128279, 128389
-recovered pasa_asmbl_7915.p1, internal, 127150, 127214
-recovered pasa_asmbl_7915.p1, internal, 128020, 128124
Valid prediction for snap_scaffold_12-snap.2098-T1
Valid prediction for GeneMark_model.52978_t
Valid prediction for GlimmerHMM_glimmerT_30689-T1
Couldn't classify 205653, 205754
Couldn't classify 207630, 207869
Sorry, prediction pasa_asmbl_7910.p1 fails validation.
(AAC)	 AG	205653-205754	GT	TGG
(ATG)	 AG	207630-207869	GT	AGG
-recovered pasa_asmbl_7910.p1, initial, 207630, 207869
-recovered pasa_asmbl_7910.p1, internal, 205653, 205754
-recovered pasa_asmbl_7910.p1, internal, 207630, 207869
Valid prediction for GeneMark_model.52976_t
Valid prediction for Augustus_model.g20467.t1
Valid prediction for GeneMark_model.52967_t
Valid prediction for GeneMark_model.52955_t
Valid prediction for Augustus_model.g20462.t1
Valid prediction for GeneMark_model.52985_t
Valid prediction for snap_scaffold_12-snap.2115-T1
Valid prediction for Augustus_model.g20465.t1
Valid prediction for snap_scaffold_12-snap.2097-T1
Valid prediction for GlimmerHMM_glimmerT_30685-T1
Valid prediction for GeneMark_model.52975_t
Couldn't classify 110609, 110679
Couldn't classify 113999, 114107
Sorry, prediction pasa_asmbl_7917.p1 fails validation.
(GTG)	 GG	110609-110679	GT	CAG
(ACA)	 AG	110797-110866	GT	AGG
(TAT)	 AG	111641-111777	GT	ATG
(CTT)	 AG	113999-114107	GT	AGG
-recovered pasa_asmbl_7917.p1, internal, 110797, 110866
-recovered pasa_asmbl_7917.p1, internal, 111641, 111777
-recovered pasa_asmbl_7917.p1, internal, 113999, 114107
Valid prediction for GlimmerHMM_glimmerT_30696-T1
Valid prediction for snap_scaffold_12-snap.2099-T1
Valid prediction for snap_scaffold_12-snap.2096-T1
Valid prediction for snap_scaffold_12-snap.2082-T1
Valid prediction for snap_scaffold_12-snap.2112-T1
Valid prediction for snap_scaffold_12-snap.2080-T1
Valid prediction for snap_scaffold_12-snap.2093-T1
Valid prediction for GeneMark_model.52981_t
Valid prediction for GeneMark_model.52960_t
Valid prediction for GeneMark_model.52991_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 71752, rend_intergenic: 70293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80871, rend_intergenic: 77107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98049, rend_intergenic: 86038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153425, rend_intergenic: 149208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154564, rend_intergenic: 153456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164341, rend_intergenic: 160604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 239571
-exon list size: 438


building trellis

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18.9    
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22.3    
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22.7    
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23.6    
23.9    
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24.8    
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25.9    
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26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
28.4    
28.6    
28.9    
29.1    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
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    
35.5    
35.7    
35.9    
36.1    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.4    
38.6    
38.9    
39.1    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
40.9    
41.1    
41.4    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.1    
46.4    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
48.0    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.0    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.6    
53.9    
54.1    
54.3    
54.5    
54.8    
55.0    
55.2    
55.5    
55.7    
55.9    
56.1    
56.4    
56.6    
56.8    
57.0    
57.3    
57.5    
57.7    
58.0    
58.2    
58.4    
58.6    
58.9    
59.1    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
60.9    
61.1    
61.4    
61.6    
61.8    
62.0    
62.3    
62.5    
62.7    
63.0    
63.2    
63.4    
63.6    
63.9    
64.1    
64.3    
64.5    
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    
68.0    
68.2    
68.4    
68.6    
68.9    
69.1    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
70.9    
71.1    
71.4    
71.6    
71.8    
72.0    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.9    
74.1    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
75.9    
76.1    
76.4    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
78.0    
78.2    
78.4    
78.6    
78.9    
79.1    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
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    
85.5    
85.7    
85.9    
86.1    
86.4    
86.6    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
90.9    
91.1    
91.4    
91.6    
91.8    
92.0    
92.3    
92.5    
92.7    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.8    
95.0    
95.2    
95.5    
95.7    
95.9    
96.1    
96.4    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 71752, rend_intergenic: 70293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80871, rend_intergenic: 77107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98049, rend_intergenic: 86038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153425, rend_intergenic: 149208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154564, rend_intergenic: 153456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164341, rend_intergenic: 160604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 210683 - 239571
-exon list size: 30


building trellis

3.1    
6.2    
9.4    
12.5    
15.6    
18.8    
21.9    
25.0    
28.1    
31.2    
34.4    
37.5    
40.6    
43.8    
46.9    
50.0    
53.1    
56.2    
59.4    
62.5    
65.6    
68.8    
71.9    
75.0    
78.1    
81.2    
84.4    
87.5    
90.6    
93.8    
96.9    
-found 2 predictions from path traversal
GOT 5prime partial gene.

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