-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_10533802-10705874

-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.56323_t
Valid prediction for GeneMark_model.56337_t
Valid prediction for snap_scaffold_13-snap.1967-T1
Valid prediction for GeneMark_model.56331_t
Valid prediction for Augustus_model.g22184.t1
Valid prediction for GeneMark_model.56320_t
Valid prediction for GlimmerHMM_glimmerT_33018-T1
Valid prediction for CodingQuarry_transcript_13196-T1
Valid prediction for Augustus_model.g22173.t1
Valid prediction for GlimmerHMM_glimmerT_33032-T1
Valid prediction for GlimmerHMM_glimmerT_33016-T1
Valid prediction for GeneMark_model.56334_t
Valid prediction for snap_scaffold_13-snap.1962-T1
Valid prediction for snap_scaffold_13-snap.1940-T1
Valid prediction for snap_scaffold_13-snap.1946-T1
Valid prediction for snap_scaffold_13-snap.1971-T1
Valid prediction for GeneMark_model.56345_t
Valid prediction for GeneMark_model.56319_t
Valid prediction for GlimmerHMM_glimmerT_33022-T1
Valid prediction for snap_scaffold_13-snap.1955-T1
Valid prediction for GeneMark_model.56342_t
Valid prediction for snap_scaffold_13-snap.1957-T1
Valid prediction for GeneMark_model.56340_t
Valid prediction for GeneMark_model.56327_t
Valid prediction for GeneMark_model.56343_t
Valid prediction for snap_scaffold_13-snap.1953-T1
Valid prediction for Augustus_model.g22185.t1
Valid prediction for HiQ_model.g22181.t1
Valid prediction for GeneMark_model.56329_t
Valid prediction for snap_scaffold_13-snap.1973-T1
Valid prediction for GeneMark_model.56350_t
Valid prediction for GlimmerHMM_glimmerT_33029-T1
Valid prediction for GeneMark_model.56314_t
Valid prediction for snap_scaffold_13-snap.1950-T1
Valid prediction for GeneMark_model.56325_t
Valid prediction for snap_scaffold_13-snap.1961-T1
Valid prediction for pasa_asmbl_11230.p1
Valid prediction for GeneMark_model.56355_t
Valid prediction for GlimmerHMM_glimmerT_33033-T1
Valid prediction for GeneMark_model.56353_t
Valid prediction for snap_scaffold_13-snap.1951-T1
Valid prediction for snap_scaffold_13-snap.1969-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.56339_t
Valid prediction for GeneMark_model.56357_t
Valid prediction for Augustus_model.g22177.t1
Valid prediction for snap_scaffold_13-snap.1963-T1
Valid prediction for GlimmerHMM_glimmerT_33020-T1
Valid prediction for GlimmerHMM_glimmerT_33006-T1
Couldn't classify 124702, 124812
Sorry, prediction pasa_asmbl_11234.p1 fails validation.
(GAG)	 AG	124702-124812	GT	TGG
(ATT)	 AG	124918-124985	GT	AGG
(AGT)	 AG	125115-125205	GT	AGG
(GAC)	 AG	125420-125503	GT	AGG
(AGG)	 AG	125609-125702	GT	AGG
(AAA)	 AG	125946-126022	TC	GAT
-recovered pasa_asmbl_11234.p1, terminal, 125946, 126022
-recovered pasa_asmbl_11234.p1, internal, 124702, 124812
-recovered pasa_asmbl_11234.p1, internal, 124918, 124985
-recovered pasa_asmbl_11234.p1, internal, 125115, 125205
-recovered pasa_asmbl_11234.p1, internal, 125420, 125503
-recovered pasa_asmbl_11234.p1, internal, 125609, 125702
Valid prediction for GeneMark_model.56317_t
Valid prediction for snap_scaffold_13-snap.1964-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.56322_t
Valid prediction for GlimmerHMM_glimmerT_33024-T1
Valid prediction for HiQ_model.g22172.t1
Valid prediction for CodingQuarry_transcript_13197-T1
Valid prediction for GlimmerHMM_glimmerT_33014-T1
Valid prediction for GeneMark_model.56333_t
Valid prediction for GlimmerHMM_glimmerT_33010-T1
Couldn't classify 27690, 28157
Sorry, prediction pasa_asmbl_11231.p1 fails validation.
(AAC)	 TC	27690-28157	GT	CAG
Valid prediction for GlimmerHMM_glimmerT_33008-T1
Valid prediction for snap_scaffold_13-snap.1952-T1
Valid prediction for GlimmerHMM_glimmerT_33023-T1
Valid prediction for GeneMark_model.56348_t
Valid prediction for GeneMark_model.56316_t
Valid prediction for Augustus_model.g22176.t1
Valid prediction for snap_scaffold_13-snap.1941-T1
Valid prediction for GeneMark_model.56346_t
Valid prediction for snap_scaffold_13-snap.1947-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_13-snap.1945-T1
Valid prediction for GlimmerHMM_glimmerT_33025-T1
Valid prediction for snap_scaffold_13-snap.1970-T1
Valid prediction for GeneMark_model.56344_t
Valid prediction for Augustus_model.g22178.t1
Valid prediction for GeneMark_model.56321_t
Valid prediction for GeneMark_model.56315_t
Valid prediction for snap_scaffold_13-snap.1960-T1
Valid prediction for GlimmerHMM_glimmerT_33011-T1
Valid prediction for Augustus_model.g22189.t1
Valid prediction for Augustus_model.g22186.t1
Valid prediction for HiQ_model.g22180.t1
Valid prediction for snap_scaffold_13-snap.1956-T1
Valid prediction for GlimmerHMM_glimmerT_33009-T1
Valid prediction for Augustus_model.g22182.t1
Valid prediction for GlimmerHMM_glimmerT_33015-T1
Valid prediction for snap_scaffold_13-snap.1948-T1
Valid prediction for GlimmerHMM_glimmerT_33034-T1
Valid prediction for snap_scaffold_13-snap.1944-T1
Valid prediction for GeneMark_model.56328_t
Valid prediction for GlimmerHMM_glimmerT_33030-T1
Valid prediction for GlimmerHMM_glimmerT_33021-T1
Valid prediction for GlimmerHMM_glimmerT_33013-T1
Valid prediction for GeneMark_model.56352_t
Valid prediction for GeneMark_model.56338_t
Valid prediction for snap_scaffold_13-snap.1974-T1
Valid prediction for Augustus_model.g22179.t1
Valid prediction for CodingQuarry_transcript_13198-T1
Valid prediction for GlimmerHMM_glimmerT_33012-T1
Valid prediction for snap_scaffold_13-snap.1949-T1
Valid prediction for GeneMark_model.56324_t
Valid prediction for Augustus_model.g22171.t1
Valid prediction for GlimmerHMM_glimmerT_33007-T1
Valid prediction for snap_scaffold_13-snap.1968-T1
Valid prediction for snap_scaffold_13-snap.1942-T1
Valid prediction for GeneMark_model.56351_t
Valid prediction for GlimmerHMM_glimmerT_33017-T1
Valid prediction for GlimmerHMM_glimmerT_33019-T1
Valid prediction for snap_scaffold_13-snap.1966-T1
Valid prediction for GlimmerHMM_glimmerT_33031-T1
Valid prediction for GeneMark_model.56335_t
Valid prediction for GeneMark_model.56341_t
Valid prediction for GeneMark_model.56354_t
Valid prediction for GeneMark_model.56349_t
Valid prediction for GeneMark_model.56326_t
Valid prediction for Augustus_model.g22187.t1
Valid prediction for snap_scaffold_13-snap.1939-T1
Valid prediction for snap_scaffold_13-snap.1958-T1
Valid prediction for snap_scaffold_13-snap.1943-T1
Valid prediction for snap_scaffold_13-snap.1959-T1
Valid prediction for GeneMark_model.56318_t
Valid prediction for snap_scaffold_13-snap.1972-T1
Valid prediction for Augustus_model.g22188.t1
Valid prediction for GeneMark_model.56330_t
Valid prediction for snap_scaffold_13-snap.1954-T1
Valid prediction for Augustus_model.g22183.t1
Valid prediction for GlimmerHMM_glimmerT_33026-T1
Valid prediction for GlimmerHMM_glimmerT_33028-T1
Valid prediction for GeneMark_model.56332_t
Valid prediction for pasa_asmbl_10020.p1
Valid prediction for GeneMark_model.56356_t
Valid prediction for GeneMark_model.56336_t
Valid prediction for Augustus_model.g22174.t1
Valid prediction for snap_scaffold_13-snap.1965-T1
Valid prediction for GeneMark_model.56347_t
Valid prediction for GlimmerHMM_glimmerT_33027-T1
Valid prediction for Augustus_model.g22175.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18497, rend_intergenic: 10362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41922, rend_intergenic: 40747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58077, rend_intergenic: 44180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134435, rend_intergenic: 132978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140371, rend_intergenic: 137485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142900, rend_intergenic: 141779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146767, rend_intergenic: 143079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148148, rend_intergenic: 146767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153277, rend_intergenic: 148290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157887, rend_intergenic: 154871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 172073
-exon list size: 586


building trellis

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11.9    
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17.7    
17.9    
18.0    
18.2    
18.4    
18.5    
18.7    
18.9    
19.0    
19.2    
19.4    
19.6    
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20.7    
20.9    
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22.6    
22.8    
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24.8    
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25.3    
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25.9    
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26.4    
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26.9    
27.0    
27.2    
27.4    
27.6    
27.7    
27.9    
28.1    
28.2    
28.4    
28.6    
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28.9    
29.1    
29.3    
29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.4    
30.6    
30.8    
31.0    
31.1    
31.3    
31.5    
31.6    
31.8    
32.0    
32.1    
32.3    
32.5    
32.7    
32.8    
33.0    
33.2    
33.3    
33.5    
33.7    
33.8    
34.0    
34.2    
34.4    
34.5    
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34.9    
35.0    
35.2    
35.4    
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35.9    
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36.6    
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36.9    
37.1    
37.2    
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37.6    
37.8    
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38.3    
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38.6    
38.8    
38.9    
39.1    
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40.0    
40.1    
40.3    
40.5    
40.6    
40.8    
41.0    
41.2    
41.3    
41.5    
41.7    
41.8    
42.0    
42.2    
42.3    
42.5    
42.7    
42.9    
43.0    
43.2    
43.4    
43.5    
43.7    
43.9    
44.0    
44.2    
44.4    
44.6    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.7    
45.9    
46.1    
46.3    
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46.8    
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47.1    
47.3    
47.4    
47.6    
47.8    
48.0    
48.1    
48.3    
48.5    
48.6    
48.8    
49.0    
49.1    
49.3    
49.5    
49.7    
49.8    
50.0    
50.2    
50.3    
50.5    
50.7    
50.9    
51.0    
51.2    
51.4    
51.5    
51.7    
51.9    
52.0    
52.2    
52.4    
52.6    
52.7    
52.9    
53.1    
53.2    
53.4    
53.6    
53.7    
53.9    
54.1    
54.3    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.4    
55.6    
55.8    
56.0    
56.1    
56.3    
56.5    
56.6    
56.8    
57.0    
57.1    
57.3    
57.5    
57.7    
57.8    
58.0    
58.2    
58.3    
58.5    
58.7    
58.8    
59.0    
59.2    
59.4    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.5    
60.7    
60.9    
61.1    
61.2    
61.4    
61.6    
61.7    
61.9    
62.1    
62.2    
62.4    
62.6    
62.8    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
63.9    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.6    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.9    
68.0    
68.2    
68.4    
68.5    
68.7    
68.9    
69.0    
69.2    
69.4    
69.6    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.7    
70.9    
71.1    
71.3    
71.4    
71.6    
71.8    
71.9    
72.1    
72.3    
72.4    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.1    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.4    
80.6    
80.8    
81.0    
81.1    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.9    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 18497, rend_intergenic: 10362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41922, rend_intergenic: 40747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58077, rend_intergenic: 44180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134435, rend_intergenic: 132978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140371, rend_intergenic: 137485  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142900, rend_intergenic: 141779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146767, rend_intergenic: 143079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148148, rend_intergenic: 146767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153277, rend_intergenic: 148290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157887, rend_intergenic: 154871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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