-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_10411346-10616409

-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_16-snap.1946-T1
Valid prediction for HiQ_model.g25991.t1
Valid prediction for GlimmerHMM_glimmerT_38954-T1
Valid prediction for CodingQuarry_transcript_20079-T1
Valid prediction for snap_scaffold_16-snap.1955-T1
Valid prediction for GlimmerHMM_glimmerT_38951-T1
Valid prediction for GlimmerHMM_glimmerT_38919-T1
Valid prediction for GlimmerHMM_glimmerT_38953-T1
Valid prediction for GlimmerHMM_glimmerT_38944-T1
Valid prediction for Augustus_model.g26002.t1
Valid prediction for GlimmerHMM_glimmerT_38932-T1
Valid prediction for GlimmerHMM_glimmerT_38941-T1
Valid prediction for snap_scaffold_16-snap.1926-T1
Valid prediction for Augustus_model.g25993.t1
Valid prediction for GlimmerHMM_glimmerT_38940-T1
Valid prediction for GlimmerHMM_glimmerT_38948-T1
Valid prediction for snap_scaffold_16-snap.1918-T1
Valid prediction for GlimmerHMM_glimmerT_38928-T1
Valid prediction for GlimmerHMM_glimmerT_38925-T1
Valid prediction for GlimmerHMM_glimmerT_38946-T1
Valid prediction for GlimmerHMM_glimmerT_38922-T1
Couldn't classify 83477, 83824
Sorry, prediction pasa_asmbl_16545.p1 fails validation.
(CAG)	 CC	83477-83824	AG	TGA
Couldn't classify 135186, 135205
Sorry, prediction pasa_asmbl_16547.p2 fails validation.
(GAT)	 TG	135186-135205	GT	GAG
(GAA)	 AG	135703-135802	GT	AGG
(TCT)	 AG	135944-136110	GT	GGG
(TAT)	 AG	136316-136453	GT	GGG
(GTA)	 AG	136853-136962	GT	TGG
(GCA)	 AG	137195-137403	GC	AGG
-recovered pasa_asmbl_16547.p2, terminal, 137195, 137403
-recovered pasa_asmbl_16547.p2, internal, 135703, 135802
-recovered pasa_asmbl_16547.p2, internal, 135944, 136110
-recovered pasa_asmbl_16547.p2, internal, 136316, 136453
-recovered pasa_asmbl_16547.p2, internal, 136853, 136962
-recovered pasa_asmbl_16547.p2, internal, 137195, 137403
Valid prediction for GlimmerHMM_glimmerT_38943-T1
Couldn't classify 53313, 53449
Sorry, prediction pasa_asmbl_16542.p1 fails validation.
(ATG)	 GC	51166-51364	GT	AGG
(GCC)	 AG	51500-51630	GT	AAG
(ATC)	 AG	51945-52104	GT	AGG
(GCA)	 AG	53313-53449	TG	GGT
-recovered pasa_asmbl_16542.p1, initial, 51166, 51364
-recovered pasa_asmbl_16542.p1, internal, 51500, 51630
-recovered pasa_asmbl_16542.p1, internal, 51945, 52104
Valid prediction for GlimmerHMM_glimmerT_38950-T1
Valid prediction for Augustus_model.g25997.t1
Valid prediction for snap_scaffold_16-snap.1938-T1
Valid prediction for snap_scaffold_16-snap.1929-T1
Valid prediction for snap_scaffold_16-snap.1921-T1
Valid prediction for snap_scaffold_16-snap.1920-T1
Valid prediction for snap_scaffold_16-snap.1923-T1
Valid prediction for snap_scaffold_16-snap.1945-T1
Valid prediction for pasa_asmbl_16536.p1
Valid prediction for snap_scaffold_16-snap.1954-T1
Valid prediction for Augustus_model.g26000.t1
Valid prediction for snap_scaffold_16-snap.1934-T1
Valid prediction for Augustus_model.g25995.t1
Valid prediction for snap_scaffold_16-snap.1958-T1
Valid prediction for CodingQuarry_transcript_20080-T1
Valid prediction for snap_scaffold_16-snap.1931-T1
Valid prediction for Augustus_model.g26009.t1
Couldn't classify 73700, 73912
Couldn't classify 76931, 76987
Sorry, prediction pasa_asmbl_16543.p1 fails validation.
(GTC)	 AG	73700-73912	GT	AGG
(ACG)	 AG	74103-74240	GT	AGG
(GTG)	 AG	75314-75442	GT	AGG
(ATG)	 AG	76931-76987	AG	ACA
-recovered pasa_asmbl_16543.p1, internal, 73700, 73912
-recovered pasa_asmbl_16543.p1, internal, 74103, 74240
-recovered pasa_asmbl_16543.p1, internal, 75314, 75442
Valid prediction for Augustus_model.g25999.t1
Valid prediction for snap_scaffold_16-snap.1942-T1
Valid prediction for GlimmerHMM_glimmerT_38924-T1
Valid prediction for GlimmerHMM_glimmerT_38931-T1
Valid prediction for GlimmerHMM_glimmerT_38926-T1
Valid prediction for snap_scaffold_16-snap.1933-T1
Valid prediction for snap_scaffold_16-snap.1952-T1
Valid prediction for Augustus_model.g26011.t1
Valid prediction for HiQ_model.g26008.t1
Valid prediction for GlimmerHMM_glimmerT_38938-T1
Valid prediction for snap_scaffold_16-snap.1949-T1
Valid prediction for GlimmerHMM_glimmerT_38927-T1
Valid prediction for HiQ_model.g25996.t1
Valid prediction for snap_scaffold_16-snap.1922-T1
Valid prediction for Augustus_model.g26001.t1
Valid prediction for HiQ_model.g25994.t1
Valid prediction for GlimmerHMM_glimmerT_38947-T1
Valid prediction for GlimmerHMM_glimmerT_38937-T1
Valid prediction for Augustus_model.g26014.t1
Valid prediction for pasa_asmbl_16527.p2
Valid prediction for snap_scaffold_16-snap.1927-T1
Valid prediction for GlimmerHMM_glimmerT_38923-T1
Couldn't classify 29542, 30156
Sorry, prediction pasa_asmbl_16530.p1 fails validation.
(GGC)	 CC	29542-30156	GT	CCG
(GGT)	 AG	30248-30328	TC	GAT
-recovered pasa_asmbl_16530.p1, terminal, 30248, 30328
Valid prediction for snap_scaffold_16-snap.1940-T1
Valid prediction for snap_scaffold_16-snap.1924-T1
Valid prediction for GlimmerHMM_glimmerT_38930-T1
Valid prediction for snap_scaffold_16-snap.1925-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 Augustus_model.g26003.t1
Valid prediction for GlimmerHMM_glimmerT_38921-T1
Valid prediction for Augustus_model.g25998.t1
Valid prediction for GlimmerHMM_glimmerT_38952-T1
Valid prediction for GlimmerHMM_glimmerT_38939-T1
Valid prediction for GlimmerHMM_glimmerT_38945-T1
Valid prediction for GlimmerHMM_glimmerT_38929-T1
Valid prediction for snap_scaffold_16-snap.1944-T1
Valid prediction for Augustus_model.g25990.t1
Valid prediction for snap_scaffold_16-snap.1937-T1
Valid prediction for snap_scaffold_16-snap.1950-T1
Valid prediction for GlimmerHMM_glimmerT_38918-T1
Couldn't classify 49737, 49920
Sorry, prediction pasa_asmbl_17315.p1 fails validation.
(ACA)	 AC	49737-49920	GT	CGG
(CAA)	 AG	49998-50093	GT	GGG
(ACC)	 AG	50213-50337	GT	AGG
(TCG)	 AG	50577-50663	GT	AGG
(AGT)	 AG	50765-50914	GT	AGG
(GCT)	 AG	51436-51545	GT	GAG
(TGA)	 AG	51698-51721	GT	AGG
(ACC)	 AG	51937-52034	GT	AGG
(ACG)	 AG	52726-52793	GT	AGG
(TGG)	 AG	52966-53118	GC	GAG
-recovered pasa_asmbl_17315.p1, terminal, 52966, 53118
-recovered pasa_asmbl_17315.p1, internal, 49998, 50093
-recovered pasa_asmbl_17315.p1, internal, 50213, 50337
-recovered pasa_asmbl_17315.p1, internal, 50577, 50663
-recovered pasa_asmbl_17315.p1, internal, 50765, 50914
-recovered pasa_asmbl_17315.p1, internal, 51436, 51545
-recovered pasa_asmbl_17315.p1, internal, 51698, 51721
-recovered pasa_asmbl_17315.p1, internal, 51937, 52034
-recovered pasa_asmbl_17315.p1, internal, 52726, 52793
-recovered pasa_asmbl_17315.p1, internal, 52966, 53118
Valid prediction for Augustus_model.g26013.t1
Valid prediction for Augustus_model.g26007.t1
Valid prediction for Augustus_model.g25992.t1
Valid prediction for snap_scaffold_16-snap.1953-T1
Valid prediction for snap_scaffold_16-snap.1917-T1
Valid prediction for GlimmerHMM_glimmerT_38933-T1
Valid prediction for GlimmerHMM_glimmerT_38935-T1
Valid prediction for snap_scaffold_16-snap.1948-T1
Valid prediction for Augustus_model.g26010.t1
Valid prediction for snap_scaffold_16-snap.1935-T1
Valid prediction for snap_scaffold_16-snap.1932-T1
Valid prediction for snap_scaffold_16-snap.1956-T1
Valid prediction for snap_scaffold_16-snap.1941-T1
Valid prediction for GlimmerHMM_glimmerT_38955-T1
Valid prediction for GlimmerHMM_glimmerT_38936-T1
Valid prediction for snap_scaffold_16-snap.1939-T1
Valid prediction for GlimmerHMM_glimmerT_38942-T1
Valid prediction for Augustus_model.g26005.t1
Valid prediction for snap_scaffold_16-snap.1951-T1
Valid prediction for snap_scaffold_16-snap.1928-T1
Valid prediction for Augustus_model.g26004.t1
Valid prediction for GlimmerHMM_glimmerT_38949-T1
Valid prediction for snap_scaffold_16-snap.1947-T1
Valid prediction for snap_scaffold_16-snap.1919-T1
Valid prediction for HiQ_model.g26012.t1
Valid prediction for snap_scaffold_16-snap.1930-T1
Valid prediction for snap_scaffold_16-snap.1943-T1
Valid prediction for CodingQuarry_transcript_20081-T1
Valid prediction for snap_scaffold_16-snap.1936-T1
Valid prediction for GlimmerHMM_glimmerT_38934-T1
Valid prediction for GlimmerHMM_glimmerT_38920-T1
Valid prediction for Augustus_model.g26006.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10684, rend_intergenic: 9125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27896, rend_intergenic: 11272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61592, rend_intergenic: 60724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71346, rend_intergenic: 61929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72012, rend_intergenic: 71594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82712, rend_intergenic: 75290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87027, rend_intergenic: 82816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99290, rend_intergenic: 88340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99879, rend_intergenic: 99438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104862, rend_intergenic: 100832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109602, rend_intergenic: 107911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151269, rend_intergenic: 148061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163440, rend_intergenic: 161463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174203, rend_intergenic: 166939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180565, rend_intergenic: 174402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205064
-exon list size: 364


building trellis

0.3    
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1.4    
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1.9    
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10.9    
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11.7    
12.0    
12.3    
12.6    
12.8    
13.1    
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14.2    
14.5    
14.8    
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15.3    
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15.8    
16.1    
16.4    
16.7    
16.9    
17.2    
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17.8    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
19.9    
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21.6    
21.9    
22.1    
22.4    
22.7    
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24.3    
24.6    
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25.7    
26.0    
26.2    
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26.8    
27.0    
27.3    
27.6    
27.9    
28.1    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.2    
37.4    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.3    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.7    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.6    
62.8    
63.1    
63.4    
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64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
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67.2    
67.5    
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68.0    
68.3    
68.6    
68.9    
69.1    
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72.4    
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73.8    
74.0    
74.3    
74.6    
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75.1    
75.4    
75.7    
76.0    
76.2    
76.5    
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77.0    
77.3    
77.6    
77.9    
78.1    
78.4    
78.7    
79.0    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.2    
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83.1    
83.3    
83.6    
83.9    
84.2    
84.4    
84.7    
85.0    
85.2    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.2    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.5    
91.8    
92.1    
92.3    
92.6    
92.9    
93.2    
93.4    
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94.0    
94.3    
94.5    
94.8    
95.1    
95.4    
95.6    
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96.2    
96.4    
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97.0    
97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 10684, rend_intergenic: 9125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27896, rend_intergenic: 11272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61592, rend_intergenic: 60724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71346, rend_intergenic: 61929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72012, rend_intergenic: 71594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82712, rend_intergenic: 75290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87027, rend_intergenic: 82816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99290, rend_intergenic: 88340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99879, rend_intergenic: 99438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104862, rend_intergenic: 100832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109602, rend_intergenic: 107911  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151269, rend_intergenic: 148061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163440, rend_intergenic: 161463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174203, rend_intergenic: 166939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180565, rend_intergenic: 174402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support