-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_14803017-14982600

-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: +)Couldn't classify 27681, 27778
Couldn't classify 35978, 36120
Sorry, prediction pasa_asmbl_2412.p1 fails validation.
(GCA)	 AA	27681-27778	GT	GAG
(CCC)	 AG	28983-29073	GT	CGG
(GTG)	 AG	30366-30518	GT	AGG
(GAA)	 AG	31394-31483	GT	AGG
(GCA)	 AG	32566-32662	GT	AGG
(TGG)	 AG	34381-34542	GT	TGG
(TGA)	 AG	35978-36120	GT	AGG
-recovered pasa_asmbl_2412.p1, internal, 28983, 29073
-recovered pasa_asmbl_2412.p1, internal, 30366, 30518
-recovered pasa_asmbl_2412.p1, internal, 31394, 31483
-recovered pasa_asmbl_2412.p1, internal, 32566, 32662
-recovered pasa_asmbl_2412.p1, internal, 34381, 34542
-recovered pasa_asmbl_2412.p1, internal, 35978, 36120
Valid prediction for GlimmerHMM_glimmerT_1941-T1
Valid prediction for snap_scaffold_1-snap.2544-T1
Valid prediction for GlimmerHMM_glimmerT_1927-T1
Valid prediction for GlimmerHMM_glimmerT_1931-T1
Valid prediction for snap_scaffold_1-snap.2577-T1
Valid prediction for snap_scaffold_1-snap.2575-T1
Valid prediction for GlimmerHMM_glimmerT_1946-T1
Valid prediction for snap_scaffold_1-snap.2558-T1
Valid prediction for Augustus_model.g1473.t1
Valid prediction for snap_scaffold_1-snap.2579-T1
Valid prediction for Augustus_model.g1472.t1
Valid prediction for snap_scaffold_1-snap.2570-T1
Valid prediction for GlimmerHMM_glimmerT_1935-T1
Valid prediction for GlimmerHMM_glimmerT_1937-T1
Valid prediction for Augustus_model.g1466.t1
Valid prediction for GlimmerHMM_glimmerT_1932-T1
Valid prediction for GlimmerHMM_glimmerT_1930-T1
Valid prediction for GlimmerHMM_glimmerT_1929-T1
Valid prediction for GlimmerHMM_glimmerT_1938-T1
Valid prediction for Augustus_model.g1461.t1
Valid prediction for snap_scaffold_1-snap.2546-T1
Valid prediction for snap_scaffold_1-snap.2568-T1
Valid prediction for Augustus_model.g1474.t1
Valid prediction for snap_scaffold_1-snap.2542-T1
Valid prediction for snap_scaffold_1-snap.2549-T1
Valid prediction for GlimmerHMM_glimmerT_1949-T1
Valid prediction for snap_scaffold_1-snap.2555-T1
Valid prediction for Augustus_model.g1465.t1
Valid prediction for snap_scaffold_1-snap.2582-T1
Valid prediction for snap_scaffold_1-snap.2573-T1
Valid prediction for CodingQuarry_transcript_2932-T1
Valid prediction for snap_scaffold_1-snap.2553-T1
Valid prediction for GlimmerHMM_glimmerT_1944-T1
Valid prediction for GlimmerHMM_glimmerT_1948-T1
Valid prediction for Augustus_model.g1462.t1
Valid prediction for snap_scaffold_1-snap.2548-T1
Valid prediction for GlimmerHMM_glimmerT_1952-T1
Valid prediction for snap_scaffold_1-snap.2547-T1
Valid prediction for Augustus_model.g1471.t1
Couldn't classify 153273, 153409
Couldn't classify 163646, 163959
Sorry, prediction pasa_asmbl_2418.p1 fails validation.
(CAC)	 GA	153273-153409	GT	CTG
(GTA)	 AG	153573-153716	GT	CTG
(TGA)	 AG	154891-155034	GT	CTG
(CCA)	 AG	155127-155270	GT	CTG
(GAA)	 AG	157007-157150	GT	CTG
(GGA)	 AG	159458-159538	GT	CTG
(AAC)	 AG	161704-161775	GT	CTG
(GAA)	 AG	162920-162991	GT	CTG
(GGT)	 AG	163218-163381	GT	TGG
(ACG)	 AG	163646-163959	GT	CAG
-recovered pasa_asmbl_2418.p1, internal, 153573, 153716
-recovered pasa_asmbl_2418.p1, internal, 154891, 155034
-recovered pasa_asmbl_2418.p1, internal, 155127, 155270
-recovered pasa_asmbl_2418.p1, internal, 157007, 157150
-recovered pasa_asmbl_2418.p1, internal, 159458, 159538
-recovered pasa_asmbl_2418.p1, internal, 161704, 161775
-recovered pasa_asmbl_2418.p1, internal, 162920, 162991
-recovered pasa_asmbl_2418.p1, internal, 163218, 163381
-recovered pasa_asmbl_2418.p1, internal, 163646, 163959
Valid prediction for pasa_asmbl_2419.p1
Valid prediction for GlimmerHMM_glimmerT_1926-T1
Valid prediction for GlimmerHMM_glimmerT_1945-T1
Valid prediction for snap_scaffold_1-snap.2560-T1
Valid prediction for snap_scaffold_1-snap.2569-T1
Valid prediction for GlimmerHMM_glimmerT_1951-T1
Valid prediction for snap_scaffold_1-snap.2561-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_1940-T1
Valid prediction for snap_scaffold_1-snap.2583-T1
Valid prediction for snap_scaffold_1-snap.2565-T1
Valid prediction for snap_scaffold_1-snap.2581-T1
Valid prediction for GlimmerHMM_glimmerT_1950-T1
Valid prediction for Augustus_model.g1463.t1
Valid prediction for snap_scaffold_1-snap.2572-T1
Valid prediction for snap_scaffold_1-snap.2551-T1
Valid prediction for snap_scaffold_1-snap.2563-T1
Valid prediction for GlimmerHMM_glimmerT_1954-T1
Valid prediction for GlimmerHMM_glimmerT_1943-T1
Valid prediction for Augustus_model.g1467.t1
Valid prediction for GlimmerHMM_glimmerT_1942-T1
Valid prediction for snap_scaffold_1-snap.2580-T1
Valid prediction for snap_scaffold_1-snap.2545-T1
Valid prediction for GlimmerHMM_glimmerT_1928-T1
Valid prediction for Augustus_model.g1476.t1
Valid prediction for GlimmerHMM_glimmerT_1933-T1
Valid prediction for snap_scaffold_1-snap.2578-T1
Valid prediction for Augustus_model.g1468.t1
Valid prediction for GlimmerHMM_glimmerT_1934-T1
Valid prediction for snap_scaffold_1-snap.2559-T1
Valid prediction for snap_scaffold_1-snap.2571-T1
Valid prediction for snap_scaffold_1-snap.2543-T1
Valid prediction for snap_scaffold_1-snap.2550-T1
Valid prediction for snap_scaffold_1-snap.2567-T1
Valid prediction for snap_scaffold_1-snap.2552-T1
Valid prediction for Augustus_model.g1469.t1
Valid prediction for snap_scaffold_1-snap.2554-T1
Valid prediction for Augustus_model.g1470.t1
Valid prediction for snap_scaffold_1-snap.2574-T1
Valid prediction for Augustus_model.g1475.t1
Valid prediction for snap_scaffold_1-snap.2557-T1
Valid prediction for snap_scaffold_1-snap.2562-T1
Valid prediction for GlimmerHMM_glimmerT_1936-T1
Valid prediction for snap_scaffold_1-snap.2556-T1
Valid prediction for snap_scaffold_1-snap.2584-T1
Valid prediction for GlimmerHMM_glimmerT_1947-T1
Valid prediction for GlimmerHMM_glimmerT_1939-T1
Valid prediction for snap_scaffold_1-snap.2566-T1
Valid prediction for Augustus_model.g1464.t1
Valid prediction for GlimmerHMM_glimmerT_1953-T1
Valid prediction for snap_scaffold_1-snap.2564-T1
Couldn't classify 78604, 78642
Couldn't classify 78805, 79077
Sorry, prediction pasa_asmbl_1245.p1 fails validation.
(GAA)	 AG	78604-78642	GT	AGG
(TTC)	 AG	78805-79077	GC	AGG
-recovered pasa_asmbl_1245.p1, internal, 78604, 78642
-recovered pasa_asmbl_1245.p1, internal, 78805, 79077
Valid prediction for snap_scaffold_1-snap.2576-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45435, rend_intergenic: 33850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46637, rend_intergenic: 45931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49435, rend_intergenic: 46815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61333, rend_intergenic: 54379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69188, rend_intergenic: 68633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74701, rend_intergenic: 69363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78932, rend_intergenic: 74716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108837, rend_intergenic: 106612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150394, rend_intergenic: 145778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152851, rend_intergenic: 150554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154718, rend_intergenic: 154605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159109, rend_intergenic: 154880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167749, rend_intergenic: 160393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173568, rend_intergenic: 171995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179584
-exon list size: 347


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
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3.4    
3.7    
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4.6    
4.9    
5.2    
5.4    
5.7    
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10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
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14.0    
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16.9    
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18.9    
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28.9    
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29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.1    
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32.7    
33.0    
33.2    
33.5    
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34.1    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
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39.8    
40.1    
40.4    
40.7    
41.0    
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42.4    
42.7    
43.0    
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43.6    
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44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
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46.4    
46.7    
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47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
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64.2    
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65.0    
65.3    
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67.0    
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67.6    
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81.4    
81.7    
81.9    
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84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 45435, rend_intergenic: 33850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46637, rend_intergenic: 45931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49435, rend_intergenic: 46815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61333, rend_intergenic: 54379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69188, rend_intergenic: 68633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74701, rend_intergenic: 69363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78932, rend_intergenic: 74716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108837, rend_intergenic: 106612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150394, rend_intergenic: 145778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152851, rend_intergenic: 150554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154718, rend_intergenic: 154605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159109, rend_intergenic: 154880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167749, rend_intergenic: 160393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173568, rend_intergenic: 171995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support