-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_14356987-14534290

-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 95565, 95674
Couldn't classify 96838, 96937
Sorry, prediction pasa_asmbl_11455.p1 fails validation.
(CAG)	 CC	95565-95674	GT	AGG
(CTC)	 AG	95831-95939	GT	AGG
(CTG)	 AG	96100-96284	GT	AAG
(GTC)	 AG	96838-96937	GC	CTG
-recovered pasa_asmbl_11455.p1, internal, 95831, 95939
-recovered pasa_asmbl_11455.p1, internal, 96100, 96284
-recovered pasa_asmbl_11455.p1, internal, 96838, 96937
Valid prediction for GlimmerHMM_glimmerT_32776-T1
Valid prediction for Augustus_model.g21865.t1
Valid prediction for snap_scaffold_13-snap.2758-T1
Valid prediction for snap_scaffold_13-snap.2754-T1
Valid prediction for snap_scaffold_13-snap.2776-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32789-T1
Valid prediction for Augustus_model.g21873.t1
Valid prediction for snap_scaffold_13-snap.2752-T1
Valid prediction for snap_scaffold_13-snap.2773-T1
Valid prediction for Augustus_model.g21877.t1
Valid prediction for GlimmerHMM_glimmerT_32769-T1
Valid prediction for GlimmerHMM_glimmerT_32778-T1
Valid prediction for CodingQuarry_transcript_13313-T1
Couldn't classify 141669, 141775
Sorry, prediction pasa_asmbl_11457.p1 fails validation.
(GCA)	 CC	141669-141775	GT	GGG
(CTT)	 AG	142235-142400	GT	AGG
(GAG)	 AG	143221-143391	CG	AAC
-recovered pasa_asmbl_11457.p1, terminal, 143221, 143391
-recovered pasa_asmbl_11457.p1, internal, 142235, 142400
Valid prediction for snap_scaffold_13-snap.2781-T1
Valid prediction for snap_scaffold_13-snap.2753-T1
Valid prediction for GlimmerHMM_glimmerT_32780-T1
Valid prediction for snap_scaffold_13-snap.2756-T1
Valid prediction for Augustus_model.g21863.t1
Valid prediction for GlimmerHMM_glimmerT_32791-T1
Valid prediction for snap_scaffold_13-snap.2749-T1
Valid prediction for GlimmerHMM_glimmerT_32793-T1
Couldn't classify 51230, 51424
Couldn't classify 52313, 52423
Sorry, prediction pasa_asmbl_11615.p1 fails validation.
(GAT)	 AG	51230-51424	GT	AGG
(GAC)	 AG	51787-51969	GT	AGG
(GAG)	 AG	52313-52423	GT	AGG
-recovered pasa_asmbl_11615.p1, internal, 51230, 51424
-recovered pasa_asmbl_11615.p1, internal, 51787, 51969
-recovered pasa_asmbl_11615.p1, internal, 52313, 52423
Valid prediction for Augustus_model.g21866.t1
Valid prediction for CodingQuarry_transcript_13314-T1
Valid prediction for Augustus_model.g21879.t1
Valid prediction for snap_scaffold_13-snap.2767-T1
Valid prediction for snap_scaffold_13-snap.2766-T1
Valid prediction for GlimmerHMM_glimmerT_32777-T1
Valid prediction for Augustus_model.g21868.t1
Valid prediction for Augustus_model.g21876.t1
Valid prediction for snap_scaffold_13-snap.2763-T1
Valid prediction for CodingQuarry_transcript_13312-T1
Valid prediction for GlimmerHMM_glimmerT_32779-T1
Couldn't classify 4832, 5137
Sorry, prediction pasa_asmbl_10186.p1 fails validation.
(ACA)	 TC	4832-5137	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_32790-T1
Couldn't classify 60003, 60110
Sorry, prediction pasa_asmbl_11667.p3 fails validation.
(ATG)	 AG	58622-58659	GT	AGG
(GAG)	 AG	59297-59618	GT	CGG
(GAG)	 AG	60003-60110	GC	GCG
-recovered pasa_asmbl_11667.p3, initial, 58622, 58659
-recovered pasa_asmbl_11667.p3, internal, 58622, 58659
-recovered pasa_asmbl_11667.p3, internal, 59297, 59618
-recovered pasa_asmbl_11667.p3, internal, 60003, 60110
Valid prediction for GlimmerHMM_glimmerT_32782-T1
Valid prediction for GlimmerHMM_glimmerT_32785-T1
Valid prediction for GlimmerHMM_glimmerT_32781-T1
Valid prediction for snap_scaffold_13-snap.2771-T1
Valid prediction for snap_scaffold_13-snap.2762-T1
Valid prediction for Augustus_model.g21862.t1
Valid prediction for snap_scaffold_13-snap.2751-T1
Valid prediction for GlimmerHMM_glimmerT_32786-T1
Valid prediction for GlimmerHMM_glimmerT_32787-T1
Valid prediction for snap_scaffold_13-snap.2764-T1
Valid prediction for snap_scaffold_13-snap.2779-T1
Valid prediction for Augustus_model.g21867.t1
Valid prediction for Augustus_model.g21864.t1
Valid prediction for GlimmerHMM_glimmerT_32774-T1
Valid prediction for Augustus_model.g21861.t1
Valid prediction for Augustus_model.g21869.t1
Valid prediction for GlimmerHMM_glimmerT_32770-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.g21874.t1
Valid prediction for snap_scaffold_13-snap.2780-T1
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2770-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2774-T1
Valid prediction for HiQ_model.g21871.t1
Valid prediction for GlimmerHMM_glimmerT_32783-T1
Valid prediction for snap_scaffold_13-snap.2761-T1
Valid prediction for snap_scaffold_13-snap.2775-T1
Valid prediction for snap_scaffold_13-snap.2765-T1
Valid prediction for snap_scaffold_13-snap.2768-T1
Valid prediction for snap_scaffold_13-snap.2748-T1
Valid prediction for pasa_asmbl_10187.p2
Valid prediction for GlimmerHMM_glimmerT_32775-T1
Valid prediction for snap_scaffold_13-snap.2783-T1
Valid prediction for Augustus_model.g21872.t1
Valid prediction for Augustus_model.g21870.t1
Valid prediction for snap_scaffold_13-snap.2759-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.2769-T1
Valid prediction for snap_scaffold_13-snap.2755-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32771-T1
Valid prediction for snap_scaffold_13-snap.2772-T1
Valid prediction for GlimmerHMM_glimmerT_32792-T1
Valid prediction for GlimmerHMM_glimmerT_32784-T1
Valid prediction for snap_scaffold_13-snap.2778-T1
Valid prediction for GlimmerHMM_glimmerT_32768-T1
Valid prediction for GlimmerHMM_glimmerT_32772-T1
Valid prediction for snap_scaffold_13-snap.2757-T1
Valid prediction for snap_scaffold_13-snap.2777-T1
Couldn't classify 92635, 92728
Sorry, prediction pasa_asmbl_10189.p2 fails validation.
(ATG)	 TC	91450-91605	GT	AGG
(ACG)	 AG	91918-92075	GT	AGG
(CCA)	 AG	92635-92728	GT	AGG
-recovered pasa_asmbl_10189.p2, initial, 91450, 91605
-recovered pasa_asmbl_10189.p2, internal, 91918, 92075
-recovered pasa_asmbl_10189.p2, internal, 92635, 92728
Valid prediction for snap_scaffold_13-snap.2760-T1
Valid prediction for GlimmerHMM_glimmerT_32773-T1
Valid prediction for GlimmerHMM_glimmerT_32788-T1
Valid prediction for snap_scaffold_13-snap.2750-T1
Valid prediction for Augustus_model.g21875.t1
Valid prediction for Augustus_model.g21878.t1
Couldn't classify 167962, 168038
Couldn't classify 169448, 169534
Sorry, prediction pasa_asmbl_10326.p1 fails validation.
(GCC)	 AT	167962-168038	GT	GGG
(GAA)	 AG	168156-168238	GT	TGG
(GAA)	 AG	168783-168907	GT	AGG
(GTG)	 AG	169448-169534	GT	GCG
-recovered pasa_asmbl_10326.p1, internal, 168156, 168238
-recovered pasa_asmbl_10326.p1, internal, 168783, 168907
-recovered pasa_asmbl_10326.p1, internal, 169448, 169534
Valid prediction for Augustus_model.g21860.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13951, rend_intergenic: 13713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16963, rend_intergenic: 13952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41358, rend_intergenic: 36751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53102, rend_intergenic: 49159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65992, rend_intergenic: 54671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66708, rend_intergenic: 66092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76484, rend_intergenic: 66986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105016, rend_intergenic: 91330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123498, rend_intergenic: 108182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128993, rend_intergenic: 123527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133463, rend_intergenic: 131321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144514, rend_intergenic: 135120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148101, rend_intergenic: 144618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163162, rend_intergenic: 152020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177304
-exon list size: 369


building trellis

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1.3    
1.6    
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3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.9    
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5.4    
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5.9    
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7.0    
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7.8    
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10.5    
10.8    
11.1    
11.3    
11.6    
11.9    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.3    
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14.8    
15.1    
15.4    
15.6    
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16.7    
17.0    
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17.8    
18.1    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
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20.5    
20.8    
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21.6    
21.8    
22.1    
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22.6    
22.9    
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24.0    
24.3    
24.5    
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25.3    
25.6    
25.9    
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26.4    
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27.0    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.5    
31.8    
32.1    
32.3    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.8    
35.0    
35.3    
35.6    
35.8    
36.1    
36.4    
36.7    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.5    
38.8    
39.1    
39.4    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.5    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
48.0    
48.2    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.8    
52.0    
52.3    
52.6    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.5    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
58.5    
58.8    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.6    
60.9    
61.2    
61.5    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.3    
63.6    
63.9    
64.2    
64.4    
64.7    
65.0    
65.2    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.7    
67.9    
68.2    
68.5    
68.7    
69.0    
69.3    
69.5    
69.8    
70.1    
70.4    
70.6    
70.9    
71.2    
71.4    
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72.0    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.7    
76.0    
76.3    
76.5    
76.8    
77.1    
77.4    
77.6    
77.9    
78.2    
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    
81.9    
82.2    
82.5    
82.7    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.1    
88.4    
88.7    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.8    
91.1    
91.4    
91.6    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 13951, rend_intergenic: 13713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16963, rend_intergenic: 13952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41358, rend_intergenic: 36751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53102, rend_intergenic: 49159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65992, rend_intergenic: 54671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66708, rend_intergenic: 66092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76484, rend_intergenic: 66986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105016, rend_intergenic: 91330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123498, rend_intergenic: 108182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128993, rend_intergenic: 123527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133463, rend_intergenic: 131321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144514, rend_intergenic: 135120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148101, rend_intergenic: 144618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163162, rend_intergenic: 152020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support