-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_13769538-13995268

-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_13-snap.2623-T1
Valid prediction for GlimmerHMM_glimmerT_32710-T1
Couldn't classify 218200, 218248
Couldn't classify 219273, 219411
Sorry, prediction pasa_asmbl_11420.p1 fails validation.
(CAC)	 CT	218200-218248	GT	AGG
(CTG)	 AG	218622-218752	GT	GCG
(TAT)	 AG	219068-219150	GT	AGG
(CCA)	 AG	219273-219411	GC	TGG
-recovered pasa_asmbl_11420.p1, internal, 218622, 218752
-recovered pasa_asmbl_11420.p1, internal, 219068, 219150
-recovered pasa_asmbl_11420.p1, internal, 219273, 219411
Valid prediction for Augustus_model.g21828.t1
Valid prediction for CodingQuarry_transcript_13291-T1
Valid prediction for snap_scaffold_13-snap.2651-T1
Valid prediction for GlimmerHMM_glimmerT_32689-T1
Valid prediction for GlimmerHMM_glimmerT_32703-T1
Couldn't classify 204317, 204386
Couldn't classify 204949, 205086
Sorry, prediction CodingQuarry_transcript_13288-T1 fails validation.
(ATG)	 GG	202374-202490	GT	AGG
(GAG)	 AG	204317-204386	AG	AAA
(CAG)	 CC	204949-205086	GT	TGG
(AGG)	 AG	205342-205436	GT	AGG
(CTA)	 AG	205579-205932	GA	GAG
-recovered CodingQuarry_transcript_13288-T1, initial, 202374, 202490
-recovered CodingQuarry_transcript_13288-T1, terminal, 205579, 205932
-recovered CodingQuarry_transcript_13288-T1, internal, 205342, 205436
Valid prediction for snap_scaffold_13-snap.2660-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 14011, 14166
Couldn't classify 19765, 19980
Sorry, prediction pasa_asmbl_11406.p1 fails validation.
(GGA)	 CA	14011-14166	GT	AGG
(CAA)	 AG	16040-16201	GT	AGG
(GAC)	 AG	16593-16742	GT	CGG
(GCT)	 AG	18591-18680	GT	TGG
(ATC)	 AG	19057-19189	GT	AGG
(GGC)	 AG	19505-19593	GT	AGG
(ATC)	 AG	19765-19980	GT	AGG
-recovered pasa_asmbl_11406.p1, internal, 16040, 16201
-recovered pasa_asmbl_11406.p1, internal, 16593, 16742
-recovered pasa_asmbl_11406.p1, internal, 18591, 18680
-recovered pasa_asmbl_11406.p1, internal, 19057, 19189
-recovered pasa_asmbl_11406.p1, internal, 19505, 19593
-recovered pasa_asmbl_11406.p1, internal, 19765, 19980
Valid prediction for GlimmerHMM_glimmerT_32697-T1
Valid prediction for GlimmerHMM_glimmerT_32702-T1
Valid prediction for snap_scaffold_13-snap.2652-T1
Valid prediction for snap_scaffold_13-snap.2628-T1
Couldn't classify 204390, 204390
Sorry, prediction pasa_asmbl_11416.p1 fails validation.
(AGT)	 GC	204390-204390	GT	CAG
(TGT)	 AG	204952-205086	GT	TGG
(AGG)	 AG	205342-205436	GT	AGG
(CTA)	 AG	205579-205932	GA	GAG
-recovered pasa_asmbl_11416.p1, terminal, 205579, 205932
-recovered pasa_asmbl_11416.p1, internal, 204952, 205086
-recovered pasa_asmbl_11416.p1, internal, 205342, 205436
Valid prediction for GlimmerHMM_glimmerT_32700-T1
Valid prediction for snap_scaffold_13-snap.2634-T1
Valid prediction for Augustus_model.g21817.t1
Valid prediction for snap_scaffold_13-snap.2645-T1
Valid prediction for snap_scaffold_13-snap.2638-T1
Couldn't classify 26234, 27124
Sorry, prediction pasa_asmbl_11407.p1 fails validation.
(CCT)	 TG	26234-27124	AA	AGA
Valid prediction for GlimmerHMM_glimmerT_32695-T1
Valid prediction for snap_scaffold_13-snap.2662-T1
Valid prediction for Augustus_model.g21826.t1
Valid prediction for snap_scaffold_13-snap.2646-T1
Valid prediction for snap_scaffold_13-snap.2659-T1
Valid prediction for snap_scaffold_13-snap.2648-T1
Valid prediction for snap_scaffold_13-snap.2642-T1
Valid prediction for Augustus_model.g21827.t1
Valid prediction for snap_scaffold_13-snap.2650-T1
Valid prediction for Augustus_model.g21819.t1
Valid prediction for snap_scaffold_13-snap.2640-T1
Valid prediction for snap_scaffold_13-snap.2629-T1
Valid prediction for Augustus_model.g21815.t1
Valid prediction for GlimmerHMM_glimmerT_32711-T1
Valid prediction for GlimmerHMM_glimmerT_32708-T1
Valid prediction for GlimmerHMM_glimmerT_32692-T1
Valid prediction for Augustus_model.g21823.t1
Valid prediction for snap_scaffold_13-snap.2635-T1
Valid prediction for GlimmerHMM_glimmerT_32699-T1
Valid prediction for snap_scaffold_13-snap.2625-T1
Valid prediction for snap_scaffold_13-snap.2643-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32706-T1
Couldn't classify 213002, 213577
Sorry, prediction pasa_asmbl_11610.p2 fails validation.
(CTC)	 TT	213002-213577	GT	AAG
Valid prediction for Augustus_model.g21814.t1
Valid prediction for GlimmerHMM_glimmerT_32696-T1
Couldn't classify 204317, 204386
Couldn't classify 204949, 205086
Sorry, prediction CodingQuarry_transcript_13289-T1 fails validation.
(ATG)	 GG	202374-202464	GT	CGG
(ATA)	 AG	204173-204201	GT	AGG
(GAG)	 AG	204317-204386	AG	AAA
(CAG)	 CC	204949-205086	GT	TGG
(AGG)	 AG	205342-205436	GT	AGG
(CTA)	 AG	205579-205932	GA	GAG
-recovered CodingQuarry_transcript_13289-T1, initial, 202374, 202464
-recovered CodingQuarry_transcript_13289-T1, terminal, 205579, 205932
-recovered CodingQuarry_transcript_13289-T1, internal, 204173, 204201
-recovered CodingQuarry_transcript_13289-T1, internal, 205342, 205436
Valid prediction for Augustus_model.g21824.t1
Valid prediction for GlimmerHMM_glimmerT_32694-T1
Valid prediction for snap_scaffold_13-snap.2656-T1
Couldn't classify 211592, 211631
Sorry, prediction pasa_asmbl_11419.p1 fails validation.
(ATG)	 AT	210181-210274	GT	TGG
(TTG)	 AG	210510-210577	GT	AGG
(CCT)	 AG	210681-210747	GT	TGG
(TCT)	 AG	211183-211273	GT	AGG
(TTA)	 AG	211592-211631	GA	CAG
-recovered pasa_asmbl_11419.p1, initial, 210181, 210274
-recovered pasa_asmbl_11419.p1, internal, 210510, 210577
-recovered pasa_asmbl_11419.p1, internal, 210681, 210747
-recovered pasa_asmbl_11419.p1, internal, 211183, 211273

-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_32690-T1
Valid prediction for Augustus_model.g21818.t1
Valid prediction for snap_scaffold_13-snap.2622-T1
Valid prediction for snap_scaffold_13-snap.2644-T1
Valid prediction for snap_scaffold_13-snap.2631-T1
Valid prediction for snap_scaffold_13-snap.2624-T1
Valid prediction for snap_scaffold_13-snap.2647-T1
Valid prediction for Augustus_model.g21821.t1
Valid prediction for snap_scaffold_13-snap.2639-T1
Valid prediction for Augustus_model.g21822.t1
Valid prediction for Augustus_model.g21813.t1
Couldn't classify 120476, 121279
Sorry, prediction pasa_asmbl_10162.p1 fails validation.
(TGT)	 TG	120476-121279	GT	AGG
(GTG)	 AG	121653-122231	AA	GAA
-recovered pasa_asmbl_10162.p1, terminal, 121653, 122231
Valid prediction for GlimmerHMM_glimmerT_32701-T1
Valid prediction for GlimmerHMM_glimmerT_32691-T1
Valid prediction for HiQ_model.g21825.t1
Valid prediction for snap_scaffold_13-snap.2641-T1
Valid prediction for snap_scaffold_13-snap.2658-T1
Valid prediction for GlimmerHMM_glimmerT_32705-T1
Valid prediction for snap_scaffold_13-snap.2630-T1
Valid prediction for snap_scaffold_13-snap.2657-T1
Valid prediction for GlimmerHMM_glimmerT_32709-T1
Valid prediction for snap_scaffold_13-snap.2626-T1
Valid prediction for GlimmerHMM_glimmerT_32707-T1
Valid prediction for snap_scaffold_13-snap.2636-T1
Valid prediction for snap_scaffold_13-snap.2627-T1
Valid prediction for snap_scaffold_13-snap.2655-T1
Valid prediction for snap_scaffold_13-snap.2654-T1
Valid prediction for Augustus_model.g21820.t1
Valid prediction for GlimmerHMM_glimmerT_32698-T1
Valid prediction for snap_scaffold_13-snap.2637-T1
Valid prediction for GlimmerHMM_glimmerT_32704-T1
Valid prediction for snap_scaffold_13-snap.2649-T1
Couldn't classify 18225, 18353
Sorry, prediction pasa_asmbl_10165.p1 fails validation.
(ATG)	 AG	16754-16951	GT	AGG
(GGA)	 AG	17047-17093	GT	TTG
(AGC)	 AG	17259-17368	GT	AGG
(TGA)	 AG	17652-17701	GT	AGG
(ATT)	 AG	17906-18046	GT	AGG
(GTG)	 AG	18225-18353	CC	CTC
-recovered pasa_asmbl_10165.p1, initial, 16754, 16951
-recovered pasa_asmbl_10165.p1, internal, 16754, 16951
-recovered pasa_asmbl_10165.p1, internal, 17047, 17093
-recovered pasa_asmbl_10165.p1, internal, 17259, 17368
-recovered pasa_asmbl_10165.p1, internal, 17652, 17701
-recovered pasa_asmbl_10165.p1, internal, 17906, 18046
Valid prediction for Augustus_model.g21816.t1
Couldn't classify 217458, 218048
Sorry, prediction pasa_asmbl_10439.p1 fails validation.
(TCC)	 TC	217458-218048	GT	AGG
(GGA)	 AG	218182-218226	CA	GAC
-recovered pasa_asmbl_10439.p1, terminal, 218182, 218226
Valid prediction for CodingQuarry_transcript_13290-T1
Valid prediction for snap_scaffold_13-snap.2663-T1
Valid prediction for GlimmerHMM_glimmerT_32688-T1
Valid prediction for snap_scaffold_13-snap.2632-T1
Valid prediction for GlimmerHMM_glimmerT_32693-T1
Valid prediction for snap_scaffold_13-snap.2633-T1
Valid prediction for snap_scaffold_13-snap.2653-T1
Valid prediction for snap_scaffold_13-snap.2661-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11620, rend_intergenic: 5946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15635, rend_intergenic: 13555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24976, rend_intergenic: 15801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28032, rend_intergenic: 25054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46707, rend_intergenic: 33496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76171, rend_intergenic: 70343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80836, rend_intergenic: 78721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84480, rend_intergenic: 81201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102740, rend_intergenic: 87606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109711, rend_intergenic: 104799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127402, rend_intergenic: 109751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140655, rend_intergenic: 127860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153069, rend_intergenic: 140948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172356, rend_intergenic: 161305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192932, rend_intergenic: 172428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206268, rend_intergenic: 201282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220378, rend_intergenic: 216432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220729, rend_intergenic: 220382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223557, rend_intergenic: 220790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225731
-exon list size: 370


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
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 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 11620, rend_intergenic: 5946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15635, rend_intergenic: 13555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24976, rend_intergenic: 15801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28032, rend_intergenic: 25054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46707, rend_intergenic: 33496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76171, rend_intergenic: 70343  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80836, rend_intergenic: 78721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84480, rend_intergenic: 81201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102740, rend_intergenic: 87606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109711, rend_intergenic: 104799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127402, rend_intergenic: 109751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140655, rend_intergenic: 127860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153069, rend_intergenic: 140948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172356, rend_intergenic: 161305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192932, rend_intergenic: 172428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206268, rend_intergenic: 201282  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220378, rend_intergenic: 216432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220729, rend_intergenic: 220382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223557, rend_intergenic: 220790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support