-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_11396942-11683097

-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 184579, 184658
Sorry, prediction pasa_asmbl_5940.p1 fails validation.
(ATA)	 AT	184579-184658	GT	AAG
(TAT)	 AG	184755-184957	GT	AGG
(AGA)	 AG	185082-185162	GT	AGG
(CAT)	 AG	185242-185276	GT	AGG
-recovered pasa_asmbl_5940.p1, terminal, 185242, 185276
-recovered pasa_asmbl_5940.p1, internal, 184755, 184957
-recovered pasa_asmbl_5940.p1, internal, 185082, 185162
-recovered pasa_asmbl_5940.p1, internal, 185242, 185276
Valid prediction for pasa_asmbl_5954.p2
Valid prediction for GlimmerHMM_glimmerT_28504-T1
Valid prediction for snap_scaffold_11-snap.2508-T1
Valid prediction for GeneMark_model.49221_t
Valid prediction for GlimmerHMM_glimmerT_28503-T1
Valid prediction for snap_scaffold_11-snap.2510-T1
Valid prediction for GlimmerHMM_glimmerT_28493-T1
Valid prediction for snap_scaffold_11-snap.2506-T1
Valid prediction for GlimmerHMM_glimmerT_28499-T1
Valid prediction for Augustus_model.g19022.t1
Valid prediction for GlimmerHMM_glimmerT_28512-T1
Valid prediction for GlimmerHMM_glimmerT_28494-T1
Valid prediction for snap_scaffold_11-snap.2486-T1
Valid prediction for GeneMark_model.49218_t
Valid prediction for GeneMark_model.49201_t
Valid prediction for snap_scaffold_11-snap.2482-T1
Valid prediction for GeneMark_model.49186_t
Couldn't classify 239001, 239243
Sorry, prediction pasa_asmbl_5946.p1 fails validation.
(GAA)	 CG	239001-239243	GT	AGG
(GGC)	 AG	240678-240722	GT	GGG
(AGA)	 AG	240894-241021	GT	AGG
(CGA)	 AG	241096-241259	GT	GGG
(GTA)	 AG	241826-242121	GT	AGG
(GTG)	 AG	242358-242482	GT	AAG
(AAG)	 AG	242592-242679	GT	AGG
(AAA)	 AG	243055-243454	GT	AGG
(AGC)	 AG	244329-244392	GT	TTG
(GAA)	 AG	244528-244699	GT	AGG
(ACC)	 AG	244810-244854	GT	AGG
(TCA)	 AG	244961-245071	TC	GAT
-recovered pasa_asmbl_5946.p1, terminal, 244961, 245071
-recovered pasa_asmbl_5946.p1, internal, 240678, 240722
-recovered pasa_asmbl_5946.p1, internal, 240894, 241021
-recovered pasa_asmbl_5946.p1, internal, 241096, 241259
-recovered pasa_asmbl_5946.p1, internal, 241826, 242121
-recovered pasa_asmbl_5946.p1, internal, 242358, 242482
-recovered pasa_asmbl_5946.p1, internal, 242592, 242679
-recovered pasa_asmbl_5946.p1, internal, 243055, 243454
-recovered pasa_asmbl_5946.p1, internal, 244329, 244392
-recovered pasa_asmbl_5946.p1, internal, 244528, 244699
-recovered pasa_asmbl_5946.p1, internal, 244810, 244854
Valid prediction for GlimmerHMM_glimmerT_28489-T1
Valid prediction for HiQ_model.g19030.t1
Valid prediction for GeneMark_model.49205_t
Valid prediction for CodingQuarry_transcript_8209-T1
Valid prediction for snap_scaffold_11-snap.2503-T1
Valid prediction for HiQ_model.g19031.t1
Valid prediction for snap_scaffold_11-snap.2504-T1
Valid prediction for CodingQuarry_transcript_8211-T1
Valid prediction for snap_scaffold_11-snap.2490-T1
Couldn't classify 229568, 229605
Couldn't classify 231289, 231315
Sorry, prediction pasa_asmbl_5943.p1 fails validation.
(CCT)	 CT	229568-229605	GT	ATG
(GGG)	 AG	230039-230084	GT	CAG
(ATA)	 AG	230183-230218	GT	TGG
(GGT)	 AG	230324-230378	GT	TGG
(ACT)	 AG	230648-230718	GT	ACG
(TTC)	 AG	230814-230892	GT	AGG
(GTT)	 AG	231078-231106	GT	AGG
(AAC)	 AG	231289-231315	AA	TGA
add_exon() Sorry, pasa_asmbl_5943.p1 230814-230892-terminal-3 is invalid.
-recovered pasa_asmbl_5943.p1, terminal, 230814, 230892
-recovered pasa_asmbl_5943.p1, internal, 230039, 230084
-recovered pasa_asmbl_5943.p1, internal, 230183, 230218
-recovered pasa_asmbl_5943.p1, internal, 230324, 230378
-recovered pasa_asmbl_5943.p1, internal, 230648, 230718
-recovered pasa_asmbl_5943.p1, internal, 230814, 230892
-recovered pasa_asmbl_5943.p1, internal, 231078, 231106
Valid prediction for HiQ_model.g19024.t1
Valid prediction for GeneMark_model.49189_t
Valid prediction for GeneMark_model.49192_t
Valid prediction for GeneMark_model.49194_t
Valid prediction for GeneMark_model.49203_t
Valid prediction for Augustus_model.g19026.t1
Valid prediction for snap_scaffold_11-snap.2502-T1
Valid prediction for Augustus_model.g19034.t1
Valid prediction for GeneMark_model.49215_t
Valid prediction for GlimmerHMM_glimmerT_28506-T1
Valid prediction for snap_scaffold_11-snap.2488-T1
Valid prediction for snap_scaffold_11-snap.2513-T1
Valid prediction for GlimmerHMM_glimmerT_28497-T1
Valid prediction for snap_scaffold_11-snap.2491-T1
Valid prediction for HiQ_model.g19032.t1
Valid prediction for GeneMark_model.49223_t
Valid prediction for snap_scaffold_11-snap.2507-T1
Couldn't classify 184221, 184399
Sorry, prediction pasa_asmbl_5939.p1 fails validation.
(ATG)	 TC	182844-183695	GT	AGG
(GAT)	 AG	183888-183990	GT	CGG
(TGG)	 AG	184221-184399	GG	GGG
-recovered pasa_asmbl_5939.p1, initial, 182844, 183695
-recovered pasa_asmbl_5939.p1, internal, 183888, 183990
Valid prediction for snap_scaffold_11-snap.2493-T1
Valid prediction for snap_scaffold_11-snap.2492-T1
Valid prediction for GeneMark_model.49207_t
Valid prediction for GeneMark_model.49195_t
Valid prediction for GlimmerHMM_glimmerT_28514-T1
Valid prediction for snap_scaffold_11-snap.2496-T1
Valid prediction for snap_scaffold_11-snap.2501-T1
Valid prediction for GlimmerHMM_glimmerT_28501-T1
Valid prediction for GeneMark_model.49210_t
Valid prediction for GlimmerHMM_glimmerT_28510-T1
Valid prediction for GlimmerHMM_glimmerT_28507-T1
Valid prediction for GeneMark_model.49217_t
Valid prediction for GeneMark_model.49214_t
Valid prediction for GeneMark_model.49204_t
Valid prediction for GeneMark_model.49199_t
Valid prediction for GlimmerHMM_glimmerT_28511-T1
Valid prediction for snap_scaffold_11-snap.2495-T1
Valid prediction for GeneMark_model.49212_t
Valid prediction for Augustus_model.g19035.t1
Valid prediction for snap_scaffold_11-snap.2485-T1
Valid prediction for GlimmerHMM_glimmerT_28490-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: -)Couldn't classify 35133, 35322
Couldn't classify 36226, 36312
Sorry, prediction pasa_asmbl_7263.p1 fails validation.
(GTG)	 AA	35133-35322	GT	CGG
(GCA)	 AG	35588-35718	GT	CGG
(ACG)	 AG	36226-36312	CT	CCC
-recovered pasa_asmbl_7263.p1, internal, 35588, 35718
Valid prediction for snap_scaffold_11-snap.2497-T1
Valid prediction for GlimmerHMM_glimmerT_28502-T1
Valid prediction for snap_scaffold_11-snap.2483-T1
Valid prediction for snap_scaffold_11-snap.2500-T1
Valid prediction for GeneMark_model.49200_t
Valid prediction for snap_scaffold_11-snap.2498-T1
Valid prediction for GeneMark_model.49184_t
Valid prediction for snap_scaffold_11-snap.2481-T1
Valid prediction for GeneMark_model.49220_t
Valid prediction for snap_scaffold_11-snap.2505-T1
Valid prediction for GeneMark_model.49216_t
Valid prediction for GeneMark_model.49211_t
Valid prediction for Augustus_model.g19019.t1
Valid prediction for GeneMark_model.49225_t
Valid prediction for snap_scaffold_11-snap.2489-T1
Valid prediction for GeneMark_model.49197_t
Valid prediction for GeneMark_model.49196_t
Valid prediction for snap_scaffold_11-snap.2494-T1
Valid prediction for GeneMark_model.49190_t
Valid prediction for CodingQuarry_transcript_8212-T1
Valid prediction for GeneMark_model.49198_t
Valid prediction for GlimmerHMM_glimmerT_28500-T1
Valid prediction for GeneMark_model.49188_t
Valid prediction for GeneMark_model.49208_t
Valid prediction for snap_scaffold_11-snap.2499-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.2509-T1
Valid prediction for GeneMark_model.49209_t
Valid prediction for Augustus_model.g19029.t1
Valid prediction for Augustus_model.g19033.t1
Valid prediction for pasa_asmbl_7001.p1
Valid prediction for GeneMark_model.49193_t
Valid prediction for GeneMark_model.49213_t
Valid prediction for GlimmerHMM_glimmerT_28496-T1
Valid prediction for Augustus_model.g19025.t1
Valid prediction for GlimmerHMM_glimmerT_28509-T1
Valid prediction for Augustus_model.g19028.t1
Valid prediction for snap_scaffold_11-snap.2484-T1
Valid prediction for GeneMark_model.49191_t
Valid prediction for GeneMark_model.49222_t
Valid prediction for GlimmerHMM_glimmerT_28505-T1
Valid prediction for snap_scaffold_11-snap.2511-T1
Valid prediction for GeneMark_model.49187_t
Valid prediction for Augustus_model.g19020.t1
Valid prediction for GeneMark_model.49224_t
Valid prediction for GlimmerHMM_glimmerT_28495-T1
Valid prediction for GlimmerHMM_glimmerT_28491-T1
Valid prediction for HiQ_model.g19021.t1
Valid prediction for snap_scaffold_11-snap.2512-T1
Valid prediction for GeneMark_model.49219_t
Valid prediction for Augustus_model.g19027.t1
Valid prediction for GeneMark_model.49206_t
Valid prediction for GlimmerHMM_glimmerT_28508-T1
Valid prediction for snap_scaffold_11-snap.2487-T1
Couldn't classify 34615, 34847
Sorry, prediction pasa_asmbl_7004.p1 fails validation.
(ATG)	 AA	32643-32709	GT	GGG
(ATG)	 AG	33013-33267	GT	TGG
(CCC)	 AG	33512-33723	GT	CGG
(GAC)	 AG	33930-34029	GT	GGG
(GTA)	 AG	34250-34396	GT	GGG
(GTT)	 AG	34615-34847	AT	ACA
-recovered pasa_asmbl_7004.p1, initial, 32643, 32709
add_exon() Sorry, pasa_asmbl_7004.p1 33013-33267-initial-1 is invalid.
-recovered pasa_asmbl_7004.p1, initial, 33013, 33267
-recovered pasa_asmbl_7004.p1, internal, 33013, 33267
-recovered pasa_asmbl_7004.p1, internal, 33512, 33723
-recovered pasa_asmbl_7004.p1, internal, 33930, 34029
-recovered pasa_asmbl_7004.p1, internal, 34250, 34396
Valid prediction for Augustus_model.g19018.t1
Valid prediction for GlimmerHMM_glimmerT_28492-T1
Valid prediction for Augustus_model.g19023.t1
Valid prediction for GlimmerHMM_glimmerT_28513-T1
Valid prediction for GlimmerHMM_glimmerT_28498-T1
Valid prediction for GeneMark_model.49185_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 208871, rend_intergenic: 207698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234875, rend_intergenic: 217385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266225, rend_intergenic: 263189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272407, rend_intergenic: 271470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 278470, rend_intergenic: 272553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 286156
-exon list size: 575


building trellis

0.2    
0.3    
0.5    
0.7    
0.9    
1.0    
1.2    
1.4    
1.6    
1.7    
1.9    
2.1    
2.3    
2.4    
2.6    
2.8    
2.9    
3.1    
3.3    
3.5    
3.6    
3.8    
4.0    
4.2    
4.3    
4.5    
4.7    
4.9    
5.0    
5.2    
5.4    
5.5    
5.7    
5.9    
6.1    
6.2    
6.4    
6.6    
6.8    
6.9    
7.1    
7.3    
7.5    
7.6    
7.8    
8.0    
8.1    
8.3    
8.5    
8.7    
8.8    
9.0    
9.2    
9.4    
9.5    
9.7    
9.9    
10.1    
10.2    
10.4    
10.6    
10.7    
10.9    
11.1    
11.3    
11.4    
11.6    
11.8    
12.0    
12.1    
12.3    
12.5    
12.7    
12.8    
13.0    
13.2    
13.3    
13.5    
13.7    
13.9    
14.0    
14.2    
14.4    
14.6    
14.7    
14.9    
15.1    
15.3    
15.4    
15.6    
15.8    
15.9    
16.1    
16.3    
16.5    
16.6    
16.8    
17.0    
17.2    
17.3    
17.5    
17.7    
17.9    
18.0    
18.2    
18.4    
18.5    
18.7    
18.9    
19.1    
19.2    
19.4    
19.6    
19.8    
19.9    
20.1    
20.3    
20.5    
20.6    
20.8    
21.0    
21.1    
21.3    
21.5    
21.7    
21.8    
22.0    
22.2    
22.4    
22.5    
22.7    
22.9    
23.1    
23.2    
23.4    
23.6    
23.7    
23.9    
24.1    
24.3    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.6    
25.8    
26.0    
26.2    
26.3    
26.5    
26.7    
26.9    
27.0    
27.2    
27.4    
27.6    
27.7    
27.9    
28.1    
28.2    
28.4    
28.6    
28.8    
28.9    
29.1    
29.3    
29.5    
29.6    
29.8    
30.0    
30.2    
30.3    
30.5    
30.7    
30.8    
31.0    
31.2    
31.4    
31.5    
31.7    
31.9    
32.1    
32.2    
32.4    
32.6    
32.8    
32.9    
33.1    
33.3    
33.4    
33.6    
33.8    
34.0    
34.1    
34.3    
34.5    
34.7    
34.8    
35.0    
35.2    
35.4    
35.5    
35.7    
35.9    
36.0    
36.2    
36.4    
36.6    
36.7    
36.9    
37.1    
37.3    
37.4    
37.6    
37.8    
38.0    
38.1    
38.3    
38.5    
38.6    
38.8    
39.0    
39.2    
39.3    
39.5    
39.7    
39.9    
40.0    
40.2    
40.4    
40.6    
40.7    
40.9    
41.1    
41.2    
41.4    
41.6    
41.8    
41.9    
42.1    
42.3    
42.5    
42.6    
42.8    
43.0    
43.2    
43.3    
43.5    
43.7    
43.8    
44.0    
44.2    
44.4    
44.5    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.8    
45.9    
46.1    
46.3    
46.4    
46.6    
46.8    
47.0    
47.1    
47.3    
47.5    
47.7    
47.8    
48.0    
48.2    
48.4    
48.5    
48.7    
48.9    
49.0    
49.2    
49.4    
49.6    
49.7    
49.9    
50.1    
50.3    
50.4    
50.6    
50.8    
51.0    
51.1    
51.3    
51.5    
51.6    
51.8    
52.0    
52.2    
52.3    
52.5    
52.7    
52.9    
53.0    
53.2    
53.4    
53.6    
53.7    
53.9    
54.1    
54.2    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.5    
55.6    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.8    
57.0    
57.2    
57.4    
57.5    
57.7    
57.9    
58.1    
58.2    
58.4    
58.6    
58.8    
58.9    
59.1    
59.3    
59.4    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.7    
60.8    
61.0    
61.2    
61.4    
61.5    
61.7    
61.9    
62.0    
62.2    
62.4    
62.6    
62.7    
62.9    
63.1    
63.3    
63.4    
63.6    
63.8    
64.0    
64.1    
64.3    
64.5    
64.6    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.9    
66.0    
66.2    
66.4    
66.6    
66.7    
66.9    
67.1    
67.2    
67.4    
67.6    
67.8    
67.9    
68.1    
68.3    
68.5    
68.6    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.1    
71.2    
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    
73.7    
73.8    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.7    
75.9    
76.1    
76.3    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
80.9    
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    
83.4    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 208871, rend_intergenic: 207698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234875, rend_intergenic: 217385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 266225, rend_intergenic: 263189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 272407, rend_intergenic: 271470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 278470, rend_intergenic: 272553  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 38435
-exon list size: 18


building trellis

5.0    
10.0    
15.0    
20.0    
25.0    
30.0    
35.0    
40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 37903
-exon list size: 15


building trellis

5.9    
11.8    
17.6    
23.5    
29.4    
35.3    
41.2    
47.1    
52.9    
58.8    
64.7    
70.6    
76.5    
82.4    
88.2    
94.1    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 31534
-exon list size: 12


building trellis

7.1    
14.3    
21.4    
28.6    
35.7    
42.9    
50.0    
57.1    
64.3    
71.4    
78.6    
85.7    
92.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 15313
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 15324 - 31534
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 15792 - 31534
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 15792 - 31268
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 20041 - 31268
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support