-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_15359376-15521208

-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 Augustus_model.g7039.t1
Valid prediction for snap_scaffold_4-snap.3092-T1
Valid prediction for snap_scaffold_4-snap.3093-T1
Valid prediction for snap_scaffold_4-snap.3095-T1
Valid prediction for Augustus_model.g7044.t1
Valid prediction for snap_scaffold_4-snap.3094-T1
Valid prediction for GlimmerHMM_glimmerT_10725-T1
Valid prediction for pasa_asmbl_41949.p1
Valid prediction for snap_scaffold_4-snap.3117-T1
Valid prediction for Augustus_model.g7037.t1
Valid prediction for GlimmerHMM_glimmerT_10723-T1
Valid prediction for snap_scaffold_4-snap.3097-T1
Valid prediction for GlimmerHMM_glimmerT_10719-T1
Valid prediction for snap_scaffold_4-snap.3099-T1
Valid prediction for snap_scaffold_4-snap.3085-T1
Valid prediction for snap_scaffold_4-snap.3090-T1
Valid prediction for snap_scaffold_4-snap.3119-T1
Valid prediction for snap_scaffold_4-snap.3109-T1
Valid prediction for GlimmerHMM_glimmerT_10716-T1
Valid prediction for GlimmerHMM_glimmerT_10717-T1
Valid prediction for snap_scaffold_4-snap.3098-T1
Valid prediction for Augustus_model.g7046.t1
Valid prediction for snap_scaffold_4-snap.3116-T1
Valid prediction for Augustus_model.g7031.t1
Valid prediction for snap_scaffold_4-snap.3103-T1
Valid prediction for Augustus_model.g7045.t1
Valid prediction for Augustus_model.g7033.t1
Couldn't classify 60330, 60444
Couldn't classify 61167, 61206
Sorry, prediction pasa_asmbl_42173.p1 fails validation.
(TGT)	 CT	60330-60444	GT	TGG
(AAA)	 AG	60550-60723	GT	AGG
(ACA)	 AG	60930-61038	GT	CGG
(GGT)	 AG	61167-61206	CC	CCC
-recovered pasa_asmbl_42173.p1, internal, 60550, 60723
-recovered pasa_asmbl_42173.p1, internal, 60930, 61038
Valid prediction for GlimmerHMM_glimmerT_10732-T1
Valid prediction for GlimmerHMM_glimmerT_10715-T1
Valid prediction for GlimmerHMM_glimmerT_10731-T1
Valid prediction for GlimmerHMM_glimmerT_10705-T1
Valid prediction for GlimmerHMM_glimmerT_10718-T1
Valid prediction for pasa_asmbl_41950.p1
Valid prediction for snap_scaffold_4-snap.3121-T1
Valid prediction for GlimmerHMM_glimmerT_10710-T1
Valid prediction for snap_scaffold_4-snap.3120-T1
Valid prediction for Augustus_model.g7032.t1
Valid prediction for snap_scaffold_4-snap.3111-T1
Valid prediction for GlimmerHMM_glimmerT_10714-T1
Valid prediction for snap_scaffold_4-snap.3096-T1
Valid prediction for Augustus_model.g7030.t1
Valid prediction for GlimmerHMM_glimmerT_10730-T1
Valid prediction for GlimmerHMM_glimmerT_10727-T1
Valid prediction for CodingQuarry_transcript_49258-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.g7024.t1
Valid prediction for snap_scaffold_4-snap.3107-T1
Valid prediction for Augustus_model.g7027.t1
Valid prediction for Augustus_model.g7040.t1
Valid prediction for GlimmerHMM_glimmerT_10720-T1
Valid prediction for GlimmerHMM_glimmerT_10721-T1
Valid prediction for snap_scaffold_4-snap.3105-T1
Valid prediction for snap_scaffold_4-snap.3108-T1
Valid prediction for CodingQuarry_transcript_49253-T1
Valid prediction for CodingQuarry_transcript_49254-T1
Valid prediction for GlimmerHMM_glimmerT_10724-T1
Valid prediction for snap_scaffold_4-snap.3112-T1
Valid prediction for snap_scaffold_4-snap.3114-T1
Valid prediction for snap_scaffold_4-snap.3087-T1
Valid prediction for snap_scaffold_4-snap.3086-T1
Valid prediction for Augustus_model.g7041.t1
Valid prediction for snap_scaffold_4-snap.3104-T1
Valid prediction for snap_scaffold_4-snap.3100-T1
Valid prediction for Augustus_model.g7036.t1
Valid prediction for snap_scaffold_4-snap.3122-T1
Valid prediction for GlimmerHMM_glimmerT_10706-T1
Valid prediction for HiQ_model.g7026.t1
Valid prediction for GlimmerHMM_glimmerT_10711-T1
Valid prediction for snap_scaffold_4-snap.3118-T1
Valid prediction for GlimmerHMM_glimmerT_10734-T1
Valid prediction for snap_scaffold_4-snap.3106-T1
Valid prediction for Augustus_model.g7047.t1
Valid prediction for Augustus_model.g7029.t1
Valid prediction for GlimmerHMM_glimmerT_10722-T1
Valid prediction for snap_scaffold_4-snap.3088-T1
Valid prediction for HiQ_model.g7042.t1
Valid prediction for Augustus_model.g7025.t1
Valid prediction for snap_scaffold_4-snap.3113-T1
Valid prediction for GlimmerHMM_glimmerT_10712-T1
Valid prediction for Augustus_model.g7035.t1
Valid prediction for Augustus_model.g7028.t1
Valid prediction for snap_scaffold_4-snap.3091-T1
Valid prediction for snap_scaffold_4-snap.3115-T1
Valid prediction for GlimmerHMM_glimmerT_10707-T1
Valid prediction for GlimmerHMM_glimmerT_10733-T1
Valid prediction for Augustus_model.g7038.t1
Valid prediction for snap_scaffold_4-snap.3110-T1
Valid prediction for HiQ_model.g7043.t1
Valid prediction for GlimmerHMM_glimmerT_10726-T1
Valid prediction for CodingQuarry_transcript_49256-T1
Valid prediction for GlimmerHMM_glimmerT_10729-T1
Valid prediction for GlimmerHMM_glimmerT_10708-T1
Valid prediction for CodingQuarry_transcript_49255-T1
Valid prediction for Augustus_model.g7049.t1
Valid prediction for GlimmerHMM_glimmerT_10713-T1
Valid prediction for snap_scaffold_4-snap.3101-T1
Valid prediction for snap_scaffold_4-snap.3089-T1
Valid prediction for HiQ_model.g7034.t1
Couldn't classify 137462, 137506
Sorry, prediction pasa_asmbl_43094.p1 fails validation.
(CTT)	 AG	137462-137506	GT	AGG
(ATG)	 AG	137844-137889	GT	AGG
(TGT)	 AG	138074-138161	GT	AGG
(GAA)	 AG	138342-138504	AC	GAA
-recovered pasa_asmbl_43094.p1, initial, 137844, 137889
-recovered pasa_asmbl_43094.p1, terminal, 138342, 138504
-recovered pasa_asmbl_43094.p1, internal, 137462, 137506
-recovered pasa_asmbl_43094.p1, internal, 137844, 137889
-recovered pasa_asmbl_43094.p1, internal, 138074, 138161
Valid prediction for pasa_asmbl_43092.p1
Valid prediction for pasa_asmbl_43097.p1
Valid prediction for Augustus_model.g7048.t1
Valid prediction for snap_scaffold_4-snap.3102-T1
Valid prediction for snap_scaffold_4-snap.3084-T1
Valid prediction for GlimmerHMM_glimmerT_10709-T1
Valid prediction for GlimmerHMM_glimmerT_10728-T1
Valid prediction for CodingQuarry_transcript_49257-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12078, rend_intergenic: 2702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34454, rend_intergenic: 30491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44460, rend_intergenic: 41132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90735, rend_intergenic: 89692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110696, rend_intergenic: 107663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111453, rend_intergenic: 110919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153059, rend_intergenic: 140769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155333, rend_intergenic: 153222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161833
-exon list size: 348


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.1    
13.4    
13.7    
14.0    
14.3    
14.6    
14.9    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
30.0    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
38.0    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
62.0    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
70.0    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.1    
85.4    
85.7    
86.0    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 12078, rend_intergenic: 2702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34454, rend_intergenic: 30491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44460, rend_intergenic: 41132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90735, rend_intergenic: 89692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110696, rend_intergenic: 107663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111453, rend_intergenic: 110919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153059, rend_intergenic: 140769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155333, rend_intergenic: 153222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support