-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_19361160-19534450

-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 GlimmerHMM_glimmerT_2599-T1
Valid prediction for GlimmerHMM_glimmerT_2618-T1
Valid prediction for snap_scaffold_1-snap.3575-T1
Valid prediction for snap_scaffold_1-snap.3592-T1
Valid prediction for GlimmerHMM_glimmerT_2601-T1
Valid prediction for snap_scaffold_1-snap.3590-T1
Valid prediction for GlimmerHMM_glimmerT_2602-T1
Valid prediction for CodingQuarry_transcript_3014-T1
Valid prediction for CodingQuarry_transcript_3015-T1
Couldn't classify 24771, 24879
Sorry, prediction pasa_asmbl_2593.p1 fails validation.
(ATG)	 AC	24041-24090	GT	AGG
(AGG)	 AG	24306-24377	GT	AGG
(AAA)	 AG	24499-24669	GT	AGG
(CTA)	 AG	24771-24879	CT	ACC
-recovered pasa_asmbl_2593.p1, initial, 24041, 24090
-recovered pasa_asmbl_2593.p1, internal, 24306, 24377
-recovered pasa_asmbl_2593.p1, internal, 24499, 24669
Valid prediction for snap_scaffold_1-snap.3605-T1
Valid prediction for Augustus_model.g1882.t1
Valid prediction for snap_scaffold_1-snap.3579-T1
Sorry, intron length (4) is less than minimum required (10)
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g1877.t1
Valid prediction for snap_scaffold_1-snap.3598-T1
Valid prediction for snap_scaffold_1-snap.3602-T1
Valid prediction for snap_scaffold_1-snap.3574-T1
Valid prediction for GlimmerHMM_glimmerT_2609-T1
Valid prediction for snap_scaffold_1-snap.3586-T1
Valid prediction for GlimmerHMM_glimmerT_2604-T1
Valid prediction for GlimmerHMM_glimmerT_2606-T1
Valid prediction for Augustus_model.g1878.t1
Valid prediction for GlimmerHMM_glimmerT_2614-T1
Valid prediction for snap_scaffold_1-snap.3582-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2617-T1
Valid prediction for snap_scaffold_1-snap.3593-T1
Valid prediction for snap_scaffold_1-snap.3585-T1
Couldn't classify 32321, 32869
Sorry, prediction pasa_asmbl_2596.p1 fails validation.
(AGG)	 AC	32321-32869	CC	GAC
Valid prediction for snap_scaffold_1-snap.3577-T1
Valid prediction for GlimmerHMM_glimmerT_2607-T1
Couldn't classify 24983, 25040
Sorry, prediction pasa_asmbl_2594.p1 fails validation.
(CTG)	 CG	24983-25040	GT	AGG
(GAT)	 AG	25289-25392	GT	AGG
(GTG)	 AG	25659-26030	GG	AAG
-recovered pasa_asmbl_2594.p1, terminal, 25659, 26030
-recovered pasa_asmbl_2594.p1, internal, 25289, 25392
Valid prediction for Augustus_model.g1879.t1
Valid prediction for Augustus_model.g1880.t1
Valid prediction for GlimmerHMM_glimmerT_2613-T1
Valid prediction for snap_scaffold_1-snap.3604-T1
Valid prediction for snap_scaffold_1-snap.3588-T1
Valid prediction for snap_scaffold_1-snap.3596-T1
Valid prediction for snap_scaffold_1-snap.3576-T1
Valid prediction for Augustus_model.g1888.t1
Valid prediction for GlimmerHMM_glimmerT_2598-T1
Valid prediction for snap_scaffold_1-snap.3594-T1
Couldn't classify 16466, 16687
Couldn't classify 20254, 20310
Sorry, prediction pasa_asmbl_2592.p1 fails validation.
(CAC)	 CC	16466-16687	GT	AGG
(GTG)	 AG	16783-16974	GT	AGG
(GTG)	 AG	17128-17309	GT	AGG
(AGC)	 AG	17403-17526	GT	AGG
(ATC)	 AG	17748-17867	GT	AGG
(ACT)	 AG	18815-18901	GT	AGG
(GTC)	 AG	19536-19720	GT	CAG
(TGT)	 AG	20017-20170	GC	AGG
(GTG)	 AG	20254-20310	CA	AGC
-recovered pasa_asmbl_2592.p1, internal, 16783, 16974
-recovered pasa_asmbl_2592.p1, internal, 17128, 17309
-recovered pasa_asmbl_2592.p1, internal, 17403, 17526
-recovered pasa_asmbl_2592.p1, internal, 17748, 17867
-recovered pasa_asmbl_2592.p1, internal, 18815, 18901
-recovered pasa_asmbl_2592.p1, internal, 19536, 19720
-recovered pasa_asmbl_2592.p1, internal, 20017, 20170

-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 snap_scaffold_1-snap.3595-T1
Valid prediction for GlimmerHMM_glimmerT_2600-T1
Valid prediction for Augustus_model.g1885.t1
Valid prediction for snap_scaffold_1-snap.3599-T1
Valid prediction for snap_scaffold_1-snap.3578-T1
Valid prediction for snap_scaffold_1-snap.3591-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g1887.t1
Valid prediction for GlimmerHMM_glimmerT_2615-T1
Valid prediction for snap_scaffold_1-snap.3580-T1
Valid prediction for snap_scaffold_1-snap.3587-T1
Valid prediction for Augustus_model.g1883.t1
Valid prediction for snap_scaffold_1-snap.3597-T1
Valid prediction for snap_scaffold_1-snap.3601-T1
Valid prediction for GlimmerHMM_glimmerT_2611-T1
Valid prediction for snap_scaffold_1-snap.3589-T1
Valid prediction for GlimmerHMM_glimmerT_2597-T1
Valid prediction for Augustus_model.g1884.t1
Valid prediction for Augustus_model.g1881.t1
Valid prediction for GlimmerHMM_glimmerT_2605-T1
Valid prediction for snap_scaffold_1-snap.3600-T1
Valid prediction for GlimmerHMM_glimmerT_2610-T1
Valid prediction for snap_scaffold_1-snap.3581-T1
Valid prediction for snap_scaffold_1-snap.3584-T1
Valid prediction for snap_scaffold_1-snap.3583-T1
Valid prediction for GlimmerHMM_glimmerT_2612-T1
Valid prediction for GlimmerHMM_glimmerT_2616-T1
Valid prediction for Augustus_model.g1886.t1
Valid prediction for GlimmerHMM_glimmerT_2603-T1
Valid prediction for Augustus_model.g1889.t1
Valid prediction for GlimmerHMM_glimmerT_2608-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26030, rend_intergenic: 20224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38732, rend_intergenic: 32192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53769, rend_intergenic: 46801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74528, rend_intergenic: 70264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79501, rend_intergenic: 74631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86049, rend_intergenic: 81270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91694, rend_intergenic: 86518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129506, rend_intergenic: 126619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139810, rend_intergenic: 138226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154772, rend_intergenic: 153257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173291
-exon list size: 255


building trellis

0.4    
0.8    
1.2    
1.6    
1.9    
2.3    
2.7    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.4    
5.8    
6.2    
6.6    
7.0    
7.4    
7.8    
8.2    
8.6    
8.9    
9.3    
9.7    
10.1    
10.5    
10.9    
11.3    
11.7    
12.1    
12.5    
12.8    
13.2    
13.6    
14.0    
14.4    
14.8    
15.2    
15.6    
16.0    
16.3    
16.7    
17.1    
17.5    
17.9    
18.3    
18.7    
19.1    
19.5    
19.8    
20.2    
20.6    
21.0    
21.4    
21.8    
22.2    
22.6    
23.0    
23.3    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.5    
26.8    
27.2    
27.6    
28.0    
28.4    
28.8    
29.2    
29.6    
30.0    
30.4    
30.7    
31.1    
31.5    
31.9    
32.3    
32.7    
33.1    
33.5    
33.9    
34.2    
34.6    
35.0    
35.4    
35.8    
36.2    
36.6    
37.0    
37.4    
37.7    
38.1    
38.5    
38.9    
39.3    
39.7    
40.1    
40.5    
40.9    
41.2    
41.6    
42.0    
42.4    
42.8    
43.2    
43.6    
44.0    
44.4    
44.7    
45.1    
45.5    
45.9    
46.3    
46.7    
47.1    
47.5    
47.9    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.1    
52.5    
52.9    
53.3    
53.7    
54.1    
54.5    
54.9    
55.3    
55.6    
56.0    
56.4    
56.8    
57.2    
57.6    
58.0    
58.4    
58.8    
59.1    
59.5    
59.9    
60.3    
60.7    
61.1    
61.5    
61.9    
62.3    
62.6    
63.0    
63.4    
63.8    
64.2    
64.6    
65.0    
65.4    
65.8    
66.1    
66.5    
66.9    
67.3    
67.7    
68.1    
68.5    
68.9    
69.3    
69.6    
70.0    
70.4    
70.8    
71.2    
71.6    
72.0    
72.4    
72.8    
73.2    
73.5    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.7    
77.0    
77.4    
77.8    
78.2    
78.6    
79.0    
79.4    
79.8    
80.2    
80.5    
80.9    
81.3    
81.7    
82.1    
82.5    
82.9    
83.3    
83.7    
84.0    
84.4    
84.8    
85.2    
85.6    
86.0    
86.4    
86.8    
87.2    
87.5    
87.9    
88.3    
88.7    
89.1    
89.5    
89.9    
90.3    
90.7    
91.1    
91.4    
91.8    
92.2    
92.6    
93.0    
93.4    
93.8    
94.2    
94.6    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.3    
97.7    
98.1    
98.4    
98.8    
99.2    
99.6    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 26030, rend_intergenic: 20224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38732, rend_intergenic: 32192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53769, rend_intergenic: 46801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74528, rend_intergenic: 70264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79501, rend_intergenic: 74631  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86049, rend_intergenic: 81270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91694, rend_intergenic: 86518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129506, rend_intergenic: 126619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139810, rend_intergenic: 138226  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154772, rend_intergenic: 153257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support