-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_18685239-18868711

-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_3-snap.3674-T1
Valid prediction for GlimmerHMM_glimmerT_8408-T1
Valid prediction for GlimmerHMM_glimmerT_8413-T1
Valid prediction for GlimmerHMM_glimmerT_8407-T1
Valid prediction for snap_scaffold_3-snap.3692-T1
Valid prediction for GlimmerHMM_glimmerT_8397-T1
Valid prediction for HiQ_model.g5527.t1
Valid prediction for snap_scaffold_3-snap.3671-T1
Couldn't classify 46371, 47498
Sorry, prediction pasa_asmbl_40742.p1 fails validation.
(CAC)	 CC	46371-47498	GT	AGG
(GAA)	 AG	48037-48222	GT	CTG
(GAA)	 AG	48382-48402	AG	AGA
-recovered pasa_asmbl_40742.p1, terminal, 48382, 48402
-recovered pasa_asmbl_40742.p1, internal, 48037, 48222
Valid prediction for pasa_asmbl_40746.p1
Valid prediction for snap_scaffold_3-snap.3676-T1
Valid prediction for HiQ_model.g5526.t1
Valid prediction for Augustus_model.g5524.t1
Valid prediction for GlimmerHMM_glimmerT_8409-T1
Valid prediction for snap_scaffold_3-snap.3673-T1
Valid prediction for snap_scaffold_3-snap.3696-T1
Valid prediction for snap_scaffold_3-snap.3680-T1
Valid prediction for snap_scaffold_3-snap.3683-T1
Valid prediction for CodingQuarry_transcript_46479-T1
Couldn't classify 45732, 46033
Sorry, prediction pasa_asmbl_40741.p1 fails validation.
(ATG)	 CC	37939-38030	GT	AGG
(TAA)	 AG	40054-40261	GT	AGG
(GCA)	 AG	40496-40721	GT	AGG
(GCC)	 AG	40930-40998	GT	AGG
(ATA)	 AG	41102-41196	GT	AGG
(TCT)	 AG	41451-41684	GT	AGG
(GAG)	 AG	41935-42103	GT	AGG
(GAG)	 AG	45030-45288	GT	AAG
(ACC)	 AG	45538-45614	GT	TGG
(GCA)	 AG	45732-46033	GC	CAG
-recovered pasa_asmbl_40741.p1, initial, 37939, 38030
-recovered pasa_asmbl_40741.p1, internal, 40054, 40261
-recovered pasa_asmbl_40741.p1, internal, 40496, 40721
-recovered pasa_asmbl_40741.p1, internal, 40930, 40998
-recovered pasa_asmbl_40741.p1, internal, 41102, 41196
-recovered pasa_asmbl_40741.p1, internal, 41451, 41684
-recovered pasa_asmbl_40741.p1, internal, 41935, 42103
-recovered pasa_asmbl_40741.p1, internal, 45030, 45288
-recovered pasa_asmbl_40741.p1, internal, 45538, 45614
-recovered pasa_asmbl_40741.p1, internal, 45732, 46033
Valid prediction for GlimmerHMM_glimmerT_8391-T1
Valid prediction for snap_scaffold_3-snap.3699-T1
Valid prediction for GlimmerHMM_glimmerT_8406-T1
Valid prediction for GlimmerHMM_glimmerT_8394-T1
Valid prediction for snap_scaffold_3-snap.3695-T1
Valid prediction for snap_scaffold_3-snap.3690-T1
Valid prediction for snap_scaffold_3-snap.3691-T1
Valid prediction for Augustus_model.g5525.t1
Valid prediction for Augustus_model.g5523.t1
Valid prediction for snap_scaffold_3-snap.3682-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8393-T1
Valid prediction for GlimmerHMM_glimmerT_8400-T1
Valid prediction for snap_scaffold_3-snap.3679-T1
Valid prediction for Augustus_model.g5530.t1
Valid prediction for Augustus_model.g5529.t1
Valid prediction for snap_scaffold_3-snap.3675-T1
Valid prediction for GlimmerHMM_glimmerT_8396-T1
Valid prediction for CodingQuarry_transcript_46478-T1
Valid prediction for GlimmerHMM_glimmerT_8402-T1
Valid prediction for snap_scaffold_3-snap.3687-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 GlimmerHMM_glimmerT_8404-T1
Valid prediction for GlimmerHMM_glimmerT_8401-T1
Valid prediction for snap_scaffold_3-snap.3689-T1
Valid prediction for snap_scaffold_3-snap.3697-T1
Valid prediction for GlimmerHMM_glimmerT_8414-T1
Valid prediction for snap_scaffold_3-snap.3686-T1
Valid prediction for GlimmerHMM_glimmerT_8399-T1
Valid prediction for snap_scaffold_3-snap.3693-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8411-T1
Valid prediction for snap_scaffold_3-snap.3698-T1
Valid prediction for snap_scaffold_3-snap.3672-T1
Valid prediction for GlimmerHMM_glimmerT_8412-T1
Valid prediction for snap_scaffold_3-snap.3684-T1
Valid prediction for GlimmerHMM_glimmerT_8415-T1
Valid prediction for Augustus_model.g5528.t1
Valid prediction for snap_scaffold_3-snap.3694-T1
Valid prediction for snap_scaffold_3-snap.3685-T1
Valid prediction for snap_scaffold_3-snap.3677-T1
Valid prediction for GlimmerHMM_glimmerT_8392-T1
Valid prediction for GlimmerHMM_glimmerT_8390-T1
Valid prediction for GlimmerHMM_glimmerT_8410-T1
Valid prediction for snap_scaffold_3-snap.3688-T1
Valid prediction for GlimmerHMM_glimmerT_8395-T1
Valid prediction for snap_scaffold_3-snap.3678-T1
Valid prediction for snap_scaffold_3-snap.3681-T1
Valid prediction for GlimmerHMM_glimmerT_8398-T1
Valid prediction for snap_scaffold_3-snap.3700-T1
Valid prediction for GlimmerHMM_glimmerT_8403-T1
Valid prediction for GlimmerHMM_glimmerT_8405-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20183, rend_intergenic: 18397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54620, rend_intergenic: 54508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79311, rend_intergenic: 75209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104470, rend_intergenic: 101774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107655, rend_intergenic: 105304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113889, rend_intergenic: 110878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154053, rend_intergenic: 149655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173097, rend_intergenic: 166760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179009, rend_intergenic: 176756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183473
-exon list size: 251


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.8    
3.2    
3.6    
4.0    
4.3    
4.7    
5.1    
5.5    
5.9    
6.3    
6.7    
7.1    
7.5    
7.9    
8.3    
8.7    
9.1    
9.5    
9.9    
10.3    
10.7    
11.1    
11.5    
11.9    
12.3    
12.6    
13.0    
13.4    
13.8    
14.2    
14.6    
15.0    
15.4    
15.8    
16.2    
16.6    
17.0    
17.4    
17.8    
18.2    
18.6    
19.0    
19.4    
19.8    
20.2    
20.6    
20.9    
21.3    
21.7    
22.1    
22.5    
22.9    
23.3    
23.7    
24.1    
24.5    
24.9    
25.3    
25.7    
26.1    
26.5    
26.9    
27.3    
27.7    
28.1    
28.5    
28.9    
29.2    
29.6    
30.0    
30.4    
30.8    
31.2    
31.6    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.8    
35.2    
35.6    
36.0    
36.4    
36.8    
37.2    
37.5    
37.9    
38.3    
38.7    
39.1    
39.5    
39.9    
40.3    
40.7    
41.1    
41.5    
41.9    
42.3    
42.7    
43.1    
43.5    
43.9    
44.3    
44.7    
45.1    
45.5    
45.8    
46.2    
46.6    
47.0    
47.4    
47.8    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.2    
52.6    
53.0    
53.4    
53.8    
54.2    
54.5    
54.9    
55.3    
55.7    
56.1    
56.5    
56.9    
57.3    
57.7    
58.1    
58.5    
58.9    
59.3    
59.7    
60.1    
60.5    
60.9    
61.3    
61.7    
62.1    
62.5    
62.8    
63.2    
63.6    
64.0    
64.4    
64.8    
65.2    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.4    
68.8    
69.2    
69.6    
70.0    
70.4    
70.8    
71.1    
71.5    
71.9    
72.3    
72.7    
73.1    
73.5    
73.9    
74.3    
74.7    
75.1    
75.5    
75.9    
76.3    
76.7    
77.1    
77.5    
77.9    
78.3    
78.7    
79.1    
79.4    
79.8    
80.2    
80.6    
81.0    
81.4    
81.8    
82.2    
82.6    
83.0    
83.4    
83.8    
84.2    
84.6    
85.0    
85.4    
85.8    
86.2    
86.6    
87.0    
87.4    
87.7    
88.1    
88.5    
88.9    
89.3    
89.7    
90.1    
90.5    
90.9    
91.3    
91.7    
92.1    
92.5    
92.9    
93.3    
93.7    
94.1    
94.5    
94.9    
95.3    
95.7    
96.0    
96.4    
96.8    
97.2    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 20183, rend_intergenic: 18397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54620, rend_intergenic: 54508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79311, rend_intergenic: 75209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104470, rend_intergenic: 101774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107655, rend_intergenic: 105304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113889, rend_intergenic: 110878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154053, rend_intergenic: 149655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173097, rend_intergenic: 166760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179009, rend_intergenic: 176756  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