-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_16086438-16278045

-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_14-snap.3399-T1
Valid prediction for snap_scaffold_14-snap.3375-T1
Valid prediction for GlimmerHMM_glimmerT_35390-T1
Valid prediction for GlimmerHMM_glimmerT_35394-T1
Valid prediction for snap_scaffold_14-snap.3380-T1
Valid prediction for GlimmerHMM_glimmerT_35397-T1
Valid prediction for snap_scaffold_14-snap.3382-T1
Valid prediction for snap_scaffold_14-snap.3391-T1
Valid prediction for snap_scaffold_14-snap.3366-T1
Valid prediction for GlimmerHMM_glimmerT_35408-T1
Valid prediction for GlimmerHMM_glimmerT_35409-T1
Valid prediction for snap_scaffold_14-snap.3372-T1
Valid prediction for snap_scaffold_14-snap.3400-T1
Valid prediction for GlimmerHMM_glimmerT_35395-T1
Valid prediction for snap_scaffold_14-snap.3396-T1
Couldn't classify 35846, 35922
Sorry, prediction pasa_asmbl_12670.p1 fails validation.
(ATG)	 AG	34483-34550	GT	AGG
(AGG)	 AG	35383-35600	GT	TGG
(GAT)	 AG	35846-35922	TA	GGT
-recovered pasa_asmbl_12670.p1, initial, 34483, 34550
-recovered pasa_asmbl_12670.p1, internal, 34483, 34550
-recovered pasa_asmbl_12670.p1, internal, 35383, 35600
Valid prediction for GlimmerHMM_glimmerT_35403-T1
Valid prediction for snap_scaffold_14-snap.3367-T1
Valid prediction for GlimmerHMM_glimmerT_35412-T1
Couldn't classify 25391, 25459
Sorry, prediction pasa_asmbl_12668.p1 fails validation.
(CGT)	 CA	25391-25459	GT	AGG
(ATG)	 AG	25853-25940	GT	TGG
(GTA)	 AG	26172-26213	GT	AGG
(ACA)	 AG	26593-26763	GT	AGG
(TGG)	 AG	26980-27124	GT	AGG
(TGA)	 AG	27546-27708	CC	AAC
-recovered pasa_asmbl_12668.p1, initial, 25853, 25940
-recovered pasa_asmbl_12668.p1, terminal, 27546, 27708
-recovered pasa_asmbl_12668.p1, internal, 25853, 25940
-recovered pasa_asmbl_12668.p1, internal, 26172, 26213
-recovered pasa_asmbl_12668.p1, internal, 26593, 26763
-recovered pasa_asmbl_12668.p1, internal, 26980, 27124
Valid prediction for snap_scaffold_14-snap.3370-T1
Valid prediction for snap_scaffold_14-snap.3377-T1
Valid prediction for snap_scaffold_14-snap.3374-T1
Valid prediction for GlimmerHMM_glimmerT_35392-T1
Valid prediction for snap_scaffold_14-snap.3368-T1
Valid prediction for snap_scaffold_14-snap.3386-T1
Valid prediction for snap_scaffold_14-snap.3393-T1
Valid prediction for snap_scaffold_14-snap.3378-T1
Valid prediction for snap_scaffold_14-snap.3389-T1
Valid prediction for snap_scaffold_14-snap.3383-T1
Valid prediction for GlimmerHMM_glimmerT_35401-T1
Valid prediction for GlimmerHMM_glimmerT_35406-T1
Valid prediction for snap_scaffold_14-snap.3387-T1
Valid prediction for snap_scaffold_14-snap.3397-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 snap_scaffold_14-snap.3388-T1
Valid prediction for snap_scaffold_14-snap.3376-T1
Valid prediction for GlimmerHMM_glimmerT_35391-T1
Valid prediction for snap_scaffold_14-snap.3401-T1
Valid prediction for GlimmerHMM_glimmerT_35399-T1
Valid prediction for GlimmerHMM_glimmerT_35405-T1
Valid prediction for snap_scaffold_14-snap.3395-T1
Valid prediction for snap_scaffold_14-snap.3379-T1
Valid prediction for GlimmerHMM_glimmerT_35396-T1
Valid prediction for snap_scaffold_14-snap.3384-T1
Valid prediction for GlimmerHMM_glimmerT_35398-T1
Valid prediction for GlimmerHMM_glimmerT_35389-T1
Valid prediction for snap_scaffold_14-snap.3369-T1
Couldn't classify 169669, 169800
Sorry, prediction pasa_asmbl_13769.p1 fails validation.
(ATG)	 AG	168241-168300	GT	AGG
(TGC)	 AG	168631-168696	GT	AGG
(GTG)	 AG	168934-169062	GT	AGG
(AGG)	 AG	169669-169800	GG	AGG
-recovered pasa_asmbl_13769.p1, initial, 168241, 168300
-recovered pasa_asmbl_13769.p1, internal, 168241, 168300
-recovered pasa_asmbl_13769.p1, internal, 168631, 168696
-recovered pasa_asmbl_13769.p1, internal, 168934, 169062
Valid prediction for snap_scaffold_14-snap.3373-T1
Valid prediction for GlimmerHMM_glimmerT_35413-T1
Valid prediction for GlimmerHMM_glimmerT_35407-T1
Couldn't classify 161631, 161737
Sorry, prediction pasa_asmbl_13770.p1 fails validation.
(CCT)	 CA	161631-161737	GT	ATG
(GTA)	 AG	162015-162104	GT	GGG
(GTT)	 AG	162240-162438	CC	AAC
-recovered pasa_asmbl_13770.p1, terminal, 162240, 162438
-recovered pasa_asmbl_13770.p1, internal, 162015, 162104
Valid prediction for snap_scaffold_14-snap.3371-T1
Valid prediction for snap_scaffold_14-snap.3394-T1
Valid prediction for GlimmerHMM_glimmerT_35411-T1
Valid prediction for snap_scaffold_14-snap.3392-T1
Valid prediction for GlimmerHMM_glimmerT_35393-T1
Valid prediction for snap_scaffold_14-snap.3398-T1
Valid prediction for snap_scaffold_14-snap.3385-T1
Valid prediction for GlimmerHMM_glimmerT_35400-T1
Couldn't classify 170361, 170473
Sorry, prediction pasa_asmbl_13768.p2 fails validation.
(TGT)	 TG	170361-170473	GT	ATG
(CCT)	 AG	170691-170834	GT	AGG
(GAA)	 AG	171274-171431	GT	AGG
(GAT)	 AG	171546-171799	GG	GAG
-recovered pasa_asmbl_13768.p2, terminal, 171546, 171799
-recovered pasa_asmbl_13768.p2, internal, 170691, 170834
-recovered pasa_asmbl_13768.p2, internal, 171274, 171431
Valid prediction for GlimmerHMM_glimmerT_35410-T1
Valid prediction for snap_scaffold_14-snap.3381-T1
Valid prediction for GlimmerHMM_glimmerT_35402-T1
Couldn't classify 145519, 145659
Sorry, prediction pasa_asmbl_13772.p1 fails validation.
(AAC)	 GA	145519-145659	GT	TGG
(CTG)	 AG	146919-146954	GT	GGG
(TGG)	 AG	147724-147782	GT	TGG
(GTA)	 AG	150023-150052	GT	AGG
(AGA)	 AG	152674-152713	TA	AGT
-recovered pasa_asmbl_13772.p1, terminal, 152674, 152713
-recovered pasa_asmbl_13772.p1, internal, 146919, 146954
-recovered pasa_asmbl_13772.p1, internal, 147724, 147782
-recovered pasa_asmbl_13772.p1, internal, 150023, 150052
Valid prediction for GlimmerHMM_glimmerT_35404-T1
Valid prediction for snap_scaffold_14-snap.3390-T1
Valid prediction for CodingQuarry_transcript_15974-T1
Valid prediction for snap_scaffold_14-snap.3365-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17727, rend_intergenic: 2040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23238, rend_intergenic: 19256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36096, rend_intergenic: 35177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52328, rend_intergenic: 37961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70556, rend_intergenic: 64171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74295, rend_intergenic: 71350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79791, rend_intergenic: 74296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84368, rend_intergenic: 84011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98188, rend_intergenic: 89924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104230, rend_intergenic: 101870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107734, rend_intergenic: 104577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123042, rend_intergenic: 112608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135941, rend_intergenic: 123307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138872, rend_intergenic: 136262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155664, rend_intergenic: 139061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160165, rend_intergenic: 156923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165333, rend_intergenic: 160521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179306, rend_intergenic: 166162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188074, rend_intergenic: 180058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 191608
-exon list size: 277


building trellis

0.4    
0.7    
1.1    
1.4    
1.8    
2.2    
2.5    
2.9    
3.2    
3.6    
3.9    
4.3    
4.7    
5.0    
5.4    
5.7    
6.1    
6.5    
6.8    
7.2    
7.5    
7.9    
8.2    
8.6    
9.0    
9.3    
9.7    
10.0    
10.4    
10.8    
11.1    
11.5    
11.8    
12.2    
12.5    
12.9    
13.3    
13.6    
14.0    
14.3    
14.7    
15.1    
15.4    
15.8    
16.1    
16.5    
16.8    
17.2    
17.6    
17.9    
18.3    
18.6    
19.0    
19.4    
19.7    
20.1    
20.4    
20.8    
21.1    
21.5    
21.9    
22.2    
22.6    
22.9    
23.3    
23.7    
24.0    
24.4    
24.7    
25.1    
25.4    
25.8    
26.2    
26.5    
26.9    
27.2    
27.6    
28.0    
28.3    
28.7    
29.0    
29.4    
29.7    
30.1    
30.5    
30.8    
31.2    
31.5    
31.9    
32.3    
32.6    
33.0    
33.3    
33.7    
34.1    
34.4    
34.8    
35.1    
35.5    
35.8    
36.2    
36.6    
36.9    
37.3    
37.6    
38.0    
38.4    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.9    
41.2    
41.6    
41.9    
42.3    
42.7    
43.0    
43.4    
43.7    
44.1    
44.4    
44.8    
45.2    
45.5    
45.9    
46.2    
46.6    
47.0    
47.3    
47.7    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.3    
52.7    
53.0    
53.4    
53.8    
54.1    
54.5    
54.8    
55.2    
55.6    
55.9    
56.3    
56.6    
57.0    
57.3    
57.7    
58.1    
58.4    
58.8    
59.1    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.6    
62.0    
62.4    
62.7    
63.1    
63.4    
63.8    
64.2    
64.5    
64.9    
65.2    
65.6    
65.9    
66.3    
66.7    
67.0    
67.4    
67.7    
68.1    
68.5    
68.8    
69.2    
69.5    
69.9    
70.3    
70.6    
71.0    
71.3    
71.7    
72.0    
72.4    
72.8    
73.1    
73.5    
73.8    
74.2    
74.6    
74.9    
75.3    
75.6    
76.0    
76.3    
76.7    
77.1    
77.4    
77.8    
78.1    
78.5    
78.9    
79.2    
79.6    
79.9    
80.3    
80.6    
81.0    
81.4    
81.7    
82.1    
82.4    
82.8    
83.2    
83.5    
83.9    
84.2    
84.6    
84.9    
85.3    
85.7    
86.0    
86.4    
86.7    
87.1    
87.5    
87.8    
88.2    
88.5    
88.9    
89.2    
89.6    
90.0    
90.3    
90.7    
91.0    
91.4    
91.8    
92.1    
92.5    
92.8    
93.2    
93.5    
93.9    
94.3    
94.6    
95.0    
95.3    
95.7    
96.1    
96.4    
96.8    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 17727, rend_intergenic: 2040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23238, rend_intergenic: 19256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36096, rend_intergenic: 35177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52328, rend_intergenic: 37961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70556, rend_intergenic: 64171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74295, rend_intergenic: 71350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79791, rend_intergenic: 74296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84368, rend_intergenic: 84011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98188, rend_intergenic: 89924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104230, rend_intergenic: 101870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107734, rend_intergenic: 104577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123042, rend_intergenic: 112608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135941, rend_intergenic: 123307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138872, rend_intergenic: 136262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155664, rend_intergenic: 139061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160165, rend_intergenic: 156923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165333, rend_intergenic: 160521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179306, rend_intergenic: 166162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188074, rend_intergenic: 180058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10698
-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 1 - 10228
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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 - 10124
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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