-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_1521544-1676212

-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_16908-T1
Valid prediction for GlimmerHMM_glimmerT_16900-T1
Valid prediction for GlimmerHMM_glimmerT_16906-T1
Valid prediction for snap_scaffold_7-snap.362-T1
Valid prediction for snap_scaffold_7-snap.383-T1
Valid prediction for snap_scaffold_7-snap.380-T1
Valid prediction for snap_scaffold_7-snap.364-T1
Valid prediction for snap_scaffold_7-snap.381-T1
Valid prediction for snap_scaffold_7-snap.371-T1
Valid prediction for snap_scaffold_7-snap.388-T1
Valid prediction for snap_scaffold_7-snap.367-T1
Valid prediction for Augustus_model.g11283.t1
Valid prediction for Augustus_model.g11289.t1
Valid prediction for snap_scaffold_7-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_16901-T1
Valid prediction for snap_scaffold_7-snap.374-T1
Valid prediction for snap_scaffold_7-snap.391-T1
Valid prediction for snap_scaffold_7-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_16903-T1
Valid prediction for GlimmerHMM_glimmerT_16917-T1
Valid prediction for snap_scaffold_7-snap.378-T1
Valid prediction for snap_scaffold_7-snap.393-T1
Valid prediction for snap_scaffold_7-snap.360-T1
Valid prediction for snap_scaffold_7-snap.377-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g11287.t1
Valid prediction for GlimmerHMM_glimmerT_16912-T1
Valid prediction for GlimmerHMM_glimmerT_16902-T1
Valid prediction for GlimmerHMM_glimmerT_16907-T1
Valid prediction for snap_scaffold_7-snap.384-T1
Valid prediction for GlimmerHMM_glimmerT_16910-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_16919-T1
Valid prediction for GlimmerHMM_glimmerT_16918-T1
Valid prediction for snap_scaffold_7-snap.386-T1
Valid prediction for snap_scaffold_7-snap.376-T1
Valid prediction for Augustus_model.g11284.t1
Valid prediction for snap_scaffold_7-snap.389-T1
Valid prediction for Augustus_model.g11285.t1
Valid prediction for snap_scaffold_7-snap.375-T1
Valid prediction for GlimmerHMM_glimmerT_16913-T1
Valid prediction for Augustus_model.g11291.t1
Valid prediction for GlimmerHMM_glimmerT_16909-T1
Valid prediction for snap_scaffold_7-snap.368-T1
Valid prediction for GlimmerHMM_glimmerT_16911-T1
Valid prediction for Augustus_model.g11286.t1
Valid prediction for GlimmerHMM_glimmerT_16916-T1
Valid prediction for snap_scaffold_7-snap.366-T1
Valid prediction for Augustus_model.g11292.t1
Valid prediction for Augustus_model.g11293.t1
Valid prediction for Augustus_model.g11281.t1
Valid prediction for Augustus_model.g11288.t1
Valid prediction for snap_scaffold_7-snap.369-T1
Valid prediction for snap_scaffold_7-snap.385-T1
Valid prediction for snap_scaffold_7-snap.373-T1
Valid prediction for snap_scaffold_7-snap.387-T1
Valid prediction for GlimmerHMM_glimmerT_16904-T1
Valid prediction for GlimmerHMM_glimmerT_16905-T1
Valid prediction for snap_scaffold_7-snap.392-T1
Valid prediction for HiQ_model.g11282.t1
Valid prediction for snap_scaffold_7-snap.370-T1
Valid prediction for snap_scaffold_7-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_16898-T1
Valid prediction for snap_scaffold_7-snap.372-T1
Couldn't classify 151535, 151623
Sorry, prediction pasa_asmbl_50744.p1 fails validation.
(ATG)	 CC	149347-149501	GT	CTG
(GGT)	 AG	150066-150151	GT	GGG
(GAG)	 AG	150357-150513	GT	AAG
(CGA)	 AG	150982-151064	GT	GGG
(TTT)	 AG	151346-151438	GT	AGG
(GTG)	 AG	151535-151623	AC	GGA
-recovered pasa_asmbl_50744.p1, initial, 149347, 149501
add_exon() Sorry, pasa_asmbl_50744.p1 151346-151438-terminal-1 is invalid.
-recovered pasa_asmbl_50744.p1, terminal, 151346, 151438
-recovered pasa_asmbl_50744.p1, internal, 150066, 150151
-recovered pasa_asmbl_50744.p1, internal, 150357, 150513
-recovered pasa_asmbl_50744.p1, internal, 150982, 151064
-recovered pasa_asmbl_50744.p1, internal, 151346, 151438
Valid prediction for GlimmerHMM_glimmerT_16914-T1
Valid prediction for GlimmerHMM_glimmerT_16915-T1
Valid prediction for snap_scaffold_7-snap.382-T1
Valid prediction for snap_scaffold_7-snap.363-T1
Valid prediction for GlimmerHMM_glimmerT_16899-T1
Valid prediction for snap_scaffold_7-snap.361-T1
Valid prediction for Augustus_model.g11290.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5894, rend_intergenic: 2374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10261, rend_intergenic: 8757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11189, rend_intergenic: 10663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13759, rend_intergenic: 13649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22490, rend_intergenic: 19746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34440, rend_intergenic: 33677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42456, rend_intergenic: 34753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43193, rend_intergenic: 43110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55107, rend_intergenic: 43229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78339, rend_intergenic: 76438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119928, rend_intergenic: 111775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134542, rend_intergenic: 130068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154669
-exon list size: 228


building trellis

0.4    
0.9    
1.3    
1.7    
2.2    
2.6    
3.0    
3.5    
3.9    
4.3    
4.8    
5.2    
5.7    
6.1    
6.5    
7.0    
7.4    
7.8    
8.3    
8.7    
9.1    
9.6    
10.0    
10.4    
10.9    
11.3    
11.7    
12.2    
12.6    
13.0    
13.5    
13.9    
14.3    
14.8    
15.2    
15.7    
16.1    
16.5    
17.0    
17.4    
17.8    
18.3    
18.7    
19.1    
19.6    
20.0    
20.4    
20.9    
21.3    
21.7    
22.2    
22.6    
23.0    
23.5    
23.9    
24.3    
24.8    
25.2    
25.7    
26.1    
26.5    
27.0    
27.4    
27.8    
28.3    
28.7    
29.1    
29.6    
30.0    
30.4    
30.9    
31.3    
31.7    
32.2    
32.6    
33.0    
33.5    
33.9    
34.3    
34.8    
35.2    
35.7    
36.1    
36.5    
37.0    
37.4    
37.8    
38.3    
38.7    
39.1    
39.6    
40.0    
40.4    
40.9    
41.3    
41.7    
42.2    
42.6    
43.0    
43.5    
43.9    
44.3    
44.8    
45.2    
45.7    
46.1    
46.5    
47.0    
47.4    
47.8    
48.3    
48.7    
49.1    
49.6    
50.0    
50.4    
50.9    
51.3    
51.7    
52.2    
52.6    
53.0    
53.5    
53.9    
54.3    
54.8    
55.2    
55.7    
56.1    
56.5    
57.0    
57.4    
57.8    
58.3    
58.7    
59.1    
59.6    
60.0    
60.4    
60.9    
61.3    
61.7    
62.2    
62.6    
63.0    
63.5    
63.9    
64.3    
64.8    
65.2    
65.7    
66.1    
66.5    
67.0    
67.4    
67.8    
68.3    
68.7    
69.1    
69.6    
70.0    
70.4    
70.9    
71.3    
71.7    
72.2    
72.6    
73.0    
73.5    
73.9    
74.3    
74.8    
75.2    
75.7    
76.1    
76.5    
77.0    
77.4    
77.8    
78.3    
78.7    
79.1    
79.6    
80.0    
80.4    
80.9    
81.3    
81.7    
82.2    
82.6    
83.0    
83.5    
83.9    
84.3    
84.8    
85.2    
85.7    
86.1    
86.5    
87.0    
87.4    
87.8    
88.3    
88.7    
89.1    
89.6    
90.0    
90.4    
90.9    
91.3    
91.7    
92.2    
92.6    
93.0    
93.5    
93.9    
94.3    
94.8    
95.2    
95.7    
96.1    
96.5    
97.0    
97.4    
97.8    
98.3    
98.7    
99.1    
99.6    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 5894, rend_intergenic: 2374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10261, rend_intergenic: 8757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11189, rend_intergenic: 10663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13759, rend_intergenic: 13649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22490, rend_intergenic: 19746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34440, rend_intergenic: 33677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42456, rend_intergenic: 34753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43193, rend_intergenic: 43110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55107, rend_intergenic: 43229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78339, rend_intergenic: 76438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119928, rend_intergenic: 111775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134542, rend_intergenic: 130068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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