-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_19923849-20125097

-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_2-snap.3906-T1
Valid prediction for GlimmerHMM_glimmerT_5739-T1
Valid prediction for GlimmerHMM_glimmerT_5742-T1
Valid prediction for snap_scaffold_2-snap.3903-T1
Valid prediction for snap_scaffold_2-snap.3885-T1
Valid prediction for GlimmerHMM_glimmerT_5735-T1
Valid prediction for GlimmerHMM_glimmerT_5740-T1
Valid prediction for snap_scaffold_2-snap.3887-T1
Valid prediction for snap_scaffold_2-snap.3907-T1
Valid prediction for snap_scaffold_2-snap.3900-T1
Valid prediction for Augustus_model.g3808.t1
Valid prediction for GlimmerHMM_glimmerT_5744-T1
Valid prediction for snap_scaffold_2-snap.3889-T1
Valid prediction for snap_scaffold_2-snap.3884-T1
Valid prediction for GlimmerHMM_glimmerT_5725-T1
Valid prediction for GlimmerHMM_glimmerT_5730-T1
Valid prediction for GlimmerHMM_glimmerT_5733-T1
Valid prediction for GlimmerHMM_glimmerT_5726-T1
Valid prediction for snap_scaffold_2-snap.3917-T1
Valid prediction for snap_scaffold_2-snap.3883-T1
Valid prediction for snap_scaffold_2-snap.3908-T1
Valid prediction for GlimmerHMM_glimmerT_5747-T1
Valid prediction for snap_scaffold_2-snap.3882-T1
Valid prediction for GlimmerHMM_glimmerT_5728-T1
Valid prediction for Augustus_model.g3810.t1
Valid prediction for snap_scaffold_2-snap.3914-T1
Valid prediction for snap_scaffold_2-snap.3888-T1
Valid prediction for snap_scaffold_2-snap.3896-T1
Valid prediction for GlimmerHMM_glimmerT_5731-T1
Valid prediction for snap_scaffold_2-snap.3878-T1
Valid prediction for snap_scaffold_2-snap.3891-T1
Valid prediction for snap_scaffold_2-snap.3898-T1
Valid prediction for snap_scaffold_2-snap.3886-T1
Valid prediction for snap_scaffold_2-snap.3910-T1
Valid prediction for snap_scaffold_2-snap.3880-T1
Valid prediction for snap_scaffold_2-snap.3915-T1
Valid prediction for GlimmerHMM_glimmerT_5743-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_2-snap.3912-T1
Valid prediction for snap_scaffold_2-snap.3894-T1
Valid prediction for snap_scaffold_2-snap.3881-T1
Valid prediction for GlimmerHMM_glimmerT_5746-T1
Valid prediction for snap_scaffold_2-snap.3919-T1
Valid prediction for snap_scaffold_2-snap.3904-T1
Valid prediction for GlimmerHMM_glimmerT_5737-T1
Valid prediction for GlimmerHMM_glimmerT_5736-T1
Valid prediction for snap_scaffold_2-snap.3916-T1
Couldn't classify 19988, 20093
Sorry, prediction pasa_asmbl_23880.p1 fails validation.
(ATG)	 CC	18824-18930	GT	AAG
(CCA)	 AG	19119-19183	GT	AGG
(ATC)	 AG	19683-19740	GT	GAG
(CCA)	 AG	19988-20093	AT	AGA
-recovered pasa_asmbl_23880.p1, initial, 18824, 18930
add_exon() Sorry, pasa_asmbl_23880.p1 19683-19740-terminal-3 is invalid.
-recovered pasa_asmbl_23880.p1, terminal, 19683, 19740
-recovered pasa_asmbl_23880.p1, internal, 19119, 19183
-recovered pasa_asmbl_23880.p1, internal, 19683, 19740
Valid prediction for snap_scaffold_2-snap.3902-T1
Valid prediction for GlimmerHMM_glimmerT_5741-T1
Valid prediction for snap_scaffold_2-snap.3921-T1
Valid prediction for snap_scaffold_2-snap.3877-T1
Valid prediction for snap_scaffold_2-snap.3890-T1
Valid prediction for GlimmerHMM_glimmerT_5729-T1
Valid prediction for snap_scaffold_2-snap.3901-T1
Valid prediction for GlimmerHMM_glimmerT_5745-T1
Valid prediction for snap_scaffold_2-snap.3897-T1
Valid prediction for Augustus_model.g3809.t1
Valid prediction for snap_scaffold_2-snap.3918-T1
Valid prediction for snap_scaffold_2-snap.3892-T1
Valid prediction for snap_scaffold_2-snap.3913-T1
Valid prediction for snap_scaffold_2-snap.3893-T1
Valid prediction for GlimmerHMM_glimmerT_5738-T1
Valid prediction for snap_scaffold_2-snap.3899-T1
Valid prediction for GlimmerHMM_glimmerT_5732-T1
Valid prediction for GlimmerHMM_glimmerT_5734-T1
Valid prediction for snap_scaffold_2-snap.3905-T1
Valid prediction for snap_scaffold_2-snap.3895-T1
Valid prediction for snap_scaffold_2-snap.3909-T1
Valid prediction for snap_scaffold_2-snap.3879-T1
Valid prediction for snap_scaffold_2-snap.3920-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_5727-T1
Valid prediction for snap_scaffold_2-snap.3911-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5154, rend_intergenic: 4067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12751, rend_intergenic: 6672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31542, rend_intergenic: 24620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85738, rend_intergenic: 73852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103306, rend_intergenic: 88016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124709, rend_intergenic: 105056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126665, rend_intergenic: 126043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128189, rend_intergenic: 126963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130993, rend_intergenic: 128296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134387, rend_intergenic: 131538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141176, rend_intergenic: 134445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150108, rend_intergenic: 141246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160662, rend_intergenic: 154015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170983, rend_intergenic: 160944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176840, rend_intergenic: 171892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200465, rend_intergenic: 184079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201249
-exon list size: 254


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.3    
2.7    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.5    
5.9    
6.2    
6.6    
7.0    
7.4    
7.8    
8.2    
8.6    
9.0    
9.4    
9.8    
10.2    
10.5    
10.9    
11.3    
11.7    
12.1    
12.5    
12.9    
13.3    
13.7    
14.1    
14.5    
14.8    
15.2    
15.6    
16.0    
16.4    
16.8    
17.2    
17.6    
18.0    
18.4    
18.8    
19.1    
19.5    
19.9    
20.3    
20.7    
21.1    
21.5    
21.9    
22.3    
22.7    
23.0    
23.4    
23.8    
24.2    
24.6    
25.0    
25.4    
25.8    
26.2    
26.6    
27.0    
27.3    
27.7    
28.1    
28.5    
28.9    
29.3    
29.7    
30.1    
30.5    
30.9    
31.2    
31.6    
32.0    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.8    
35.2    
35.5    
35.9    
36.3    
36.7    
37.1    
37.5    
37.9    
38.3    
38.7    
39.1    
39.5    
39.8    
40.2    
40.6    
41.0    
41.4    
41.8    
42.2    
42.6    
43.0    
43.4    
43.8    
44.1    
44.5    
44.9    
45.3    
45.7    
46.1    
46.5    
46.9    
47.3    
47.7    
48.0    
48.4    
48.8    
49.2    
49.6    
50.0    
50.4    
50.8    
51.2    
51.6    
52.0    
52.3    
52.7    
53.1    
53.5    
53.9    
54.3    
54.7    
55.1    
55.5    
55.9    
56.2    
56.6    
57.0    
57.4    
57.8    
58.2    
58.6    
59.0    
59.4    
59.8    
60.2    
60.5    
60.9    
61.3    
61.7    
62.1    
62.5    
62.9    
63.3    
63.7    
64.1    
64.5    
64.8    
65.2    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
68.0    
68.4    
68.8    
69.1    
69.5    
69.9    
70.3    
70.7    
71.1    
71.5    
71.9    
72.3    
72.7    
73.0    
73.4    
73.8    
74.2    
74.6    
75.0    
75.4    
75.8    
76.2    
76.6    
77.0    
77.3    
77.7    
78.1    
78.5    
78.9    
79.3    
79.7    
80.1    
80.5    
80.9    
81.2    
81.6    
82.0    
82.4    
82.8    
83.2    
83.6    
84.0    
84.4    
84.8    
85.2    
85.5    
85.9    
86.3    
86.7    
87.1    
87.5    
87.9    
88.3    
88.7    
89.1    
89.5    
89.8    
90.2    
90.6    
91.0    
91.4    
91.8    
92.2    
92.6    
93.0    
93.4    
93.8    
94.1    
94.5    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.3    
97.7    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 5154, rend_intergenic: 4067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12751, rend_intergenic: 6672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31542, rend_intergenic: 24620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85738, rend_intergenic: 73852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103306, rend_intergenic: 88016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124709, rend_intergenic: 105056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126665, rend_intergenic: 126043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128189, rend_intergenic: 126963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130993, rend_intergenic: 128296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134387, rend_intergenic: 131538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141176, rend_intergenic: 134445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150108, rend_intergenic: 141246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160662, rend_intergenic: 154015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170983, rend_intergenic: 160944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176840, rend_intergenic: 171892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200465, rend_intergenic: 184079  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