-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_3072092-3230280

-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.746-T1
Valid prediction for snap_scaffold_2-snap.718-T1
Valid prediction for GlimmerHMM_glimmerT_3476-T1
Valid prediction for GlimmerHMM_glimmerT_3460-T1
Valid prediction for Augustus_model.g2324.t1
Valid prediction for snap_scaffold_2-snap.717-T1
Valid prediction for GlimmerHMM_glimmerT_3485-T1
Valid prediction for snap_scaffold_2-snap.741-T1
Valid prediction for snap_scaffold_2-snap.725-T1
Valid prediction for GlimmerHMM_glimmerT_3462-T1
Valid prediction for snap_scaffold_2-snap.726-T1
Valid prediction for pasa_asmbl_24271.p1
Valid prediction for snap_scaffold_2-snap.742-T1
Valid prediction for snap_scaffold_2-snap.735-T1
Valid prediction for snap_scaffold_2-snap.739-T1
Valid prediction for snap_scaffold_2-snap.750-T1
Valid prediction for GlimmerHMM_glimmerT_3471-T1
Valid prediction for snap_scaffold_2-snap.716-T1
Valid prediction for snap_scaffold_2-snap.736-T1
Valid prediction for GlimmerHMM_glimmerT_3465-T1
Valid prediction for GlimmerHMM_glimmerT_3466-T1
Valid prediction for snap_scaffold_2-snap.732-T1
Valid prediction for snap_scaffold_2-snap.748-T1
Couldn't classify 33123, 33279
Sorry, prediction pasa_asmbl_24273.p1 fails validation.
(ATG)	 TC	31354-31464	GT	AGG
(GAC)	 AG	32324-32502	GT	AGG
(AGA)	 AG	33123-33279	CA	GAC
-recovered pasa_asmbl_24273.p1, initial, 31354, 31464
add_exon() Sorry, pasa_asmbl_24273.p1 32324-32502-terminal-2 is invalid.
-recovered pasa_asmbl_24273.p1, terminal, 32324, 32502
-recovered pasa_asmbl_24273.p1, internal, 32324, 32502
Valid prediction for snap_scaffold_2-snap.730-T1
Valid prediction for HiQ_model.g2321.t1
Valid prediction for GlimmerHMM_glimmerT_3472-T1
Valid prediction for GlimmerHMM_glimmerT_3478-T1
Valid prediction for snap_scaffold_2-snap.721-T1
Valid prediction for snap_scaffold_2-snap.727-T1
Valid prediction for snap_scaffold_2-snap.744-T1
Valid prediction for Augustus_model.g2328.t1
Valid prediction for Augustus_model.g2330.t1
Valid prediction for Augustus_model.g2327.t1
Valid prediction for snap_scaffold_2-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_3464-T1
Valid prediction for snap_scaffold_2-snap.747-T1
Valid prediction for GlimmerHMM_glimmerT_3483-T1
Valid prediction for snap_scaffold_2-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_3468-T1
Valid prediction for GlimmerHMM_glimmerT_3484-T1
Valid prediction for GlimmerHMM_glimmerT_3469-T1
Valid prediction for snap_scaffold_2-snap.720-T1
Valid prediction for CodingQuarry_transcript_28492-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_3461-T1
Valid prediction for HiQ_model.g2320.t1
Valid prediction for snap_scaffold_2-snap.719-T1
Valid prediction for Augustus_model.g2331.t1
Valid prediction for snap_scaffold_2-snap.738-T1
Valid prediction for snap_scaffold_2-snap.731-T1
Valid prediction for snap_scaffold_2-snap.737-T1
Valid prediction for Augustus_model.g2332.t1
Valid prediction for snap_scaffold_2-snap.745-T1
Valid prediction for GlimmerHMM_glimmerT_3474-T1
Valid prediction for GlimmerHMM_glimmerT_3481-T1
Valid prediction for GlimmerHMM_glimmerT_3473-T1
Valid prediction for pasa_asmbl_22963.p2
Valid prediction for GlimmerHMM_glimmerT_3480-T1
Valid prediction for snap_scaffold_2-snap.740-T1
Valid prediction for snap_scaffold_2-snap.733-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.728-T1
Valid prediction for pasa_asmbl_22964.p1
Valid prediction for GlimmerHMM_glimmerT_3470-T1
Valid prediction for snap_scaffold_2-snap.724-T1
Valid prediction for Augustus_model.g2333.t1
Couldn't classify 140105, 140403
Sorry, prediction pasa_asmbl_22965.p1 fails validation.
(ATG)	 GC	138971-139073	GT	AGG
(GTC)	 AG	140105-140403	GG	CGG
-recovered pasa_asmbl_22965.p1, initial, 138971, 139073
Valid prediction for GlimmerHMM_glimmerT_3477-T1
Couldn't classify 97807, 98136
Sorry, prediction pasa_asmbl_23996.p1 fails validation.
(AAG)	 CA	97807-98136	GA	AGG
Valid prediction for snap_scaffold_2-snap.749-T1
Valid prediction for HiQ_model.g2322.t1
Valid prediction for GlimmerHMM_glimmerT_3463-T1
Valid prediction for GlimmerHMM_glimmerT_3459-T1
Valid prediction for snap_scaffold_2-snap.729-T1
Valid prediction for snap_scaffold_2-snap.723-T1
Valid prediction for GlimmerHMM_glimmerT_3482-T1
Valid prediction for Augustus_model.g2325.t1
Valid prediction for GlimmerHMM_glimmerT_3467-T1
Couldn't classify 98899, 99399
Sorry, prediction pasa_asmbl_22968.p1 fails validation.
(CAC)	 CT	98899-99399	CC	GAC
Valid prediction for GlimmerHMM_glimmerT_3479-T1
Valid prediction for Augustus_model.g2323.t1
Valid prediction for snap_scaffold_2-snap.743-T1
Valid prediction for snap_scaffold_2-snap.715-T1
Valid prediction for Augustus_model.g2329.t1
Valid prediction for Augustus_model.g2326.t1
Valid prediction for GlimmerHMM_glimmerT_3475-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24316, rend_intergenic: 13755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47280, rend_intergenic: 46445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78580, rend_intergenic: 75879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81380, rend_intergenic: 78619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85639, rend_intergenic: 81383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96218, rend_intergenic: 86447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107304, rend_intergenic: 96381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110541, rend_intergenic: 108250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112546, rend_intergenic: 111808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124830, rend_intergenic: 113649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136246, rend_intergenic: 135047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137455, rend_intergenic: 136737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140097, rend_intergenic: 138214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151208, rend_intergenic: 150513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156387, rend_intergenic: 151243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158189
-exon list size: 272


building trellis

0.4    
0.7    
1.1    
1.5    
1.8    
2.2    
2.6    
2.9    
3.3    
3.6    
4.0    
4.4    
4.7    
5.1    
5.5    
5.8    
6.2    
6.6    
6.9    
7.3    
7.7    
8.0    
8.4    
8.8    
9.1    
9.5    
9.9    
10.2    
10.6    
10.9    
11.3    
11.7    
12.0    
12.4    
12.8    
13.1    
13.5    
13.9    
14.2    
14.6    
15.0    
15.3    
15.7    
16.1    
16.4    
16.8    
17.2    
17.5    
17.9    
18.2    
18.6    
19.0    
19.3    
19.7    
20.1    
20.4    
20.8    
21.2    
21.5    
21.9    
22.3    
22.6    
23.0    
23.4    
23.7    
24.1    
24.5    
24.8    
25.2    
25.5    
25.9    
26.3    
26.6    
27.0    
27.4    
27.7    
28.1    
28.5    
28.8    
29.2    
29.6    
29.9    
30.3    
30.7    
31.0    
31.4    
31.8    
32.1    
32.5    
32.8    
33.2    
33.6    
33.9    
34.3    
34.7    
35.0    
35.4    
35.8    
36.1    
36.5    
36.9    
37.2    
37.6    
38.0    
38.3    
38.7    
39.1    
39.4    
39.8    
40.1    
40.5    
40.9    
41.2    
41.6    
42.0    
42.3    
42.7    
43.1    
43.4    
43.8    
44.2    
44.5    
44.9    
45.3    
45.6    
46.0    
46.4    
46.7    
47.1    
47.4    
47.8    
48.2    
48.5    
48.9    
49.3    
49.6    
50.0    
50.4    
50.7    
51.1    
51.5    
51.8    
52.2    
52.6    
52.9    
53.3    
53.6    
54.0    
54.4    
54.7    
55.1    
55.5    
55.8    
56.2    
56.6    
56.9    
57.3    
57.7    
58.0    
58.4    
58.8    
59.1    
59.5    
59.9    
60.2    
60.6    
60.9    
61.3    
61.7    
62.0    
62.4    
62.8    
63.1    
63.5    
63.9    
64.2    
64.6    
65.0    
65.3    
65.7    
66.1    
66.4    
66.8    
67.2    
67.5    
67.9    
68.2    
68.6    
69.0    
69.3    
69.7    
70.1    
70.4    
70.8    
71.2    
71.5    
71.9    
72.3    
72.6    
73.0    
73.4    
73.7    
74.1    
74.5    
74.8    
75.2    
75.5    
75.9    
76.3    
76.6    
77.0    
77.4    
77.7    
78.1    
78.5    
78.8    
79.2    
79.6    
79.9    
80.3    
80.7    
81.0    
81.4    
81.8    
82.1    
82.5    
82.8    
83.2    
83.6    
83.9    
84.3    
84.7    
85.0    
85.4    
85.8    
86.1    
86.5    
86.9    
87.2    
87.6    
88.0    
88.3    
88.7    
89.1    
89.4    
89.8    
90.1    
90.5    
90.9    
91.2    
91.6    
92.0    
92.3    
92.7    
93.1    
93.4    
93.8    
94.2    
94.5    
94.9    
95.3    
95.6    
96.0    
96.4    
96.7    
97.1    
97.4    
97.8    
98.2    
98.5    
98.9    
99.3    
99.6    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 24316, rend_intergenic: 13755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47280, rend_intergenic: 46445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78580, rend_intergenic: 75879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81380, rend_intergenic: 78619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85639, rend_intergenic: 81383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96218, rend_intergenic: 86447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107304, rend_intergenic: 96381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110541, rend_intergenic: 108250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112546, rend_intergenic: 111808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124830, rend_intergenic: 113649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136246, rend_intergenic: 135047  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137455, rend_intergenic: 136737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140097, rend_intergenic: 138214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151208, rend_intergenic: 150513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156387, rend_intergenic: 151243  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