-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_1357320-1516173

-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 Augustus_model.g2164.t1
Valid prediction for snap_scaffold_2-snap.317-T1
Valid prediction for snap_scaffold_2-snap.339-T1
Valid prediction for GlimmerHMM_glimmerT_3202-T1
Valid prediction for Augustus_model.g2178.t1
Valid prediction for GlimmerHMM_glimmerT_3201-T1
Valid prediction for GlimmerHMM_glimmerT_3206-T1
Valid prediction for GlimmerHMM_glimmerT_3216-T1
Valid prediction for snap_scaffold_2-snap.324-T1
Valid prediction for snap_scaffold_2-snap.326-T1
Couldn't classify 19555, 19752
Sorry, prediction pasa_asmbl_24194.p1 fails validation.
(ATA)	 AG	19555-19752	GT	AGG
(GCC)	 AG	20278-20356	GT	TGG
(CGA)	 AG	23234-23313	GT	AGG
(ATC)	 AG	23894-23929	TG	GAT
-recovered pasa_asmbl_24194.p1, terminal, 23894, 23929
-recovered pasa_asmbl_24194.p1, internal, 19555, 19752
-recovered pasa_asmbl_24194.p1, internal, 20278, 20356
-recovered pasa_asmbl_24194.p1, internal, 23234, 23313
Valid prediction for snap_scaffold_2-snap.319-T1
Valid prediction for Augustus_model.g2179.t1
Valid prediction for CodingQuarry_transcript_28461-T1
Valid prediction for snap_scaffold_2-snap.347-T1
Valid prediction for snap_scaffold_2-snap.330-T1
Valid prediction for pasa_asmbl_24198.p1
Couldn't classify 98981, 99658
Sorry, prediction pasa_asmbl_24201.p1 fails validation.
(CTT)	 GG	98981-99658	AG	GAA
Valid prediction for Augustus_model.g2163.t1
Valid prediction for snap_scaffold_2-snap.313-T1
Valid prediction for snap_scaffold_2-snap.335-T1
Valid prediction for CodingQuarry_transcript_28460-T1
Valid prediction for Augustus_model.g2174.t1
Couldn't classify 123446, 123506
Sorry, prediction pasa_asmbl_25395.p2 fails validation.
(ATG)	 TA	122572-122700	GT	AGG
(GAG)	 AG	122819-122864	GT	CGG
(AGG)	 AG	122951-123042	GT	TGG
(GGA)	 AG	123212-123255	GT	ATG
(AGA)	 AG	123446-123506	GT	AGG
-recovered pasa_asmbl_25395.p2, initial, 122572, 122700
-recovered pasa_asmbl_25395.p2, internal, 122819, 122864
-recovered pasa_asmbl_25395.p2, internal, 122951, 123042
-recovered pasa_asmbl_25395.p2, internal, 123212, 123255
-recovered pasa_asmbl_25395.p2, internal, 123446, 123506
Valid prediction for GlimmerHMM_glimmerT_3222-T1
Valid prediction for GlimmerHMM_glimmerT_3221-T1
Valid prediction for snap_scaffold_2-snap.311-T1
Valid prediction for snap_scaffold_2-snap.344-T1
Valid prediction for snap_scaffold_2-snap.340-T1
Valid prediction for snap_scaffold_2-snap.333-T1
Valid prediction for CodingQuarry_transcript_28459-T1
Valid prediction for GlimmerHMM_glimmerT_3212-T1
Valid prediction for GlimmerHMM_glimmerT_3218-T1
Valid prediction for HiQ_model.g2176.t1
Valid prediction for GlimmerHMM_glimmerT_3199-T1
Valid prediction for snap_scaffold_2-snap.312-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.337-T1
Valid prediction for snap_scaffold_2-snap.318-T1
Valid prediction for GlimmerHMM_glimmerT_3203-T1
Valid prediction for GlimmerHMM_glimmerT_3200-T1
Valid prediction for Augustus_model.g2171.t1
Valid prediction for Augustus_model.g2173.t1
Valid prediction for CodingQuarry_transcript_28458-T1
Valid prediction for Augustus_model.g2162.t1
Valid prediction for snap_scaffold_2-snap.342-T1
Valid prediction for snap_scaffold_2-snap.346-T1
Valid prediction for GlimmerHMM_glimmerT_3204-T1
Valid prediction for snap_scaffold_2-snap.338-T1
Couldn't classify 37608, 38102
Sorry, prediction pasa_asmbl_24197.p1 fails validation.
(TTA)	 CC	37608-38102	AA	GAA
Valid prediction for pasa_asmbl_24209.p1
Valid prediction for snap_scaffold_2-snap.316-T1
Valid prediction for snap_scaffold_2-snap.332-T1
Valid prediction for GlimmerHMM_glimmerT_3208-T1
Valid prediction for GlimmerHMM_glimmerT_3217-T1
Valid prediction for GlimmerHMM_glimmerT_3215-T1
Valid prediction for Augustus_model.g2175.t1
Valid prediction for GlimmerHMM_glimmerT_3220-T1
Valid prediction for snap_scaffold_2-snap.315-T1
Valid prediction for snap_scaffold_2-snap.348-T1
Valid prediction for Augustus_model.g2166.t1
Couldn't classify 124796, 124870
Sorry, prediction pasa_asmbl_24203.p2 fails validation.
(GCA)	 CG	124796-124870	GT	CAG
(GTA)	 AG	125104-125177	GT	TGG
(GGA)	 AG	126128-126398	TG	GAT
-recovered pasa_asmbl_24203.p2, terminal, 126128, 126398
-recovered pasa_asmbl_24203.p2, internal, 125104, 125177
Valid prediction for Augustus_model.g2165.t1
Valid prediction for GlimmerHMM_glimmerT_3207-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: -)Couldn't classify 19144, 19995
Sorry, prediction pasa_asmbl_22852.p1 fails validation.
(ACT)	 GC	19144-19995	TT	GAT
Valid prediction for snap_scaffold_2-snap.325-T1
Valid prediction for GlimmerHMM_glimmerT_3213-T1
Valid prediction for snap_scaffold_2-snap.334-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_3214-T1
Valid prediction for snap_scaffold_2-snap.322-T1
Valid prediction for snap_scaffold_2-snap.320-T1
Valid prediction for Augustus_model.g2170.t1
Valid prediction for Augustus_model.g2167.t1
Valid prediction for Augustus_model.g2177.t1
Valid prediction for GlimmerHMM_glimmerT_3210-T1
Valid prediction for Augustus_model.g2168.t1
Valid prediction for GlimmerHMM_glimmerT_3209-T1
Valid prediction for snap_scaffold_2-snap.329-T1
Valid prediction for GlimmerHMM_glimmerT_3211-T1
Valid prediction for snap_scaffold_2-snap.336-T1
Valid prediction for snap_scaffold_2-snap.323-T1
Valid prediction for snap_scaffold_2-snap.343-T1
Valid prediction for GlimmerHMM_glimmerT_3219-T1
Valid prediction for snap_scaffold_2-snap.331-T1
Valid prediction for snap_scaffold_2-snap.314-T1
Valid prediction for Augustus_model.g2169.t1
Valid prediction for Augustus_model.g2172.t1
Valid prediction for snap_scaffold_2-snap.327-T1
Valid prediction for GlimmerHMM_glimmerT_3223-T1
Valid prediction for snap_scaffold_2-snap.321-T1
Valid prediction for snap_scaffold_2-snap.341-T1
Valid prediction for GlimmerHMM_glimmerT_3205-T1
Valid prediction for snap_scaffold_2-snap.345-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9875, rend_intergenic: 6806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13084, rend_intergenic: 10271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71589, rend_intergenic: 65018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80811, rend_intergenic: 77572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89758, rend_intergenic: 87157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96206, rend_intergenic: 91400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103684, rend_intergenic: 98458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135653, rend_intergenic: 135383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137694, rend_intergenic: 136185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158854
-exon list size: 260


building trellis

0.4    
0.8    
1.1    
1.5    
1.9    
2.3    
2.7    
3.1    
3.4    
3.8    
4.2    
4.6    
5.0    
5.3    
5.7    
6.1    
6.5    
6.9    
7.3    
7.6    
8.0    
8.4    
8.8    
9.2    
9.5    
9.9    
10.3    
10.7    
11.1    
11.5    
11.8    
12.2    
12.6    
13.0    
13.4    
13.7    
14.1    
14.5    
14.9    
15.3    
15.6    
16.0    
16.4    
16.8    
17.2    
17.6    
17.9    
18.3    
18.7    
19.1    
19.5    
19.8    
20.2    
20.6    
21.0    
21.4    
21.8    
22.1    
22.5    
22.9    
23.3    
23.7    
24.0    
24.4    
24.8    
25.2    
25.6    
26.0    
26.3    
26.7    
27.1    
27.5    
27.9    
28.2    
28.6    
29.0    
29.4    
29.8    
30.2    
30.5    
30.9    
31.3    
31.7    
32.1    
32.4    
32.8    
33.2    
33.6    
34.0    
34.4    
34.7    
35.1    
35.5    
35.9    
36.3    
36.6    
37.0    
37.4    
37.8    
38.2    
38.5    
38.9    
39.3    
39.7    
40.1    
40.5    
40.8    
41.2    
41.6    
42.0    
42.4    
42.7    
43.1    
43.5    
43.9    
44.3    
44.7    
45.0    
45.4    
45.8    
46.2    
46.6    
46.9    
47.3    
47.7    
48.1    
48.5    
48.9    
49.2    
49.6    
50.0    
50.4    
50.8    
51.1    
51.5    
51.9    
52.3    
52.7    
53.1    
53.4    
53.8    
54.2    
54.6    
55.0    
55.3    
55.7    
56.1    
56.5    
56.9    
57.3    
57.6    
58.0    
58.4    
58.8    
59.2    
59.5    
59.9    
60.3    
60.7    
61.1    
61.5    
61.8    
62.2    
62.6    
63.0    
63.4    
63.7    
64.1    
64.5    
64.9    
65.3    
65.6    
66.0    
66.4    
66.8    
67.2    
67.6    
67.9    
68.3    
68.7    
69.1    
69.5    
69.8    
70.2    
70.6    
71.0    
71.4    
71.8    
72.1    
72.5    
72.9    
73.3    
73.7    
74.0    
74.4    
74.8    
75.2    
75.6    
76.0    
76.3    
76.7    
77.1    
77.5    
77.9    
78.2    
78.6    
79.0    
79.4    
79.8    
80.2    
80.5    
80.9    
81.3    
81.7    
82.1    
82.4    
82.8    
83.2    
83.6    
84.0    
84.4    
84.7    
85.1    
85.5    
85.9    
86.3    
86.6    
87.0    
87.4    
87.8    
88.2    
88.5    
88.9    
89.3    
89.7    
90.1    
90.5    
90.8    
91.2    
91.6    
92.0    
92.4    
92.7    
93.1    
93.5    
93.9    
94.3    
94.7    
95.0    
95.4    
95.8    
96.2    
96.6    
96.9    
97.3    
97.7    
98.1    
98.5    
98.9    
99.2    
99.6    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 9875, rend_intergenic: 6806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13084, rend_intergenic: 10271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71589, rend_intergenic: 65018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80811, rend_intergenic: 77572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89758, rend_intergenic: 87157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96206, rend_intergenic: 91400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103684, rend_intergenic: 98458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135653, rend_intergenic: 135383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137694, rend_intergenic: 136185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support