-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_1-126539

-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_13861-T1
Valid prediction for snap_scaffold_6-snap.22-T1
Valid prediction for GlimmerHMM_glimmerT_13880-T1
Valid prediction for pasa_asmbl_46630.p1
Valid prediction for Augustus_model.g9221.t1
Valid prediction for GlimmerHMM_glimmerT_13875-T1
Valid prediction for snap_scaffold_6-snap.6-T1
Valid prediction for pasa_asmbl_46627.p1
Valid prediction for snap_scaffold_6-snap.9-T1
Valid prediction for snap_scaffold_6-snap.20-T1
Valid prediction for snap_scaffold_6-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_13881-T1
Couldn't classify 51565, 52141
Sorry, prediction pasa_asmbl_47890.p1 fails validation.
(GTT)	 GA	51565-52141	GT	TAG
(TGA)	 AG	52271-52341	CC	GAC
-recovered pasa_asmbl_47890.p1, terminal, 52271, 52341
Valid prediction for snap_scaffold_6-snap.19-T1
Valid prediction for Augustus_model.g9214.t1
Valid prediction for CodingQuarry_transcript_54882-T1
Valid prediction for GlimmerHMM_glimmerT_13872-T1
Valid prediction for snap_scaffold_6-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_13864-T1
Valid prediction for Augustus_model.g9219.t1
Valid prediction for snap_scaffold_6-snap.14-T1
Valid prediction for snap_scaffold_6-snap.38-T1
Valid prediction for snap_scaffold_6-snap.4-T1
Valid prediction for GlimmerHMM_glimmerT_13883-T1
Valid prediction for snap_scaffold_6-snap.29-T1
Couldn't classify 50365, 51152
Sorry, prediction pasa_asmbl_46625.p1 fails validation.
(ATG)	 AG	50121-50151	GT	GGG
(CAG)	 AG	50365-51152	GG	GAG
-recovered pasa_asmbl_46625.p1, initial, 50121, 50151
-recovered pasa_asmbl_46625.p1, internal, 50121, 50151
Valid prediction for Augustus_model.g9211.t1
Couldn't classify 10665, 10985
Sorry, prediction pasa_asmbl_48012.p1 fails validation.
(ATG)	 CA	10665-10985	CT	TCC
Valid prediction for GlimmerHMM_glimmerT_13882-T1
Valid prediction for HiQ_model.g9220.t1
Valid prediction for GlimmerHMM_glimmerT_13871-T1
Couldn't classify 89523, 90114
Sorry, prediction pasa_asmbl_46631.p1 fails validation.
(GTC)	 CT	89523-90114	GT	TGG
(ATA)	 AG	90302-90588	AA	AGA
-recovered pasa_asmbl_46631.p1, terminal, 90302, 90588
Valid prediction for Augustus_model.g9209.t1
Valid prediction for Augustus_model.g9222.t1
Valid prediction for GlimmerHMM_glimmerT_13866-T1
Valid prediction for Augustus_model.g9208.t1
add_exon() Sorry, Augustus_model.g9208.t1 711-848-initial-1 is invalid.
add_exon() Sorry, Augustus_model.g9208.t1 1010-1091-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g9208.t1 2552-3128-terminal-1 is invalid.
Valid prediction for snap_scaffold_6-snap.37-T1
Valid prediction for CodingQuarry_transcript_54883-T1
Valid prediction for Augustus_model.g9223.t1
Valid prediction for snap_scaffold_6-snap.25-T1
Valid prediction for snap_scaffold_6-snap.30-T1
Valid prediction for snap_scaffold_6-snap.16-T1
Valid prediction for snap_scaffold_6-snap.18-T1
Valid prediction for HiQ_model.g9217.t1
Valid prediction for snap_scaffold_6-snap.2-T1
add_exon() Sorry, snap_scaffold_6-snap.2-T1 711-848-initial-1 is invalid.
add_exon() Sorry, snap_scaffold_6-snap.2-T1 1010-1091-internal-1 is invalid.
add_exon() Sorry, snap_scaffold_6-snap.2-T1 2538-3096-internal-2 is invalid.
add_exon() Sorry, snap_scaffold_6-snap.2-T1 5300-5436-internal-3 is invalid.
add_exon() Sorry, snap_scaffold_6-snap.2-T1 7161-7268-terminal-2 is invalid.
Valid prediction for snap_scaffold_6-snap.31-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_13874-T1
Valid prediction for snap_scaffold_6-snap.21-T1
Valid prediction for snap_scaffold_6-snap.34-T1
Valid prediction for snap_scaffold_6-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_13862-T1
Valid prediction for snap_scaffold_6-snap.8-T1
Valid prediction for GlimmerHMM_glimmerT_13869-T1
Valid prediction for Augustus_model.g9216.t1
Valid prediction for GlimmerHMM_glimmerT_13879-T1
Valid prediction for GlimmerHMM_glimmerT_13873-T1
Valid prediction for GlimmerHMM_glimmerT_13870-T1
Couldn't classify 112881, 113420
Sorry, prediction pasa_asmbl_48015.p1 fails validation.
(CTT)	 CA	112881-113420	TT	GGT
Valid prediction for GlimmerHMM_glimmerT_13868-T1
Couldn't classify 125726, 125846
Sorry, prediction snap_scaffold_6-snap.1-T1 fails validation.
(ATG)	 GC	123929-123975	GT	AGG
(AGC)	 AG	124516-125324	GT	AGG
(CCA)	 AG	125726-125846	GT	AAG
-recovered snap_scaffold_6-snap.1-T1, initial, 123929, 123975
-recovered snap_scaffold_6-snap.1-T1, internal, 124516, 125324
-recovered snap_scaffold_6-snap.1-T1, internal, 125726, 125846
Valid prediction for CodingQuarry_transcript_54881-T1
Valid prediction for CodingQuarry_transcript_54880-T1
Couldn't classify 111989, 112183
Couldn't classify 112452, 112565
Sorry, prediction pasa_asmbl_49316.p1 fails validation.
(GAT)	 CA	111989-112183	GT	AGG
(GTG)	 AG	112452-112565	AA	CCA
Valid prediction for GlimmerHMM_glimmerT_13867-T1
Valid prediction for GlimmerHMM_glimmerT_13878-T1
Valid prediction for GlimmerHMM_glimmerT_13865-T1
Valid prediction for snap_scaffold_6-snap.13-T1
Valid prediction for Augustus_model.g9218.t1
Valid prediction for snap_scaffold_6-snap.35-T1
Valid prediction for snap_scaffold_6-snap.15-T1
Valid prediction for snap_scaffold_6-snap.10-T1
Valid prediction for GlimmerHMM_glimmerT_13876-T1
Valid prediction for snap_scaffold_6-snap.26-T1
Valid prediction for snap_scaffold_6-snap.36-T1
Valid prediction for pasa_asmbl_49415.p1
Valid prediction for snap_scaffold_6-snap.28-T1
Valid prediction for snap_scaffold_6-snap.3-T1
Valid prediction for pasa_asmbl_48020.p1
Valid prediction for snap_scaffold_6-snap.17-T1
Valid prediction for CodingQuarry_transcript_54884-T1
Valid prediction for snap_scaffold_6-snap.7-T1
Valid prediction for snap_scaffold_6-snap.5-T1
Valid prediction for pasa_asmbl_48017.p1
Valid prediction for GlimmerHMM_glimmerT_13877-T1
Valid prediction for HiQ_model.g9213.t1
Valid prediction for Augustus_model.g9215.t1
Valid prediction for GlimmerHMM_glimmerT_13863-T1
Valid prediction for snap_scaffold_6-snap.23-T1
Valid prediction for Augustus_model.g9212.t1
Valid prediction for Augustus_model.g9210.t1
Valid prediction for snap_scaffold_6-snap.12-T1
Valid prediction for snap_scaffold_6-snap.32-T1
Valid prediction for snap_scaffold_6-snap.24-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2611, rend_intergenic: 711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7268, rend_intergenic: 3865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9093, rend_intergenic: 7355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10607, rend_intergenic: 9551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14554, rend_intergenic: 11110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18729, rend_intergenic: 15636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34958, rend_intergenic: 23872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42699, rend_intergenic: 39645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43659, rend_intergenic: 42892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63287, rend_intergenic: 60442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72006, rend_intergenic: 67650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103638, rend_intergenic: 101210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111291, rend_intergenic: 108281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 126539
-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: 2611, rend_intergenic: 711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7268, rend_intergenic: 3865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9093, rend_intergenic: 7355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10607, rend_intergenic: 9551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14554, rend_intergenic: 11110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18729, rend_intergenic: 15636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34958, rend_intergenic: 23872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42699, rend_intergenic: 39645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43659, rend_intergenic: 42892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63287, rend_intergenic: 60442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72006, rend_intergenic: 67650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103638, rend_intergenic: 101210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111291, rend_intergenic: 108281  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