-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_10677381-10875925

-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_15447-T1
Valid prediction for snap_scaffold_6-snap.2318-T1
Valid prediction for snap_scaffold_6-snap.2308-T1
Valid prediction for GlimmerHMM_glimmerT_15444-T1
Valid prediction for snap_scaffold_6-snap.2310-T1
Valid prediction for Augustus_model.g10272.t1
Valid prediction for snap_scaffold_6-snap.2326-T1
Valid prediction for snap_scaffold_6-snap.2332-T1
Valid prediction for snap_scaffold_6-snap.2311-T1
Valid prediction for snap_scaffold_6-snap.2304-T1
Valid prediction for snap_scaffold_6-snap.2330-T1
Valid prediction for GlimmerHMM_glimmerT_15445-T1
Valid prediction for snap_scaffold_6-snap.2331-T1
Valid prediction for GlimmerHMM_glimmerT_15435-T1
Valid prediction for GlimmerHMM_glimmerT_15428-T1
Valid prediction for snap_scaffold_6-snap.2323-T1
Valid prediction for GlimmerHMM_glimmerT_15425-T1
Valid prediction for GlimmerHMM_glimmerT_15430-T1
Valid prediction for snap_scaffold_6-snap.2317-T1
Valid prediction for GlimmerHMM_glimmerT_15432-T1
Valid prediction for snap_scaffold_6-snap.2329-T1
Valid prediction for Augustus_model.g10273.t1
Valid prediction for CodingQuarry_transcript_55212-T1
Valid prediction for GlimmerHMM_glimmerT_15424-T1
Valid prediction for snap_scaffold_6-snap.2312-T1
Valid prediction for snap_scaffold_6-snap.2303-T1
Valid prediction for snap_scaffold_6-snap.2315-T1
Valid prediction for Augustus_model.g10278.t1
Valid prediction for snap_scaffold_6-snap.2314-T1
Valid prediction for snap_scaffold_6-snap.2321-T1
Valid prediction for snap_scaffold_6-snap.2301-T1
Valid prediction for snap_scaffold_6-snap.2307-T1
Valid prediction for snap_scaffold_6-snap.2328-T1
Valid prediction for snap_scaffold_6-snap.2302-T1
Valid prediction for Augustus_model.g10275.t1
Valid prediction for snap_scaffold_6-snap.2305-T1
Valid prediction for Augustus_model.g10280.t1
Valid prediction for CodingQuarry_transcript_55213-T1
Valid prediction for GlimmerHMM_glimmerT_15426-T1
Valid prediction for GlimmerHMM_glimmerT_15446-T1
Valid prediction for snap_scaffold_6-snap.2327-T1
Valid prediction for GlimmerHMM_glimmerT_15433-T1
Valid prediction for HiQ_model.g10270.t1
Valid prediction for pasa_asmbl_47290.p1
Valid prediction for HiQ_model.g10279.t1
Valid prediction for GlimmerHMM_glimmerT_15438-T1
Couldn't classify 69285, 69376
Sorry, prediction pasa_asmbl_47292.p1 fails validation.
(CAA)	 GA	69285-69376	GT	AGG
(AAT)	 AG	71335-71450	GT	TGG
(CCA)	 AG	72429-72609	GT	GAG
(GTG)	 AG	74626-74735	GT	GGG
(GTA)	 AG	74945-75026	GT	GGG
(ATT)	 AG	75362-75421	GT	AGG
(GGT)	 AG	75548-75806	TG	AGT
-recovered pasa_asmbl_47292.p1, terminal, 75548, 75806
-recovered pasa_asmbl_47292.p1, internal, 71335, 71450
-recovered pasa_asmbl_47292.p1, internal, 72429, 72609
-recovered pasa_asmbl_47292.p1, internal, 74626, 74735
-recovered pasa_asmbl_47292.p1, internal, 74945, 75026
-recovered pasa_asmbl_47292.p1, internal, 75362, 75421
Valid prediction for CodingQuarry_transcript_55210-T1
Valid prediction for pasa_asmbl_47299.p1
Valid prediction for GlimmerHMM_glimmerT_15439-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_6-snap.2309-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g10276.t1
Valid prediction for GlimmerHMM_glimmerT_15427-T1
Valid prediction for Augustus_model.g10274.t1
Valid prediction for GlimmerHMM_glimmerT_15429-T1
Valid prediction for snap_scaffold_6-snap.2320-T1
Valid prediction for GlimmerHMM_glimmerT_15431-T1
Valid prediction for Augustus_model.g10277.t1
Valid prediction for Augustus_model.g10271.t1
Valid prediction for snap_scaffold_6-snap.2319-T1
Sorry, intron length (6) is less than minimum required (10)
Couldn't classify 46246, 46480
Couldn't classify 47612, 47758
Sorry, prediction pasa_asmbl_48711.p1 fails validation.
(CCA)	 CA	46246-46480	GT	AGG
(CTT)	 AG	46939-47114	GT	CCG
(GTG)	 AG	47612-47758	GT	AGG
-recovered pasa_asmbl_48711.p1, internal, 46939, 47114
-recovered pasa_asmbl_48711.p1, internal, 47612, 47758
Valid prediction for GlimmerHMM_glimmerT_15441-T1
Couldn't classify 27672, 27796
Couldn't classify 31091, 31186
Sorry, prediction pasa_asmbl_48718.p1 fails validation.
(CTT)	 CA	27672-27796	GT	GGG
(GCC)	 AG	29677-29755	GT	CGG
(GTG)	 AG	30356-30505	GT	AGG
(GCC)	 AG	31091-31186	GA	CAG
-recovered pasa_asmbl_48718.p1, internal, 29677, 29755
-recovered pasa_asmbl_48718.p1, internal, 30356, 30505
Valid prediction for GlimmerHMM_glimmerT_15443-T1
Couldn't classify 36096, 36164
Sorry, prediction pasa_asmbl_48715.p1 fails validation.
(CTG)	 AG	36096-36164	GT	TGG
(ATC)	 AG	38274-38333	GT	TGG
(AAA)	 AG	38999-39035	GT	AGG
(AGT)	 AG	39218-39372	AC	AGA
-recovered pasa_asmbl_48715.p1, terminal, 39218, 39372
-recovered pasa_asmbl_48715.p1, internal, 36096, 36164
-recovered pasa_asmbl_48715.p1, internal, 38274, 38333
-recovered pasa_asmbl_48715.p1, internal, 38999, 39035
Valid prediction for CodingQuarry_transcript_55211-T1
Valid prediction for snap_scaffold_6-snap.2322-T1
Valid prediction for GlimmerHMM_glimmerT_15437-T1
Valid prediction for GlimmerHMM_glimmerT_15440-T1
Couldn't classify 52358, 52464
Sorry, prediction pasa_asmbl_48710.p1 fails validation.
(GAC)	 TG	52358-52464	GT	GGG
(TGA)	 AG	52576-52685	GT	CGG
(GAT)	 AG	54583-54715	GT	GAG
(GAG)	 AG	55176-55341	GT	AGG
(GTG)	 AG	56036-56245	GT	GGG
(TTG)	 AG	56909-57020	GT	AGG
(AGG)	 AG	57202-57422	AG	AGA
-recovered pasa_asmbl_48710.p1, terminal, 57202, 57422
-recovered pasa_asmbl_48710.p1, internal, 52576, 52685
-recovered pasa_asmbl_48710.p1, internal, 54583, 54715
-recovered pasa_asmbl_48710.p1, internal, 55176, 55341
-recovered pasa_asmbl_48710.p1, internal, 56036, 56245
-recovered pasa_asmbl_48710.p1, internal, 56909, 57020
Valid prediction for GlimmerHMM_glimmerT_15434-T1
Valid prediction for snap_scaffold_6-snap.2316-T1
Valid prediction for snap_scaffold_6-snap.2300-T1
Valid prediction for snap_scaffold_6-snap.2324-T1
Valid prediction for snap_scaffold_6-snap.2313-T1
Valid prediction for GlimmerHMM_glimmerT_15442-T1
Valid prediction for snap_scaffold_6-snap.2325-T1
Valid prediction for GlimmerHMM_glimmerT_15436-T1
Valid prediction for snap_scaffold_6-snap.2306-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 56620, rend_intergenic: 50872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71579, rend_intergenic: 66108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82731, rend_intergenic: 81178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93731, rend_intergenic: 83193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115022, rend_intergenic: 94135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119822, rend_intergenic: 115166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138030, rend_intergenic: 122346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144420, rend_intergenic: 140652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152726, rend_intergenic: 144709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174245, rend_intergenic: 172166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198545
-exon list size: 321


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.9    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.8    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.7    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.6    
26.9    
27.2    
27.6    
27.9    
28.2    
28.5    
28.8    
29.1    
29.4    
29.7    
30.0    
30.3    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.1    
34.4    
34.7    
35.0    
35.3    
35.6    
35.9    
36.2    
36.5    
36.8    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.6    
39.9    
40.2    
40.6    
40.9    
41.2    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.8    
59.1    
59.4    
59.8    
60.1    
60.4    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.2    
63.5    
63.8    
64.1    
64.4    
64.7    
65.0    
65.3    
65.6    
65.9    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.7    
70.0    
70.3    
70.6    
70.9    
71.2    
71.5    
71.8    
72.1    
72.4    
72.8    
73.1    
73.4    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.3    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.2    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.1    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 56620, rend_intergenic: 50872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71579, rend_intergenic: 66108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82731, rend_intergenic: 81178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93731, rend_intergenic: 83193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115022, rend_intergenic: 94135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119822, rend_intergenic: 115166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138030, rend_intergenic: 122346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144420, rend_intergenic: 140652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152726, rend_intergenic: 144709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174245, rend_intergenic: 172166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 34492
-exon list size: 13


building trellis

6.7    
13.3    
20.0    
26.7    
33.3    
40.0    
46.7    
53.3    
60.0    
66.7    
73.3    
80.0    
86.7    
93.3    
-found 3 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11759
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support