-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_16342744-16492326

-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_4-snap.3311-T1
Valid prediction for snap_scaffold_4-snap.3324-T1
Valid prediction for snap_scaffold_4-snap.3309-T1
Valid prediction for GlimmerHMM_glimmerT_10857-T1
Valid prediction for pasa_asmbl_41968.p1
Valid prediction for snap_scaffold_4-snap.3338-T1
Valid prediction for snap_scaffold_4-snap.3332-T1
Valid prediction for snap_scaffold_4-snap.3325-T1
Valid prediction for snap_scaffold_4-snap.3342-T1
Valid prediction for Augustus_model.g7115.t1
Valid prediction for snap_scaffold_4-snap.3318-T1
Valid prediction for snap_scaffold_4-snap.3303-T1
Valid prediction for snap_scaffold_4-snap.3313-T1
Valid prediction for GlimmerHMM_glimmerT_10849-T1
Valid prediction for CodingQuarry_transcript_49272-T1
Valid prediction for GlimmerHMM_glimmerT_10851-T1
Valid prediction for snap_scaffold_4-snap.3335-T1
Valid prediction for snap_scaffold_4-snap.3334-T1
Valid prediction for snap_scaffold_4-snap.3312-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10867-T1
Valid prediction for snap_scaffold_4-snap.3327-T1
Valid prediction for GlimmerHMM_glimmerT_10859-T1
Valid prediction for snap_scaffold_4-snap.3337-T1
Valid prediction for snap_scaffold_4-snap.3314-T1
Valid prediction for snap_scaffold_4-snap.3304-T1
Valid prediction for snap_scaffold_4-snap.3330-T1
Valid prediction for GlimmerHMM_glimmerT_10850-T1
Valid prediction for snap_scaffold_4-snap.3333-T1
Valid prediction for snap_scaffold_4-snap.3316-T1
Valid prediction for snap_scaffold_4-snap.3317-T1
Valid prediction for snap_scaffold_4-snap.3340-T1
Valid prediction for snap_scaffold_4-snap.3328-T1
Valid prediction for GlimmerHMM_glimmerT_10865-T1
Valid prediction for GlimmerHMM_glimmerT_10870-T1
Valid prediction for Augustus_model.g7112.t1
Couldn't classify 97447, 97514
Sorry, prediction pasa_asmbl_41970.p1 fails validation.
(ATG)	 GT	94516-94698	GT	AGG
(ATC)	 AG	95438-95556	GT	GTG
(TGA)	 AG	96522-96727	GT	AGG
(ATG)	 AG	97447-97514	CC	GTC
-recovered pasa_asmbl_41970.p1, initial, 94516, 94698
-recovered pasa_asmbl_41970.p1, internal, 95438, 95556
-recovered pasa_asmbl_41970.p1, internal, 96522, 96727
Valid prediction for snap_scaffold_4-snap.3322-T1
Valid prediction for Augustus_model.g7113.t1
Valid prediction for HiQ_model.g7108.t1
Valid prediction for GlimmerHMM_glimmerT_10863-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_10868-T1
Valid prediction for snap_scaffold_4-snap.3307-T1
Valid prediction for snap_scaffold_4-snap.3320-T1
Valid prediction for snap_scaffold_4-snap.3310-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_10866-T1
Valid prediction for pasa_asmbl_43177.p1
Couldn't classify 23744, 23804
Sorry, prediction pasa_asmbl_43173.p1 fails validation.
(CAC)	 GC	23744-23804	GT	AGG
(AAA)	 AG	25227-25315	GT	AGG
(TGC)	 AG	28302-28504	GT	TGG
(GTG)	 AG	28829-28934	GT	AGG
(GTG)	 AG	29125-29294	GT	GGG
(GCT)	 AG	30746-30785	GG	GAG
-recovered pasa_asmbl_43173.p1, terminal, 30746, 30785
-recovered pasa_asmbl_43173.p1, internal, 25227, 25315
-recovered pasa_asmbl_43173.p1, internal, 28302, 28504
-recovered pasa_asmbl_43173.p1, internal, 28829, 28934
-recovered pasa_asmbl_43173.p1, internal, 29125, 29294
Valid prediction for snap_scaffold_4-snap.3341-T1
Valid prediction for pasa_asmbl_43544.p1
Valid prediction for GlimmerHMM_glimmerT_10869-T1
Valid prediction for GlimmerHMM_glimmerT_10858-T1
Valid prediction for GlimmerHMM_glimmerT_10864-T1
Valid prediction for GlimmerHMM_glimmerT_10855-T1
Valid prediction for snap_scaffold_4-snap.3321-T1
Valid prediction for GlimmerHMM_glimmerT_10852-T1
Couldn't classify 109891, 109911
Couldn't classify 114409, 114595
Sorry, prediction pasa_asmbl_43164.p1 fails validation.
(AGC)	 CC	109891-109911	GT	AGG
(GTG)	 AG	110163-110315	GT	AGG
(GTG)	 AG	110814-110961	GT	CGG
(ACG)	 AG	113482-113584	GT	GGG
(GGT)	 AG	114409-114595	GT	AGG
-recovered pasa_asmbl_43164.p1, internal, 110163, 110315
-recovered pasa_asmbl_43164.p1, internal, 110814, 110961
-recovered pasa_asmbl_43164.p1, internal, 113482, 113584
-recovered pasa_asmbl_43164.p1, internal, 114409, 114595
Valid prediction for snap_scaffold_4-snap.3326-T1
Valid prediction for pasa_asmbl_43161.p1
Couldn't classify 58503, 58592
Sorry, prediction pasa_asmbl_43172.p1 fails validation.
(ATG)	 TC	56762-56771	GT	AGG
(CAG)	 AG	57171-57293	GT	AGG
(ATA)	 AG	58258-58421	GT	AGG
(GTT)	 AG	58503-58592	AG	ACA
-recovered pasa_asmbl_43172.p1, initial, 56762, 56771
-recovered pasa_asmbl_43172.p1, internal, 57171, 57293
-recovered pasa_asmbl_43172.p1, internal, 58258, 58421
Valid prediction for snap_scaffold_4-snap.3343-T1
Valid prediction for snap_scaffold_4-snap.3336-T1
Valid prediction for snap_scaffold_4-snap.3319-T1
Valid prediction for GlimmerHMM_glimmerT_10861-T1
Valid prediction for GlimmerHMM_glimmerT_10848-T1
Valid prediction for snap_scaffold_4-snap.3339-T1
Valid prediction for snap_scaffold_4-snap.3305-T1
Valid prediction for GlimmerHMM_glimmerT_10871-T1
Valid prediction for CodingQuarry_transcript_49275-T1
Couldn't classify 14317, 14385
Couldn't classify 17816, 17904
Sorry, prediction pasa_asmbl_43635.p1 fails validation.
(ACG)	 AA	14317-14385	GT	AGG
(ATG)	 AG	15372-15494	GT	AGG
(CTG)	 AG	16221-16296	GT	AGG
(AAA)	 AG	17816-17904	GT	AGG
-recovered pasa_asmbl_43635.p1, initial, 15372, 15494
-recovered pasa_asmbl_43635.p1, internal, 15372, 15494
-recovered pasa_asmbl_43635.p1, internal, 16221, 16296
-recovered pasa_asmbl_43635.p1, internal, 17816, 17904
Valid prediction for CodingQuarry_transcript_49271-T1
Valid prediction for Augustus_model.g7117.t1
Valid prediction for snap_scaffold_4-snap.3329-T1
Valid prediction for snap_scaffold_4-snap.3315-T1
Couldn't classify 61193, 61356
Couldn't classify 62013, 62177
Sorry, prediction pasa_asmbl_43601.p1 fails validation.
(CAC)	 AC	61193-61356	GT	CGG
(TAT)	 AG	61458-61536	GT	AGG
(TCT)	 AG	61617-61775	GT	CGG
(GAG)	 AG	62013-62177	GG	GAG
-recovered pasa_asmbl_43601.p1, internal, 61458, 61536
-recovered pasa_asmbl_43601.p1, internal, 61617, 61775
Valid prediction for GlimmerHMM_glimmerT_10862-T1
Valid prediction for snap_scaffold_4-snap.3323-T1
Valid prediction for snap_scaffold_4-snap.3306-T1
Valid prediction for snap_scaffold_4-snap.3308-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 119349, 119400
Couldn't classify 122591, 122815
Sorry, prediction pasa_asmbl_43162.p1 fails validation.
(TTC)	 AG	119349-119400	GT	TGG
(AGC)	 AG	119555-119713	GT	CGG
(AAC)	 AG	120645-120698	GT	AGG
(GAG)	 AG	122057-122223	GT	AGG
(GCC)	 AG	122591-122815	GG	CAG
-recovered pasa_asmbl_43162.p1, internal, 119349, 119400
-recovered pasa_asmbl_43162.p1, internal, 119555, 119713
-recovered pasa_asmbl_43162.p1, internal, 120645, 120698
-recovered pasa_asmbl_43162.p1, internal, 122057, 122223
Valid prediction for Augustus_model.g7111.t1
Valid prediction for Augustus_model.g7109.t1
Valid prediction for GlimmerHMM_glimmerT_10860-T1
Valid prediction for Augustus_model.g7107.t1
Valid prediction for Augustus_model.g7116.t1
Valid prediction for CodingQuarry_transcript_49274-T1
Valid prediction for snap_scaffold_4-snap.3302-T1
Valid prediction for Augustus_model.g7114.t1
Valid prediction for snap_scaffold_4-snap.3331-T1
Valid prediction for GlimmerHMM_glimmerT_10853-T1
Valid prediction for GlimmerHMM_glimmerT_10856-T1
Couldn't classify 65665, 65747
Sorry, prediction pasa_asmbl_43168.p1 fails validation.
(ATG)	 TT	63912-63984	GT	AGG
(GTG)	 AG	64785-64938	GT	AGG
(GTT)	 AG	65386-65522	GT	AGG
(GTC)	 AG	65665-65747	GA	GAG
-recovered pasa_asmbl_43168.p1, initial, 63912, 63984
-recovered pasa_asmbl_43168.p1, internal, 64785, 64938
-recovered pasa_asmbl_43168.p1, internal, 65386, 65522
Valid prediction for GlimmerHMM_glimmerT_10854-T1
Valid prediction for Augustus_model.g7110.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7949, rend_intergenic: 5061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17635, rend_intergenic: 11501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22092, rend_intergenic: 21050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24315, rend_intergenic: 22168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46017, rend_intergenic: 24586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61512, rend_intergenic: 56126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84749, rend_intergenic: 81035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93201, rend_intergenic: 88910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101937, rend_intergenic: 95406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112812, rend_intergenic: 111418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116978, rend_intergenic: 116112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127088, rend_intergenic: 117192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134212, rend_intergenic: 129889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140566, rend_intergenic: 140333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143846, rend_intergenic: 140793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 149583
-exon list size: 337


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 7949, rend_intergenic: 5061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17635, rend_intergenic: 11501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22092, rend_intergenic: 21050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24315, rend_intergenic: 22168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46017, rend_intergenic: 24586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61512, rend_intergenic: 56126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84749, rend_intergenic: 81035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93201, rend_intergenic: 88910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101937, rend_intergenic: 95406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112812, rend_intergenic: 111418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116978, rend_intergenic: 116112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127088, rend_intergenic: 117192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134212, rend_intergenic: 129889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140566, rend_intergenic: 140333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143846, rend_intergenic: 140793  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