-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_1980356-2114784

-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_58259-T1
Valid prediction for snap_scaffold_28-snap.514-T1
Valid prediction for GlimmerHMM_glimmerT_58278-T1
Couldn't classify 125451, 125540
Sorry, prediction CodingQuarry_transcript_43544-T1 fails validation.
(ATG)	 CA	125032-125045	GT	TGG
(CTG)	 CA	125451-125540	GT	GAG
(CTT)	 AG	125670-125748	GT	AGG
(GTG)	 AG	126000-126171	GT	CGG
(AAA)	 AG	126318-126397	GT	AGG
(CAA)	 AG	126661-126806	GT	GGG
(AGG)	 AG	126969-127134	GT	AGG
(CAT)	 AG	127229-127448	GT	AGG
(CGG)	 AG	127569-127678	GT	GGG
(CAC)	 AG	127804-127992	GT	CGG
(GCG)	 AG	128252-128492	GT	GCG
(TGG)	 AG	128687-128769	GT	AGG
(ATC)	 AG	128909-129029	GT	AGG
(GTG)	 AG	129123-129220	GT	AGG
(ATG)	 AG	129350-129424	GT	AGG
(ATC)	 AG	129799-129904	GT	CGG
(GTT)	 AG	130103-130289	GT	AGG
(GCA)	 AG	130417-130573	GT	AGG
(GCC)	 AG	130685-130771	TC	AGT
-recovered CodingQuarry_transcript_43544-T1, initial, 125032, 125045
-recovered CodingQuarry_transcript_43544-T1, initial, 129350, 129424
-recovered CodingQuarry_transcript_43544-T1, terminal, 130685, 130771
-recovered CodingQuarry_transcript_43544-T1, internal, 125670, 125748
-recovered CodingQuarry_transcript_43544-T1, internal, 126000, 126171
-recovered CodingQuarry_transcript_43544-T1, internal, 126318, 126397
-recovered CodingQuarry_transcript_43544-T1, internal, 126661, 126806
-recovered CodingQuarry_transcript_43544-T1, internal, 126969, 127134
-recovered CodingQuarry_transcript_43544-T1, internal, 127229, 127448
-recovered CodingQuarry_transcript_43544-T1, internal, 127569, 127678
-recovered CodingQuarry_transcript_43544-T1, internal, 127804, 127992
-recovered CodingQuarry_transcript_43544-T1, internal, 128252, 128492
-recovered CodingQuarry_transcript_43544-T1, internal, 128687, 128769
-recovered CodingQuarry_transcript_43544-T1, internal, 128909, 129029
-recovered CodingQuarry_transcript_43544-T1, internal, 129123, 129220
-recovered CodingQuarry_transcript_43544-T1, internal, 129350, 129424
-recovered CodingQuarry_transcript_43544-T1, internal, 129799, 129904
-recovered CodingQuarry_transcript_43544-T1, internal, 130103, 130289
-recovered CodingQuarry_transcript_43544-T1, internal, 130417, 130573
Valid prediction for snap_scaffold_28-snap.509-T1
Valid prediction for GlimmerHMM_glimmerT_58258-T1
Valid prediction for snap_scaffold_28-snap.502-T1
Valid prediction for GlimmerHMM_glimmerT_58276-T1
Valid prediction for GlimmerHMM_glimmerT_58255-T1
Valid prediction for Augustus_model.g38574.t1
Valid prediction for snap_scaffold_28-snap.495-T1
Valid prediction for GlimmerHMM_glimmerT_58275-T1
Valid prediction for snap_scaffold_28-snap.489-T1
Valid prediction for snap_scaffold_28-snap.494-T1
Valid prediction for GlimmerHMM_glimmerT_58263-T1
Valid prediction for GlimmerHMM_glimmerT_58267-T1
Valid prediction for snap_scaffold_28-snap.485-T1
Valid prediction for snap_scaffold_28-snap.479-T1
Valid prediction for snap_scaffold_28-snap.510-T1
Valid prediction for Augustus_model.g38560.t1
Couldn't classify 70212, 70268
Couldn't classify 71293, 71389
Sorry, prediction pasa_asmbl_37855.p1 fails validation.
(GAT)	 AG	70212-70268	GT	CTG
(AGC)	 AG	70370-70420	GT	ATG
(CTG)	 AG	70755-70927	GT	AAG
(GTC)	 AG	71293-71389	AG	AGA
-recovered pasa_asmbl_37855.p1, internal, 70212, 70268
-recovered pasa_asmbl_37855.p1, internal, 70370, 70420
-recovered pasa_asmbl_37855.p1, internal, 70755, 70927
Valid prediction for GlimmerHMM_glimmerT_58256-T1
Valid prediction for pasa_asmbl_37323.p1
Valid prediction for GlimmerHMM_glimmerT_58274-T1
Valid prediction for Augustus_model.g38561.t1
Valid prediction for snap_scaffold_28-snap.499-T1
Valid prediction for snap_scaffold_28-snap.511-T1
Valid prediction for Augustus_model.g38562.t1
Valid prediction for snap_scaffold_28-snap.512-T1
Valid prediction for GlimmerHMM_glimmerT_58273-T1
Valid prediction for snap_scaffold_28-snap.488-T1
Valid prediction for snap_scaffold_28-snap.480-T1
Valid prediction for GlimmerHMM_glimmerT_58272-T1
Valid prediction for snap_scaffold_28-snap.487-T1
Valid prediction for snap_scaffold_28-snap.504-T1
Valid prediction for snap_scaffold_28-snap.500-T1
Valid prediction for Augustus_model.g38565.t1
Valid prediction for snap_scaffold_28-snap.482-T1
Valid prediction for GlimmerHMM_glimmerT_58265-T1
Valid prediction for snap_scaffold_28-snap.493-T1
Couldn't classify 122488, 122508
Sorry, prediction pasa_asmbl_37321.p1 fails validation.
(ATG)	 TA	119008-119461	GT	AGG
(GTT)	 AG	120037-120261	GT	CGG
(TGT)	 AG	120402-120497	GT	TGG
(GAG)	 AG	120606-120642	GT	AGG
(AAG)	 AG	120886-120961	GT	AGG
(TCA)	 AG	122488-122508	GT	TGG
-recovered pasa_asmbl_37321.p1, initial, 119008, 119461
-recovered pasa_asmbl_37321.p1, internal, 120037, 120261
-recovered pasa_asmbl_37321.p1, internal, 120402, 120497
-recovered pasa_asmbl_37321.p1, internal, 120606, 120642
-recovered pasa_asmbl_37321.p1, internal, 120886, 120961
-recovered pasa_asmbl_37321.p1, internal, 122488, 122508
Valid prediction for snap_scaffold_28-snap.490-T1
Valid prediction for GlimmerHMM_glimmerT_58262-T1
Valid prediction for HiQ_model.g38575.t1
Valid prediction for GlimmerHMM_glimmerT_58261-T1
Valid prediction for snap_scaffold_28-snap.501-T1
Valid prediction for Augustus_model.g38569.t1
Valid prediction for Augustus_model.g38563.t1
Valid prediction for Augustus_model.g38564.t1
Valid prediction for GlimmerHMM_glimmerT_58277-T1
Valid prediction for snap_scaffold_28-snap.513-T1
Valid prediction for Augustus_model.g38566.t1
Valid prediction for snap_scaffold_28-snap.491-T1
Valid prediction for GlimmerHMM_glimmerT_58279-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_28-snap.503-T1
Valid prediction for snap_scaffold_28-snap.486-T1
Valid prediction for GlimmerHMM_glimmerT_58280-T1
Valid prediction for snap_scaffold_28-snap.516-T1
Valid prediction for GlimmerHMM_glimmerT_58264-T1
Valid prediction for GlimmerHMM_glimmerT_58269-T1
Valid prediction for GlimmerHMM_glimmerT_58271-T1
Valid prediction for Augustus_model.g38571.t1
Valid prediction for snap_scaffold_28-snap.508-T1
Valid prediction for snap_scaffold_28-snap.496-T1
Valid prediction for snap_scaffold_28-snap.497-T1
Valid prediction for Augustus_model.g38568.t1
Valid prediction for Augustus_model.g38576.t1
Valid prediction for snap_scaffold_28-snap.481-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.505-T1
Valid prediction for Augustus_model.g38573.t1
Valid prediction for snap_scaffold_28-snap.483-T1
Valid prediction for Augustus_model.g38570.t1
Valid prediction for snap_scaffold_28-snap.492-T1
Valid prediction for snap_scaffold_28-snap.484-T1
Valid prediction for GlimmerHMM_glimmerT_58270-T1
Valid prediction for Augustus_model.g38572.t1
Valid prediction for GlimmerHMM_glimmerT_58266-T1
Valid prediction for snap_scaffold_28-snap.498-T1
Valid prediction for snap_scaffold_28-snap.515-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58257-T1
Valid prediction for GlimmerHMM_glimmerT_58268-T1
Valid prediction for GlimmerHMM_glimmerT_58260-T1
Valid prediction for snap_scaffold_28-snap.506-T1
Valid prediction for snap_scaffold_28-snap.507-T1
Valid prediction for Augustus_model.g38567.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16116, rend_intergenic: 14232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23220, rend_intergenic: 22729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43944, rend_intergenic: 42797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84463, rend_intergenic: 81932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130771, rend_intergenic: 123741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 134429
-exon list size: 296


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.7    
3.0    
3.4    
3.7    
4.0    
4.4    
4.7    
5.0    
5.4    
5.7    
6.0    
6.4    
6.7    
7.0    
7.4    
7.7    
8.1    
8.4    
8.7    
9.1    
9.4    
9.7    
10.1    
10.4    
10.7    
11.1    
11.4    
11.7    
12.1    
12.4    
12.8    
13.1    
13.4    
13.8    
14.1    
14.4    
14.8    
15.1    
15.4    
15.8    
16.1    
16.4    
16.8    
17.1    
17.4    
17.8    
18.1    
18.5    
18.8    
19.1    
19.5    
19.8    
20.1    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.5    
22.8    
23.2    
23.5    
23.8    
24.2    
24.5    
24.8    
25.2    
25.5    
25.8    
26.2    
26.5    
26.8    
27.2    
27.5    
27.9    
28.2    
28.5    
28.9    
29.2    
29.5    
29.9    
30.2    
30.5    
30.9    
31.2    
31.5    
31.9    
32.2    
32.6    
32.9    
33.2    
33.6    
33.9    
34.2    
34.6    
34.9    
35.2    
35.6    
35.9    
36.2    
36.6    
36.9    
37.2    
37.6    
37.9    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.3    
41.6    
41.9    
42.3    
42.6    
43.0    
43.3    
43.6    
44.0    
44.3    
44.6    
45.0    
45.3    
45.6    
46.0    
46.3    
46.6    
47.0    
47.3    
47.7    
48.0    
48.3    
48.7    
49.0    
49.3    
49.7    
50.0    
50.3    
50.7    
51.0    
51.3    
51.7    
52.0    
52.3    
52.7    
53.0    
53.4    
53.7    
54.0    
54.4    
54.7    
55.0    
55.4    
55.7    
56.0    
56.4    
56.7    
57.0    
57.4    
57.7    
58.1    
58.4    
58.7    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.1    
62.4    
62.8    
63.1    
63.4    
63.8    
64.1    
64.4    
64.8    
65.1    
65.4    
65.8    
66.1    
66.4    
66.8    
67.1    
67.4    
67.8    
68.1    
68.5    
68.8    
69.1    
69.5    
69.8    
70.1    
70.5    
70.8    
71.1    
71.5    
71.8    
72.1    
72.5    
72.8    
73.2    
73.5    
73.8    
74.2    
74.5    
74.8    
75.2    
75.5    
75.8    
76.2    
76.5    
76.8    
77.2    
77.5    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.9    
80.2    
80.5    
80.9    
81.2    
81.5    
81.9    
82.2    
82.6    
82.9    
83.2    
83.6    
83.9    
84.2    
84.6    
84.9    
85.2    
85.6    
85.9    
86.2    
86.6    
86.9    
87.2    
87.6    
87.9    
88.3    
88.6    
88.9    
89.3    
89.6    
89.9    
90.3    
90.6    
90.9    
91.3    
91.6    
91.9    
92.3    
92.6    
93.0    
93.3    
93.6    
94.0    
94.3    
94.6    
95.0    
95.3    
95.6    
96.0    
96.3    
96.6    
97.0    
97.3    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 16116, rend_intergenic: 14232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23220, rend_intergenic: 22729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43944, rend_intergenic: 42797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84463, rend_intergenic: 81932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130771, rend_intergenic: 123741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support