-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_6141798-6294799

-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_24-snap.1217-T1
Valid prediction for Augustus_model.g35045.t1
Valid prediction for GlimmerHMM_glimmerT_52615-T1
Valid prediction for snap_scaffold_24-snap.1227-T1
Valid prediction for GlimmerHMM_glimmerT_52613-T1
Valid prediction for GlimmerHMM_glimmerT_52614-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.1234-T1
Valid prediction for Augustus_model.g35036.t1
Couldn't classify 13324, 13411
Couldn't classify 15575, 15667
Sorry, prediction pasa_asmbl_32663.p1 fails validation.
(GTC)	 AG	13324-13411	GT	TCG
(TCG)	 AG	14269-14359	GT	GGG
(GGG)	 AG	15223-15328	GT	TGG
(ATC)	 AG	15575-15667	GG	AAG
-recovered pasa_asmbl_32663.p1, internal, 13324, 13411
-recovered pasa_asmbl_32663.p1, internal, 14269, 14359
-recovered pasa_asmbl_32663.p1, internal, 15223, 15328
Valid prediction for snap_scaffold_24-snap.1236-T1
Valid prediction for snap_scaffold_24-snap.1238-T1
Valid prediction for snap_scaffold_24-snap.1225-T1
Valid prediction for snap_scaffold_24-snap.1242-T1
Couldn't classify 107813, 107873
Couldn't classify 109538, 109655
Sorry, prediction pasa_asmbl_32292.p1 fails validation.
(ACC)	 AC	107813-107873	GT	CGG
(TCA)	 AG	108014-108165	GT	AGG
(GTT)	 AG	108365-108484	GT	AGG
(AAG)	 AG	109075-109220	GT	AGG
(GCG)	 AG	109538-109655	CC	CCC
-recovered pasa_asmbl_32292.p1, internal, 108014, 108165
-recovered pasa_asmbl_32292.p1, internal, 108365, 108484
-recovered pasa_asmbl_32292.p1, internal, 109075, 109220
Valid prediction for snap_scaffold_24-snap.1240-T1
Valid prediction for snap_scaffold_24-snap.1231-T1
Couldn't classify 151268, 151284
Couldn't classify 152487, 152540
Sorry, prediction pasa_asmbl_32672.p1 fails validation.
(GAC)	 AT	151268-151284	GT	TGG
(CCA)	 AG	151491-151602	GT	GGG
(CTG)	 AG	151739-151828	GT	AGG
(GCC)	 AG	151923-152109	GT	TGG
(GAG)	 AG	152204-152364	GT	CGG
(CCC)	 AG	152487-152540	GA	ACG
-recovered pasa_asmbl_32672.p1, internal, 151491, 151602
-recovered pasa_asmbl_32672.p1, internal, 151739, 151828
-recovered pasa_asmbl_32672.p1, internal, 151923, 152109
-recovered pasa_asmbl_32672.p1, internal, 152204, 152364
Valid prediction for GlimmerHMM_glimmerT_52627-T1
Valid prediction for snap_scaffold_24-snap.1223-T1
Valid prediction for Augustus_model.g35035.t1
Valid prediction for snap_scaffold_24-snap.1220-T1
Valid prediction for Augustus_model.g35046.t1
Valid prediction for Augustus_model.g35044.t1
Valid prediction for GlimmerHMM_glimmerT_52629-T1
Valid prediction for GlimmerHMM_glimmerT_52621-T1
Valid prediction for snap_scaffold_24-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_52626-T1
Valid prediction for pasa_asmbl_32289.p1
Valid prediction for snap_scaffold_24-snap.1237-T1
Couldn't classify 110193, 110200
Couldn't classify 113312, 113407
Sorry, prediction pasa_asmbl_32293.p1 fails validation.
(GAG)	 AC	110193-110200	GT	GGG
(GAC)	 AG	110406-110574	GT	CGG
(AAC)	 AG	111409-111589	GT	AGG
(GTG)	 AG	113062-113150	GT	AGG
(GCC)	 AG	113312-113407	GT	GGG
-recovered pasa_asmbl_32293.p1, internal, 110406, 110574
-recovered pasa_asmbl_32293.p1, internal, 111409, 111589
-recovered pasa_asmbl_32293.p1, internal, 113062, 113150
-recovered pasa_asmbl_32293.p1, internal, 113312, 113407
Couldn't classify 151133, 151261
Sorry, prediction pasa_asmbl_32298.p1 fails validation.
(ATG)	 CG	147960-147984	GT	CGG
(ATC)	 AG	148699-148872	GT	ACG
(ATC)	 AG	149427-149465	GT	AGG
(ATA)	 AG	150268-150434	GT	AGG
(GAG)	 AG	150864-151001	GT	CGG
(GCC)	 AG	151133-151261	AC	TGA
-recovered pasa_asmbl_32298.p1, initial, 147960, 147984
-recovered pasa_asmbl_32298.p1, internal, 148699, 148872
-recovered pasa_asmbl_32298.p1, internal, 149427, 149465
-recovered pasa_asmbl_32298.p1, internal, 150268, 150434
-recovered pasa_asmbl_32298.p1, internal, 150864, 151001
Valid prediction for snap_scaffold_24-snap.1239-T1
Couldn't classify 20879, 20960
Sorry, prediction pasa_asmbl_32287.p1 fails validation.
(GGG)	 CA	20879-20960	GT	CGG
(CCT)	 AG	22065-22432	CC	GAC
-recovered pasa_asmbl_32287.p1, terminal, 22065, 22432
Valid prediction for snap_scaffold_24-snap.1233-T1
Valid prediction for Augustus_model.g35047.t1
Valid prediction for Augustus_model.g35041.t1
Valid prediction for CodingQuarry_transcript_37325-T1
Valid prediction for snap_scaffold_24-snap.1219-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.1230-T1
Valid prediction for Augustus_model.g35039.t1
Valid prediction for GlimmerHMM_glimmerT_52625-T1
Valid prediction for snap_scaffold_24-snap.1222-T1
Valid prediction for GlimmerHMM_glimmerT_52618-T1
Couldn't classify 41622, 43277
Sorry, prediction pasa_asmbl_32288.p1 fails validation.
(ATG)	 AC	41622-43277	TA	GGT
Valid prediction for snap_scaffold_24-snap.1229-T1
Valid prediction for Augustus_model.g35038.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 Augustus_model.g35043.t1
Valid prediction for Augustus_model.g35048.t1
Valid prediction for snap_scaffold_24-snap.1216-T1
Valid prediction for CodingQuarry_transcript_37327-T1
Valid prediction for snap_scaffold_24-snap.1241-T1
Valid prediction for GlimmerHMM_glimmerT_52628-T1
Valid prediction for snap_scaffold_24-snap.1235-T1
Valid prediction for snap_scaffold_24-snap.1228-T1
Valid prediction for Augustus_model.g35037.t1
Valid prediction for Augustus_model.g35040.t1
Valid prediction for GlimmerHMM_glimmerT_52617-T1
Valid prediction for GlimmerHMM_glimmerT_52612-T1
Valid prediction for CodingQuarry_transcript_37328-T1
Valid prediction for CodingQuarry_transcript_37326-T1
Valid prediction for CodingQuarry_transcript_37324-T1
Valid prediction for snap_scaffold_24-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_52619-T1
Valid prediction for GlimmerHMM_glimmerT_52611-T1
Valid prediction for GlimmerHMM_glimmerT_52620-T1
Valid prediction for snap_scaffold_24-snap.1215-T1
Valid prediction for HiQ_model.g35042.t1
Valid prediction for GlimmerHMM_glimmerT_52623-T1
Valid prediction for snap_scaffold_24-snap.1232-T1
Valid prediction for pasa_asmbl_32946.p1
Valid prediction for snap_scaffold_24-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_52616-T1
Valid prediction for GlimmerHMM_glimmerT_52622-T1
Valid prediction for snap_scaffold_24-snap.1224-T1
Valid prediction for GlimmerHMM_glimmerT_52624-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12623, rend_intergenic: 9187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91994, rend_intergenic: 90646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101246, rend_intergenic: 92121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105819, rend_intergenic: 104367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110546, rend_intergenic: 106353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114332, rend_intergenic: 113058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145644, rend_intergenic: 143989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 127969, rend_intergenic: 127966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153002
-exon list size: 265


building trellis

0.4    
0.7    
1.1    
1.5    
1.9    
2.2    
2.6    
3.0    
3.4    
3.7    
4.1    
4.5    
4.9    
5.2    
5.6    
6.0    
6.4    
6.7    
7.1    
7.5    
7.9    
8.2    
8.6    
9.0    
9.4    
9.7    
10.1    
10.5    
10.9    
11.2    
11.6    
12.0    
12.4    
12.7    
13.1    
13.5    
13.9    
14.2    
14.6    
15.0    
15.4    
15.7    
16.1    
16.5    
16.9    
17.2    
17.6    
18.0    
18.4    
18.7    
19.1    
19.5    
19.9    
20.2    
20.6    
21.0    
21.3    
21.7    
22.1    
22.5    
22.8    
23.2    
23.6    
24.0    
24.3    
24.7    
25.1    
25.5    
25.8    
26.2    
26.6    
27.0    
27.3    
27.7    
28.1    
28.5    
28.8    
29.2    
29.6    
30.0    
30.3    
30.7    
31.1    
31.5    
31.8    
32.2    
32.6    
33.0    
33.3    
33.7    
34.1    
34.5    
34.8    
35.2    
35.6    
36.0    
36.3    
36.7    
37.1    
37.5    
37.8    
38.2    
38.6    
39.0    
39.3    
39.7    
40.1    
40.4    
40.8    
41.2    
41.6    
41.9    
42.3    
42.7    
43.1    
43.4    
43.8    
44.2    
44.6    
44.9    
45.3    
45.7    
46.1    
46.4    
46.8    
47.2    
47.6    
47.9    
48.3    
48.7    
49.1    
49.4    
49.8    
50.2    
50.6    
50.9    
51.3    
51.7    
52.1    
52.4    
52.8    
53.2    
53.6    
53.9    
54.3    
54.7    
55.1    
55.4    
55.8    
56.2    
56.6    
56.9    
57.3    
57.7    
58.1    
58.4    
58.8    
59.2    
59.6    
59.9    
60.3    
60.7    
61.0    
61.4    
61.8    
62.2    
62.5    
62.9    
63.3    
63.7    
64.0    
64.4    
64.8    
65.2    
65.5    
65.9    
66.3    
66.7    
67.0    
67.4    
67.8    
68.2    
68.5    
68.9    
69.3    
69.7    
70.0    
70.4    
70.8    
71.2    
71.5    
71.9    
72.3    
72.7    
73.0    
73.4    
73.8    
74.2    
74.5    
74.9    
75.3    
75.7    
76.0    
76.4    
76.8    
77.2    
77.5    
77.9    
78.3    
78.7    
79.0    
79.4    
79.8    
80.1    
80.5    
80.9    
81.3    
81.6    
82.0    
82.4    
82.8    
83.1    
83.5    
83.9    
84.3    
84.6    
85.0    
85.4    
85.8    
86.1    
86.5    
86.9    
87.3    
87.6    
88.0    
88.4    
88.8    
89.1    
89.5    
89.9    
90.3    
90.6    
91.0    
91.4    
91.8    
92.1    
92.5    
92.9    
93.3    
93.6    
94.0    
94.4    
94.8    
95.1    
95.5    
95.9    
96.3    
96.6    
97.0    
97.4    
97.8    
98.1    
98.5    
98.9    
99.3    
99.6    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 12623, rend_intergenic: 9187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91994, rend_intergenic: 90646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101246, rend_intergenic: 92121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105819, rend_intergenic: 104367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110546, rend_intergenic: 106353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114332, rend_intergenic: 113058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145644, rend_intergenic: 143989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 127969, rend_intergenic: 127966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11670
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 3 predictions from path traversal

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