-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_15989272-16139478

-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_32990-T1
Valid prediction for Augustus_model.g22008.t1
Couldn't classify 87101, 87553
Sorry, prediction pasa_asmbl_11551.p2 fails validation.
(ATG)	 TG	87101-87553	GA	GCG
Valid prediction for snap_scaffold_13-snap.3125-T1
Valid prediction for GlimmerHMM_glimmerT_33006-T1
Valid prediction for GlimmerHMM_glimmerT_32999-T1
Valid prediction for Augustus_model.g22016.t1
Valid prediction for Augustus_model.g22011.t1
Valid prediction for Augustus_model.g22013.t1
Valid prediction for GlimmerHMM_glimmerT_33010-T1
Valid prediction for Augustus_model.g22027.t1
Valid prediction for HiQ_model.g22014.t1
Valid prediction for snap_scaffold_13-snap.3135-T1
Valid prediction for GlimmerHMM_glimmerT_33014-T1
Valid prediction for Augustus_model.g22032.t1
Valid prediction for snap_scaffold_13-snap.3137-T1
Valid prediction for Augustus_model.g22024.t1
Valid prediction for GlimmerHMM_glimmerT_33000-T1
Valid prediction for snap_scaffold_13-snap.3142-T1
Valid prediction for GlimmerHMM_glimmerT_32996-T1
Valid prediction for snap_scaffold_13-snap.3151-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 1410, 1660
Sorry, prediction pasa_asmbl_11641.p1 fails validation.
(ATG)	 CC	1018-1294	GT	ACG
(CAA)	 AG	1410-1660	TC	GTT
-recovered pasa_asmbl_11641.p1, initial, 1018, 1294
Valid prediction for snap_scaffold_13-snap.3128-T1
Valid prediction for snap_scaffold_13-snap.3147-T1
Valid prediction for snap_scaffold_13-snap.3149-T1
Valid prediction for snap_scaffold_13-snap.3146-T1
Valid prediction for Augustus_model.g22020.t1
Couldn't classify 56303, 56574
Sorry, prediction pasa_asmbl_11548.p1 fails validation.
(AAG)	 CC	56303-56574	GT	AGG
(CCA)	 AG	57845-57930	GT	GGG
(CGG)	 AG	58950-59425	TG	GAT
-recovered pasa_asmbl_11548.p1, terminal, 58950, 59425
-recovered pasa_asmbl_11548.p1, internal, 57845, 57930
Valid prediction for GlimmerHMM_glimmerT_32993-T1
Valid prediction for snap_scaffold_13-snap.3161-T1
Valid prediction for Augustus_model.g22030.t1
Valid prediction for snap_scaffold_13-snap.3138-T1
Valid prediction for GlimmerHMM_glimmerT_33007-T1
Valid prediction for GlimmerHMM_glimmerT_32989-T1
Valid prediction for GlimmerHMM_glimmerT_32998-T1
Valid prediction for snap_scaffold_13-snap.3143-T1
Valid prediction for Augustus_model.g22019.t1
Valid prediction for snap_scaffold_13-snap.3159-T1
Valid prediction for snap_scaffold_13-snap.3157-T1
Valid prediction for CodingQuarry_transcript_13350-T1
Valid prediction for snap_scaffold_13-snap.3162-T1
Valid prediction for snap_scaffold_13-snap.3130-T1
Valid prediction for GlimmerHMM_glimmerT_33002-T1
Couldn't classify 89393, 89749
Sorry, prediction pasa_asmbl_11552.p1 fails validation.
(GGG)	 CA	89393-89749	TT	GAT
Couldn't classify 12634, 12693
Sorry, prediction CodingQuarry_transcript_13345-T1 fails validation.
(ATG)	 GA	9579-9651	GT	AGG
(GTA)	 AG	10430-10678	GT	GGG
(ACC)	 AG	10771-10872	GT	AGG
(GGG)	 AG	10996-11087	GT	AGG
(GTA)	 AG	11391-11573	GT	AGG
(TGT)	 AA	12634-12693	GT	AGG
(GTG)	 AG	12902-12997	CA	GAC
-recovered CodingQuarry_transcript_13345-T1, initial, 9579, 9651
-recovered CodingQuarry_transcript_13345-T1, terminal, 12902, 12997
-recovered CodingQuarry_transcript_13345-T1, internal, 10430, 10678
-recovered CodingQuarry_transcript_13345-T1, internal, 10771, 10872
-recovered CodingQuarry_transcript_13345-T1, internal, 10996, 11087
-recovered CodingQuarry_transcript_13345-T1, internal, 11391, 11573
Valid prediction for GlimmerHMM_glimmerT_32992-T1
Valid prediction for snap_scaffold_13-snap.3164-T1
Valid prediction for snap_scaffold_13-snap.3153-T1
Valid prediction for Augustus_model.g22021.t1
Valid prediction for GlimmerHMM_glimmerT_33012-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g22015.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_33013-T1
Valid prediction for Augustus_model.g22025.t1
Valid prediction for snap_scaffold_13-snap.3155-T1
Valid prediction for snap_scaffold_13-snap.3160-T1
Couldn't classify 119032, 119132
Sorry, prediction pasa_asmbl_10261.p1 fails validation.
(ATG)	 CC	117098-117328	GT	AGG
(GTT)	 AG	117922-118042	GT	AGG
(GCG)	 AG	119032-119132	GT	GGG
-recovered pasa_asmbl_10261.p1, initial, 117098, 117328
-recovered pasa_asmbl_10261.p1, internal, 117922, 118042
-recovered pasa_asmbl_10261.p1, internal, 119032, 119132
Valid prediction for GlimmerHMM_glimmerT_32997-T1
Couldn't classify 17998, 18211
Couldn't classify 18316, 18398
Sorry, prediction pasa_asmbl_10318.p1 fails validation.
(GAG)	 AT	17998-18211	GT	AGG
(CTG)	 AG	18316-18398	GA	GAG
Valid prediction for snap_scaffold_13-snap.3145-T1
Valid prediction for snap_scaffold_13-snap.3134-T1
Valid prediction for Augustus_model.g22017.t1
Valid prediction for snap_scaffold_13-snap.3154-T1
Valid prediction for Augustus_model.g22023.t1
Valid prediction for snap_scaffold_13-snap.3127-T1
Valid prediction for GlimmerHMM_glimmerT_33004-T1
Valid prediction for snap_scaffold_13-snap.3152-T1
Valid prediction for Augustus_model.g22009.t1
Valid prediction for snap_scaffold_13-snap.3132-T1
Valid prediction for CodingQuarry_transcript_13349-T1
Valid prediction for Augustus_model.g22026.t1
Valid prediction for snap_scaffold_13-snap.3163-T1
Valid prediction for snap_scaffold_13-snap.3124-T1
Valid prediction for Augustus_model.g22022.t1
Couldn't classify 121711, 121796
Couldn't classify 123052, 123262
Sorry, prediction pasa_asmbl_10260.p1 fails validation.
(TAC)	 CG	121711-121796	GT	AAG
(GTA)	 AG	122446-122685	GT	TCG
(GAT)	 AG	123052-123262	TC	CCT
-recovered pasa_asmbl_10260.p1, internal, 122446, 122685
Valid prediction for GlimmerHMM_glimmerT_33015-T1
Valid prediction for GlimmerHMM_glimmerT_33008-T1
Valid prediction for snap_scaffold_13-snap.3150-T1
Valid prediction for GlimmerHMM_glimmerT_33016-T1
Valid prediction for snap_scaffold_13-snap.3126-T1
Valid prediction for snap_scaffold_13-snap.3131-T1
Valid prediction for Augustus_model.g22031.t1
Valid prediction for snap_scaffold_13-snap.3141-T1
Valid prediction for GlimmerHMM_glimmerT_33005-T1
Valid prediction for HiQ_model.g22010.t1
Couldn't classify 25514, 25604
Couldn't classify 26963, 27189
Sorry, prediction pasa_asmbl_10264.p1 fails validation.
(CTA)	 GT	25514-25604	GT	TGG
(ATG)	 AG	26963-27189	TG	AGT
Valid prediction for snap_scaffold_13-snap.3156-T1
Valid prediction for GlimmerHMM_glimmerT_33003-T1
Valid prediction for GlimmerHMM_glimmerT_32995-T1
Valid prediction for Augustus_model.g22018.t1
Valid prediction for Augustus_model.g22028.t1
Valid prediction for GlimmerHMM_glimmerT_33001-T1
Valid prediction for snap_scaffold_13-snap.3136-T1
Couldn't classify 142386, 142752
Sorry, prediction pasa_asmbl_10256.p1 fails validation.
(ATG)	 AT	140932-140936	GT	AGG
(TCG)	 AG	142386-142752	GA	AGG
-recovered pasa_asmbl_10256.p1, initial, 140932, 140936
Valid prediction for GlimmerHMM_glimmerT_32991-T1
Valid prediction for snap_scaffold_13-snap.3148-T1
Valid prediction for GlimmerHMM_glimmerT_32994-T1
Valid prediction for CodingQuarry_transcript_13346-T1
Valid prediction for snap_scaffold_13-snap.3133-T1
Valid prediction for Augustus_model.g22012.t1
Valid prediction for GlimmerHMM_glimmerT_33011-T1
Valid prediction for GlimmerHMM_glimmerT_33009-T1
Couldn't classify 128927, 129143
Sorry, prediction pasa_asmbl_10258.p1 fails validation.
(AGT)	 AG	128927-129143	GT	TGG
(CCG)	 AG	129808-129901	GT	CGG
(GAT)	 AG	130556-130649	GT	AGG
(ACT)	 AG	130762-130932	GT	AGG
(GAG)	 AG	131108-131205	GT	GGG
(GGA)	 AG	131591-131747	AA	AGA
-recovered pasa_asmbl_10258.p1, terminal, 131591, 131747
-recovered pasa_asmbl_10258.p1, internal, 128927, 129143
-recovered pasa_asmbl_10258.p1, internal, 129808, 129901
-recovered pasa_asmbl_10258.p1, internal, 130556, 130649
-recovered pasa_asmbl_10258.p1, internal, 130762, 130932
-recovered pasa_asmbl_10258.p1, internal, 131108, 131205
Valid prediction for Augustus_model.g22029.t1
Valid prediction for snap_scaffold_13-snap.3139-T1
Valid prediction for snap_scaffold_13-snap.3144-T1
Valid prediction for snap_scaffold_13-snap.3140-T1
Valid prediction for snap_scaffold_13-snap.3158-T1
Valid prediction for snap_scaffold_13-snap.3129-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13403, rend_intergenic: 10354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32900, rend_intergenic: 18139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49044, rend_intergenic: 38924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62243, rend_intergenic: 56087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66821, rend_intergenic: 62469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70736, rend_intergenic: 68298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86477, rend_intergenic: 82304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89749, rend_intergenic: 87211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94885, rend_intergenic: 92642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98241, rend_intergenic: 95204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100699, rend_intergenic: 98948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118472, rend_intergenic: 108540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129317, rend_intergenic: 125792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135446, rend_intergenic: 134203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139494, rend_intergenic: 135917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143710, rend_intergenic: 140874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150207
-exon list size: 351


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.3    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.6    
7.9    
8.2    
8.5    
8.8    
9.1    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.4    
14.7    
15.0    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
17.0    
17.3    
17.6    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.5    
19.8    
20.1    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.5    
27.8    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.7    
30.0    
30.3    
30.6    
30.9    
31.2    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.3    
43.6    
43.9    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.9    
46.2    
46.5    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.5    
53.8    
54.1    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.1    
56.4    
56.7    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.0    
62.3    
62.6    
62.9    
63.2    
63.5    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.8    
69.1    
69.4    
69.7    
70.0    
70.3    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.2    
72.5    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.9    
80.2    
80.5    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.4    
82.7    
83.0    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
85.0    
85.3    
85.6    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
90.9    
91.2    
91.5    
91.8    
92.1    
92.4    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.7    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 13403, rend_intergenic: 10354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32900, rend_intergenic: 18139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49044, rend_intergenic: 38924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62243, rend_intergenic: 56087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66821, rend_intergenic: 62469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70736, rend_intergenic: 68298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86477, rend_intergenic: 82304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89749, rend_intergenic: 87211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94885, rend_intergenic: 92642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98241, rend_intergenic: 95204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100699, rend_intergenic: 98948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118472, rend_intergenic: 108540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129317, rend_intergenic: 125792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135446, rend_intergenic: 134203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139494, rend_intergenic: 135917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143710, rend_intergenic: 140874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support