-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_20019941-20227641

-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 Augustus_model.g1926.t1
Valid prediction for snap_scaffold_1-snap.3702-T1
Valid prediction for snap_scaffold_1-snap.3714-T1
Valid prediction for snap_scaffold_1-snap.3722-T1
Valid prediction for snap_scaffold_1-snap.3728-T1
Valid prediction for GlimmerHMM_glimmerT_2711-T1
Valid prediction for GlimmerHMM_glimmerT_2713-T1
Valid prediction for GlimmerHMM_glimmerT_2684-T1
Valid prediction for snap_scaffold_1-snap.3738-T1
Couldn't classify 110023, 110043
Sorry, prediction pasa_asmbl_2608.p2 fails validation.
(GGT)	 CC	110023-110043	GT	AGG
(ATG)	 AG	110551-110700	GT	AGG
(TCT)	 AG	111270-111444	GT	GGG
(GTA)	 AG	111941-112018	GT	ACG
(CTG)	 AG	112584-112639	GT	TCG
(AGG)	 AG	112988-113032	AA	AAA
-recovered pasa_asmbl_2608.p2, initial, 110551, 110700
-recovered pasa_asmbl_2608.p2, terminal, 112988, 113032
-recovered pasa_asmbl_2608.p2, internal, 110551, 110700
-recovered pasa_asmbl_2608.p2, internal, 111270, 111444
-recovered pasa_asmbl_2608.p2, internal, 111941, 112018
-recovered pasa_asmbl_2608.p2, internal, 112584, 112639
Valid prediction for GlimmerHMM_glimmerT_2699-T1
Valid prediction for snap_scaffold_1-snap.3709-T1
Valid prediction for snap_scaffold_1-snap.3720-T1
Valid prediction for snap_scaffold_1-snap.3698-T1
Valid prediction for snap_scaffold_1-snap.3745-T1
Valid prediction for snap_scaffold_1-snap.3700-T1
Valid prediction for snap_scaffold_1-snap.3730-T1
Valid prediction for snap_scaffold_1-snap.3703-T1
Valid prediction for GlimmerHMM_glimmerT_2700-T1
Valid prediction for GlimmerHMM_glimmerT_2708-T1
Valid prediction for Augustus_model.g1919.t1
Valid prediction for GlimmerHMM_glimmerT_2695-T1
Valid prediction for Augustus_model.g1929.t1
Valid prediction for snap_scaffold_1-snap.3713-T1
Valid prediction for snap_scaffold_1-snap.3737-T1
Valid prediction for Augustus_model.g1923.t1
Valid prediction for snap_scaffold_1-snap.3711-T1
Valid prediction for GlimmerHMM_glimmerT_2697-T1
Valid prediction for snap_scaffold_1-snap.3723-T1
Valid prediction for snap_scaffold_1-snap.3704-T1
Valid prediction for GlimmerHMM_glimmerT_2688-T1
Valid prediction for snap_scaffold_1-snap.3705-T1
Valid prediction for snap_scaffold_1-snap.3735-T1
Valid prediction for GlimmerHMM_glimmerT_2705-T1
Valid prediction for snap_scaffold_1-snap.3726-T1
Valid prediction for snap_scaffold_1-snap.3707-T1
Valid prediction for snap_scaffold_1-snap.3716-T1
Valid prediction for GlimmerHMM_glimmerT_2706-T1
Valid prediction for snap_scaffold_1-snap.3744-T1
Valid prediction for Augustus_model.g1921.t1
Valid prediction for GlimmerHMM_glimmerT_2712-T1
Valid prediction for snap_scaffold_1-snap.3741-T1
Valid prediction for snap_scaffold_1-snap.3706-T1
Valid prediction for Augustus_model.g1924.t1
Valid prediction for GlimmerHMM_glimmerT_2701-T1
Valid prediction for GlimmerHMM_glimmerT_2692-T1
Couldn't classify 61017, 61213
Sorry, prediction pasa_asmbl_2605.p1 fails validation.
(ATG)	 CA	59738-59895	GT	TGG
(GAA)	 AG	60586-60740	GT	AGG
(GTG)	 AG	61017-61213	GG	GAG
-recovered pasa_asmbl_2605.p1, initial, 59738, 59895
-recovered pasa_asmbl_2605.p1, internal, 60586, 60740

-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_1-snap.3733-T1
Valid prediction for snap_scaffold_1-snap.3731-T1
Valid prediction for GlimmerHMM_glimmerT_2686-T1
Valid prediction for GlimmerHMM_glimmerT_2685-T1
Valid prediction for GlimmerHMM_glimmerT_2696-T1
Valid prediction for snap_scaffold_1-snap.3718-T1
Valid prediction for Augustus_model.g1928.t1
Valid prediction for CodingQuarry_transcript_3022-T1
Valid prediction for snap_scaffold_1-snap.3715-T1
Valid prediction for GlimmerHMM_glimmerT_2702-T1
Valid prediction for snap_scaffold_1-snap.3727-T1
Valid prediction for HiQ_model.g1922.t1
Valid prediction for snap_scaffold_1-snap.3701-T1
Valid prediction for snap_scaffold_1-snap.3732-T1
Valid prediction for snap_scaffold_1-snap.3746-T1
Valid prediction for GlimmerHMM_glimmerT_2698-T1
Valid prediction for snap_scaffold_1-snap.3717-T1
Valid prediction for snap_scaffold_1-snap.3712-T1
Valid prediction for Augustus_model.g1918.t1
Valid prediction for snap_scaffold_1-snap.3710-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3729-T1
Valid prediction for Augustus_model.g1925.t1
Valid prediction for HiQ_model.g1927.t1
Couldn't classify 148493, 148530
Sorry, prediction pasa_asmbl_1166.p2 fails validation.
(CAG)	 GG	148493-148530	GT	AAG
(ATT)	 AG	148959-149001	GT	CGG
(CCG)	 AG	149107-149215	GT	AAG
(CGG)	 AG	149363-149422	GT	AGG
(GGG)	 AG	149911-150015	GT	AGG
(GTC)	 AG	150712-150833	GG	AGG
-recovered pasa_asmbl_1166.p2, terminal, 150712, 150833
-recovered pasa_asmbl_1166.p2, internal, 148959, 149001
-recovered pasa_asmbl_1166.p2, internal, 149107, 149215
-recovered pasa_asmbl_1166.p2, internal, 149363, 149422
-recovered pasa_asmbl_1166.p2, internal, 149911, 150015
Valid prediction for snap_scaffold_1-snap.3721-T1
Couldn't classify 194960, 195145
Sorry, prediction pasa_asmbl_1165.p1 fails validation.
(ATG)	 AC	189792-189869	GT	GGG
(GTG)	 AG	190233-190379	GT	ATG
(GTC)	 AG	191480-191587	GT	GGG
(TTC)	 AG	192324-192503	GT	TTG
(GAC)	 AG	192776-192913	GT	GCG
(TAC)	 AG	193571-193642	GT	GGG
(AAA)	 AG	193928-194011	GT	AGG
(ACC)	 AG	194283-194420	GT	TGG
(ACA)	 AG	194960-195145	AC	TCA
-recovered pasa_asmbl_1165.p1, initial, 189792, 189869
-recovered pasa_asmbl_1165.p1, internal, 190233, 190379
-recovered pasa_asmbl_1165.p1, internal, 191480, 191587
-recovered pasa_asmbl_1165.p1, internal, 192324, 192503
-recovered pasa_asmbl_1165.p1, internal, 192776, 192913
-recovered pasa_asmbl_1165.p1, internal, 193571, 193642
-recovered pasa_asmbl_1165.p1, internal, 193928, 194011
-recovered pasa_asmbl_1165.p1, internal, 194283, 194420
Valid prediction for snap_scaffold_1-snap.3734-T1
Valid prediction for CodingQuarry_transcript_3023-T1
Couldn't classify 112378, 112467
Couldn't classify 115106, 115123
Sorry, prediction pasa_asmbl_1169.p1 fails validation.
(GAG)	 TA	112378-112467	GT	AGG
(GTG)	 AG	112941-113097	GT	AGG
(GCC)	 AG	113351-113586	GT	AGG
(CTG)	 AG	114293-114448	GT	AGG
(GCC)	 AG	115106-115123	CG	AGC
-recovered pasa_asmbl_1169.p1, internal, 112941, 113097
-recovered pasa_asmbl_1169.p1, internal, 113351, 113586
-recovered pasa_asmbl_1169.p1, internal, 114293, 114448
Valid prediction for GlimmerHMM_glimmerT_2690-T1
Valid prediction for GlimmerHMM_glimmerT_2691-T1
Valid prediction for GlimmerHMM_glimmerT_2687-T1
Valid prediction for GlimmerHMM_glimmerT_2710-T1
Valid prediction for snap_scaffold_1-snap.3739-T1
Valid prediction for snap_scaffold_1-snap.3724-T1
Valid prediction for snap_scaffold_1-snap.3719-T1
Valid prediction for snap_scaffold_1-snap.3740-T1
Valid prediction for snap_scaffold_1-snap.3747-T1
Valid prediction for snap_scaffold_1-snap.3736-T1
Valid prediction for GlimmerHMM_glimmerT_2694-T1
Valid prediction for snap_scaffold_1-snap.3699-T1
Valid prediction for GlimmerHMM_glimmerT_2703-T1
Valid prediction for GlimmerHMM_glimmerT_2707-T1
Valid prediction for GlimmerHMM_glimmerT_2689-T1
Valid prediction for GlimmerHMM_glimmerT_2693-T1
Valid prediction for CodingQuarry_transcript_3024-T1
Valid prediction for snap_scaffold_1-snap.3742-T1
Valid prediction for pasa_asmbl_1171.p1
Valid prediction for CodingQuarry_transcript_3020-T1
Valid prediction for snap_scaffold_1-snap.3708-T1
Valid prediction for GlimmerHMM_glimmerT_2714-T1
Valid prediction for snap_scaffold_1-snap.3725-T1
Valid prediction for Augustus_model.g1920.t1
Valid prediction for GlimmerHMM_glimmerT_2709-T1
Valid prediction for snap_scaffold_1-snap.3743-T1
Valid prediction for GlimmerHMM_glimmerT_2704-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3229, rend_intergenic: 2996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6714, rend_intergenic: 5215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7727, rend_intergenic: 7466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26511, rend_intergenic: 8006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30483, rend_intergenic: 26862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37383, rend_intergenic: 34171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40592, rend_intergenic: 38567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41849, rend_intergenic: 40824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47001, rend_intergenic: 41852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54721, rend_intergenic: 47051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74359, rend_intergenic: 69558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78531, rend_intergenic: 77107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84628, rend_intergenic: 80389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93888, rend_intergenic: 90770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94347, rend_intergenic: 94020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95294, rend_intergenic: 94852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104561, rend_intergenic: 95324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162344, rend_intergenic: 147089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174697, rend_intergenic: 173751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190146, rend_intergenic: 182733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193575, rend_intergenic: 192355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207701
-exon list size: 371


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.4    
6.7    
7.0    
7.2    
7.5    
7.8    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.5    
11.8    
12.1    
12.3    
12.6    
12.9    
13.1    
13.4    
13.7    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.5    
15.8    
16.1    
16.4    
16.6    
16.9    
17.2    
17.4    
17.7    
18.0    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.4    
21.7    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.2    
28.4    
28.7    
29.0    
29.2    
29.5    
29.8    
30.0    
30.3    
30.6    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
36.2    
36.5    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.6    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.4    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.8    
57.1    
57.4    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.1    
61.4    
61.7    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.5    
63.8    
64.1    
64.3    
64.6    
64.9    
65.1    
65.4    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.6    
68.9    
69.2    
69.4    
69.7    
70.0    
70.2    
70.5    
70.8    
71.0    
71.3    
71.6    
71.8    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.3    
78.6    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.0    
82.3    
82.6    
82.8    
83.1    
83.4    
83.6    
83.9    
84.2    
84.5    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.3    
86.6    
86.9    
87.1    
87.4    
87.7    
87.9    
88.2    
88.5    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 3229, rend_intergenic: 2996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6714, rend_intergenic: 5215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7727, rend_intergenic: 7466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26511, rend_intergenic: 8006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30483, rend_intergenic: 26862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37383, rend_intergenic: 34171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40592, rend_intergenic: 38567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41849, rend_intergenic: 40824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47001, rend_intergenic: 41852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54721, rend_intergenic: 47051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74359, rend_intergenic: 69558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78531, rend_intergenic: 77107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84628, rend_intergenic: 80389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93888, rend_intergenic: 90770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94347, rend_intergenic: 94020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95294, rend_intergenic: 94852  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104561, rend_intergenic: 95324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162344, rend_intergenic: 147089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174697, rend_intergenic: 173751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190146, rend_intergenic: 182733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193575, rend_intergenic: 192355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 190822 - 207701
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 2 predictions from path traversal

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