-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_947063-1162403

-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_3149-T1
Valid prediction for snap_scaffold_2-snap.253-T1
Valid prediction for Augustus_model.g2141.t1
Valid prediction for snap_scaffold_2-snap.259-T1
Valid prediction for snap_scaffold_2-snap.254-T1
Valid prediction for snap_scaffold_2-snap.231-T1
Valid prediction for CodingQuarry_transcript_28445-T1
Valid prediction for GlimmerHMM_glimmerT_3160-T1
Valid prediction for GlimmerHMM_glimmerT_3162-T1
Valid prediction for snap_scaffold_2-snap.227-T1
Valid prediction for snap_scaffold_2-snap.222-T1
Valid prediction for Augustus_model.g2139.t1
Valid prediction for Augustus_model.g2144.t1
Valid prediction for snap_scaffold_2-snap.251-T1
Valid prediction for snap_scaffold_2-snap.256-T1
Valid prediction for snap_scaffold_2-snap.257-T1
Valid prediction for snap_scaffold_2-snap.234-T1
Valid prediction for snap_scaffold_2-snap.260-T1
Valid prediction for GlimmerHMM_glimmerT_3143-T1
Valid prediction for Augustus_model.g2138.t1
Valid prediction for snap_scaffold_2-snap.236-T1
Valid prediction for snap_scaffold_2-snap.224-T1
Valid prediction for snap_scaffold_2-snap.229-T1
Valid prediction for snap_scaffold_2-snap.232-T1
Valid prediction for snap_scaffold_2-snap.246-T1
Valid prediction for snap_scaffold_2-snap.221-T1
Valid prediction for CodingQuarry_transcript_28444-T1
Valid prediction for GlimmerHMM_glimmerT_3161-T1
Couldn't classify 2446, 2523
Sorry, prediction pasa_asmbl_24169.p1 fails validation.
(GAG)	 AG	2446-2523	GT	AGG
(GAG)	 AG	2955-3068	GT	AGG
(GCG)	 AG	3317-3433	AC	AAA
-recovered pasa_asmbl_24169.p1, terminal, 3317, 3433
-recovered pasa_asmbl_24169.p1, internal, 2446, 2523
-recovered pasa_asmbl_24169.p1, internal, 2955, 3068
Valid prediction for snap_scaffold_2-snap.226-T1
Valid prediction for snap_scaffold_2-snap.241-T1
Valid prediction for snap_scaffold_2-snap.247-T1
Valid prediction for snap_scaffold_2-snap.245-T1
Valid prediction for GlimmerHMM_glimmerT_3159-T1
Valid prediction for GlimmerHMM_glimmerT_3153-T1
Valid prediction for GlimmerHMM_glimmerT_3154-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_2-snap.244-T1
Valid prediction for CodingQuarry_transcript_28447-T1
Couldn't classify 89879, 89987
Sorry, prediction pasa_asmbl_22834.p2 fails validation.
(GGG)	 TA	89879-89987	GT	TGG
(GTC)	 AG	90085-90210	GT	AGG
(GAG)	 AG	90711-90821	GT	AGG
(GTC)	 AG	91147-91262	GT	AGG
(GTG)	 AG	91948-92148	GT	AGG
(ATC)	 AG	93767-93943	AG	GAA
-recovered pasa_asmbl_22834.p2, terminal, 93767, 93943
-recovered pasa_asmbl_22834.p2, internal, 90085, 90210
-recovered pasa_asmbl_22834.p2, internal, 90711, 90821
-recovered pasa_asmbl_22834.p2, internal, 91147, 91262
-recovered pasa_asmbl_22834.p2, internal, 91948, 92148
Valid prediction for GlimmerHMM_glimmerT_3148-T1
Valid prediction for snap_scaffold_2-snap.233-T1
Valid prediction for snap_scaffold_2-snap.239-T1
Valid prediction for GlimmerHMM_glimmerT_3163-T1
Valid prediction for snap_scaffold_2-snap.228-T1
Valid prediction for snap_scaffold_2-snap.223-T1
Valid prediction for Augustus_model.g2135.t1
Valid prediction for snap_scaffold_2-snap.255-T1
Valid prediction for GlimmerHMM_glimmerT_3141-T1
Valid prediction for GlimmerHMM_glimmerT_3142-T1
Valid prediction for GlimmerHMM_glimmerT_3157-T1
Valid prediction for Augustus_model.g2143.t1
Valid prediction for snap_scaffold_2-snap.237-T1
Valid prediction for GlimmerHMM_glimmerT_3151-T1
Valid prediction for GlimmerHMM_glimmerT_3144-T1
Valid prediction for snap_scaffold_2-snap.219-T1
Valid prediction for Augustus_model.g2145.t1
Couldn't classify 83997, 84122
Sorry, prediction pasa_asmbl_22836.p1 fails validation.
(ATG)	 GA	82148-82279	GT	GGG
(AAT)	 AG	82603-82684	GT	AGG
(ACG)	 AG	82907-83007	GT	AGG
(GGA)	 AG	83234-83383	GT	TGG
(GTC)	 AG	83480-83554	GT	CGG
(AAC)	 AG	83997-84122	TG	GGT
-recovered pasa_asmbl_22836.p1, initial, 82148, 82279
-recovered pasa_asmbl_22836.p1, internal, 82603, 82684
-recovered pasa_asmbl_22836.p1, internal, 82907, 83007
-recovered pasa_asmbl_22836.p1, internal, 83234, 83383
-recovered pasa_asmbl_22836.p1, internal, 83480, 83554
Valid prediction for snap_scaffold_2-snap.238-T1
Valid prediction for GlimmerHMM_glimmerT_3152-T1
Valid prediction for snap_scaffold_2-snap.250-T1
Valid prediction for snap_scaffold_2-snap.258-T1
Valid prediction for Augustus_model.g2140.t1
Valid prediction for snap_scaffold_2-snap.248-T1
Valid prediction for HiQ_model.g2133.t1
Valid prediction for Augustus_model.g2142.t1
Valid prediction for snap_scaffold_2-snap.243-T1
Valid prediction for snap_scaffold_2-snap.230-T1
Valid prediction for snap_scaffold_2-snap.235-T1
Valid prediction for pasa_asmbl_22826.p1
Valid prediction for snap_scaffold_2-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_3155-T1
Valid prediction for GlimmerHMM_glimmerT_3164-T1
Valid prediction for Augustus_model.g2137.t1
Valid prediction for GlimmerHMM_glimmerT_3156-T1
Valid prediction for GlimmerHMM_glimmerT_3150-T1
Valid prediction for CodingQuarry_transcript_28446-T1
Couldn't classify 26424, 26966
Sorry, prediction pasa_asmbl_22837.p1 fails validation.
(GCC)	 GT	26424-26966	GG	AAG
Valid prediction for Augustus_model.g2136.t1
Valid prediction for pasa_asmbl_22829.p1
Valid prediction for HiQ_model.g2134.t1
Valid prediction for GlimmerHMM_glimmerT_3146-T1
Valid prediction for CodingQuarry_transcript_28449-T1
Couldn't classify 11545, 11618
Couldn't classify 12694, 12817
Sorry, prediction pasa_asmbl_23934.p1 fails validation.
(GAC)	 TC	11545-11618	GT	ATG
(GAT)	 AG	12223-12324	GT	AAG
(GTT)	 AG	12694-12817	GC	ACG
-recovered pasa_asmbl_23934.p1, internal, 12223, 12324
-recovered pasa_asmbl_23934.p1, internal, 12694, 12817
Valid prediction for snap_scaffold_2-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_3165-T1
Valid prediction for snap_scaffold_2-snap.242-T1
Valid prediction for snap_scaffold_2-snap.225-T1
Valid prediction for snap_scaffold_2-snap.240-T1
Valid prediction for GlimmerHMM_glimmerT_3147-T1
Valid prediction for GlimmerHMM_glimmerT_3140-T1
Valid prediction for GlimmerHMM_glimmerT_3145-T1
Valid prediction for CodingQuarry_transcript_28450-T1
Valid prediction for snap_scaffold_2-snap.249-T1
Valid prediction for GlimmerHMM_glimmerT_3158-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18771, rend_intergenic: 16509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21433, rend_intergenic: 19181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27807, rend_intergenic: 25135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33743, rend_intergenic: 32604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39549, rend_intergenic: 34929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59218, rend_intergenic: 52844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88917, rend_intergenic: 74423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94632, rend_intergenic: 91845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105326, rend_intergenic: 95217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115924, rend_intergenic: 107103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145410, rend_intergenic: 136847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158160, rend_intergenic: 145422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165982, rend_intergenic: 162892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167972, rend_intergenic: 166349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182229, rend_intergenic: 180381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210889, rend_intergenic: 182267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215341
-exon list size: 361


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
1.9    
2.2    
2.5    
2.8    
3.0    
3.3    
3.6    
3.9    
4.1    
4.4    
4.7    
5.0    
5.2    
5.5    
5.8    
6.1    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.5    
8.8    
9.1    
9.4    
9.6    
9.9    
10.2    
10.5    
10.7    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.7    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.3    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.7    
19.0    
19.3    
19.6    
19.8    
20.1    
20.4    
20.7    
20.9    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.9    
23.1    
23.4    
23.7    
24.0    
24.2    
24.5    
24.8    
25.1    
25.3    
25.6    
25.9    
26.2    
26.4    
26.7    
27.0    
27.3    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.0    
30.3    
30.6    
30.9    
31.1    
31.4    
31.7    
32.0    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.4    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.4    
36.6    
36.9    
37.2    
37.5    
37.7    
38.0    
38.3    
38.6    
38.8    
39.1    
39.4    
39.7    
39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.5    
45.7    
46.0    
46.3    
46.6    
46.8    
47.1    
47.4    
47.7    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.3    
52.6    
52.9    
53.2    
53.4    
53.7    
54.0    
54.3    
54.5    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.2    
59.5    
59.8    
60.1    
60.3    
60.6    
60.9    
61.2    
61.4    
61.7    
62.0    
62.3    
62.5    
62.8    
63.1    
63.4    
63.6    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.6    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.0    
68.3    
68.6    
68.9    
69.1    
69.4    
69.7    
70.0    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.7    
73.0    
73.3    
73.6    
73.8    
74.1    
74.4    
74.7    
74.9    
75.2    
75.5    
75.8    
76.0    
76.3    
76.6    
76.9    
77.1    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.1    
79.3    
79.6    
79.9    
80.2    
80.4    
80.7    
81.0    
81.3    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.3    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.3    
89.5    
89.8    
90.1    
90.4    
90.6    
90.9    
91.2    
91.5    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
93.9    
94.2    
94.5    
94.8    
95.0    
95.3    
95.6    
95.9    
96.1    
96.4    
96.7    
97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 18771, rend_intergenic: 16509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21433, rend_intergenic: 19181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27807, rend_intergenic: 25135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33743, rend_intergenic: 32604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39549, rend_intergenic: 34929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59218, rend_intergenic: 52844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88917, rend_intergenic: 74423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94632, rend_intergenic: 91845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105326, rend_intergenic: 95217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115924, rend_intergenic: 107103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145410, rend_intergenic: 136847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158160, rend_intergenic: 145422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165982, rend_intergenic: 162892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167972, rend_intergenic: 166349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182229, rend_intergenic: 180381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210889, rend_intergenic: 182267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support