-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_5166665-5417004

-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_28-snap.1230-T1
Valid prediction for Augustus_model.g38967.t1
Valid prediction for GlimmerHMM_glimmerT_58799-T1
Valid prediction for Augustus_model.g38955.t1
Couldn't classify 75949, 75949
Sorry, prediction CodingQuarry_transcript_43659-T1 fails validation.
(AGG)	 TC	75949-75949	GG	CAG
(TGG)	 AG	77047-77174	GT	AGG
(GTG)	 AG	77428-77628	GG	GAG
-recovered CodingQuarry_transcript_43659-T1, terminal, 77428, 77628
-recovered CodingQuarry_transcript_43659-T1, internal, 77047, 77174
Valid prediction for Augustus_model.g38938.t1
Valid prediction for Augustus_model.g38942.t1
Valid prediction for snap_scaffold_28-snap.1222-T1
Couldn't classify 160955, 161017
Sorry, prediction pasa_asmbl_37581.p1 fails validation.
(CTG)	 TG	160955-161017	GT	AGG
(ACG)	 AG	161249-161344	GT	AGG
(TTC)	 AG	162348-162464	GT	CGG
(GTG)	 AG	163626-163676	GT	ATG
(CGT)	 AG	164018-164134	GT	AGG
(CTG)	 AG	164558-164896	GA	GAG
-recovered pasa_asmbl_37581.p1, terminal, 164558, 164896
-recovered pasa_asmbl_37581.p1, internal, 161249, 161344
-recovered pasa_asmbl_37581.p1, internal, 162348, 162464
-recovered pasa_asmbl_37581.p1, internal, 163626, 163676
-recovered pasa_asmbl_37581.p1, internal, 164018, 164134
Valid prediction for CodingQuarry_transcript_43660-T1
Valid prediction for GlimmerHMM_glimmerT_58792-T1
Valid prediction for snap_scaffold_28-snap.1243-T1
Valid prediction for CodingQuarry_transcript_43669-T1
Valid prediction for GlimmerHMM_glimmerT_58791-T1
Valid prediction for HiQ_model.g38949.t1
Valid prediction for GlimmerHMM_glimmerT_58801-T1
Valid prediction for Augustus_model.g38968.t1
Valid prediction for snap_scaffold_28-snap.1227-T1
Valid prediction for snap_scaffold_28-snap.1209-T1
Valid prediction for pasa_asmbl_37576.p1
Valid prediction for pasa_asmbl_37588.p1
Valid prediction for Augustus_model.g38940.t1
Valid prediction for Augustus_model.g38970.t1
Valid prediction for GlimmerHMM_glimmerT_58790-T1
Valid prediction for snap_scaffold_28-snap.1204-T1
Valid prediction for snap_scaffold_28-snap.1235-T1
Valid prediction for GlimmerHMM_glimmerT_58775-T1
Valid prediction for snap_scaffold_28-snap.1210-T1
Valid prediction for snap_scaffold_28-snap.1238-T1
Valid prediction for snap_scaffold_28-snap.1231-T1
Valid prediction for snap_scaffold_28-snap.1217-T1
Valid prediction for snap_scaffold_28-snap.1237-T1
Valid prediction for snap_scaffold_28-snap.1229-T1
Valid prediction for CodingQuarry_transcript_43670-T1
Valid prediction for snap_scaffold_28-snap.1241-T1
Valid prediction for GlimmerHMM_glimmerT_58773-T1
Valid prediction for snap_scaffold_28-snap.1200-T1
Valid prediction for snap_scaffold_28-snap.1239-T1
Valid prediction for snap_scaffold_28-snap.1202-T1
Valid prediction for Augustus_model.g38963.t1
Valid prediction for GlimmerHMM_glimmerT_58783-T1
Valid prediction for GlimmerHMM_glimmerT_58779-T1
Valid prediction for Augustus_model.g38962.t1
Valid prediction for snap_scaffold_28-snap.1198-T1
Valid prediction for snap_scaffold_28-snap.1219-T1
Valid prediction for Augustus_model.g38956.t1
Valid prediction for GlimmerHMM_glimmerT_58782-T1
Valid prediction for snap_scaffold_28-snap.1197-T1
Valid prediction for snap_scaffold_28-snap.1226-T1
Valid prediction for GlimmerHMM_glimmerT_58798-T1
Valid prediction for GlimmerHMM_glimmerT_58771-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 pasa_asmbl_38290.p2
Valid prediction for GlimmerHMM_glimmerT_58777-T1
Valid prediction for Augustus_model.g38957.t1
Valid prediction for CodingQuarry_transcript_43672-T1
Valid prediction for snap_scaffold_28-snap.1196-T1
Valid prediction for pasa_asmbl_38256.p1
Valid prediction for GlimmerHMM_glimmerT_58770-T1
Valid prediction for CodingQuarry_transcript_43656-T1
Couldn't classify 144228, 144671
Sorry, prediction pasa_asmbl_37580.p1 fails validation.
(GCT)	 TG	144228-144671	GG	TGG
Valid prediction for pasa_asmbl_38271.p1
Valid prediction for HiQ_model.g38944.t1
Valid prediction for HiQ_model.g38952.t1
Valid prediction for snap_scaffold_28-snap.1194-T1
Valid prediction for HiQ_model.g38946.t1
Valid prediction for Augustus_model.g38954.t1
Valid prediction for GlimmerHMM_glimmerT_58776-T1
Valid prediction for GlimmerHMM_glimmerT_58794-T1
Valid prediction for snap_scaffold_28-snap.1240-T1
Valid prediction for snap_scaffold_28-snap.1221-T1
Valid prediction for CodingQuarry_transcript_43664-T1
Valid prediction for Augustus_model.g38966.t1
Valid prediction for pasa_asmbl_38286.p1
Valid prediction for pasa_asmbl_38587.p1
Valid prediction for CodingQuarry_transcript_43662-T1
Valid prediction for GlimmerHMM_glimmerT_58784-T1
Valid prediction for snap_scaffold_28-snap.1201-T1
Valid prediction for snap_scaffold_28-snap.1225-T1
Valid prediction for snap_scaffold_28-snap.1211-T1
Valid prediction for snap_scaffold_28-snap.1208-T1
Valid prediction for pasa_asmbl_38260.p1
Valid prediction for HiQ_model.g38969.t1
Valid prediction for CodingQuarry_transcript_43671-T1
Valid prediction for Augustus_model.g38937.t1
Valid prediction for snap_scaffold_28-snap.1242-T1
Valid prediction for CodingQuarry_transcript_43657-T1
Valid prediction for snap_scaffold_28-snap.1212-T1
Valid prediction for snap_scaffold_28-snap.1207-T1
Valid prediction for GlimmerHMM_glimmerT_58778-T1
Valid prediction for snap_scaffold_28-snap.1206-T1
Valid prediction for GlimmerHMM_glimmerT_58797-T1
Valid prediction for snap_scaffold_28-snap.1228-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1195-T1
Valid prediction for pasa_asmbl_38277.p1
Valid prediction for Augustus_model.g38953.t1
Valid prediction for HiQ_model.g38965.t1
Valid prediction for snap_scaffold_28-snap.1218-T1
Valid prediction for snap_scaffold_28-snap.1224-T1
Valid prediction for GlimmerHMM_glimmerT_58781-T1
Valid prediction for snap_scaffold_28-snap.1203-T1
Valid prediction for GlimmerHMM_glimmerT_58780-T1
Valid prediction for snap_scaffold_28-snap.1213-T1
Valid prediction for Augustus_model.g38959.t1
Valid prediction for CodingQuarry_transcript_43666-T1
Valid prediction for snap_scaffold_28-snap.1216-T1
Couldn't classify 208177, 208335
Sorry, prediction pasa_asmbl_38253.p1 fails validation.
(AGC)	 TC	208177-208335	GT	GGG
(GTG)	 AG	208558-208668	GT	AGG
(GAA)	 AG	208758-208838	GT	AGG
(ACC)	 AG	209474-209521	CA	AGC
-recovered pasa_asmbl_38253.p1, terminal, 209474, 209521
-recovered pasa_asmbl_38253.p1, internal, 208558, 208668
-recovered pasa_asmbl_38253.p1, internal, 208758, 208838
Valid prediction for snap_scaffold_28-snap.1214-T1
Couldn't classify 177756, 177921
Sorry, prediction pasa_asmbl_38270.p1 fails validation.
(GTC)	 AG	177756-177921	GT	AGG
(ATA)	 AG	178355-178401	GT	AGG
(CTG)	 AG	178856-178882	GT	TGG
(CAG)	 AG	178971-179042	GT	AAG
add_exon() Sorry, pasa_asmbl_38270.p1 177756-177921-terminal-3 is invalid.
-recovered pasa_asmbl_38270.p1, terminal, 177756, 177921
-recovered pasa_asmbl_38270.p1, terminal, 178971, 179042
-recovered pasa_asmbl_38270.p1, internal, 177756, 177921
-recovered pasa_asmbl_38270.p1, internal, 178355, 178401
-recovered pasa_asmbl_38270.p1, internal, 178856, 178882
-recovered pasa_asmbl_38270.p1, internal, 178971, 179042
Valid prediction for pasa_asmbl_38291.p1
Valid prediction for snap_scaffold_28-snap.1236-T1
Valid prediction for Augustus_model.g38948.t1
Valid prediction for HiQ_model.g38951.t1
Valid prediction for GlimmerHMM_glimmerT_58796-T1
Valid prediction for snap_scaffold_28-snap.1234-T1
Valid prediction for CodingQuarry_transcript_43667-T1
Valid prediction for Augustus_model.g38945.t1
Valid prediction for snap_scaffold_28-snap.1220-T1
Valid prediction for GlimmerHMM_glimmerT_58772-T1
Valid prediction for snap_scaffold_28-snap.1205-T1
Couldn't classify 53459, 53651
Sorry, prediction pasa_asmbl_38288.p1 fails validation.
(ACG)	 TG	53459-53651	GT	AGG
(GCC)	 AG	54125-54232	GT	TAG
(GTT)	 AG	54600-54730	GT	CTG
(CCT)	 AG	55037-55195	GT	AGG
(ATC)	 AG	55467-55651	GT	AGG
(GGC)	 AG	55792-55885	GT	AGG
(GGG)	 AG	56092-56211	CA	GAC
-recovered pasa_asmbl_38288.p1, terminal, 56092, 56211
-recovered pasa_asmbl_38288.p1, internal, 54125, 54232
-recovered pasa_asmbl_38288.p1, internal, 54600, 54730
-recovered pasa_asmbl_38288.p1, internal, 55037, 55195
-recovered pasa_asmbl_38288.p1, internal, 55467, 55651
-recovered pasa_asmbl_38288.p1, internal, 55792, 55885
Valid prediction for snap_scaffold_28-snap.1215-T1
Valid prediction for snap_scaffold_28-snap.1199-T1
Valid prediction for CodingQuarry_transcript_43665-T1
Valid prediction for snap_scaffold_28-snap.1232-T1
Valid prediction for GlimmerHMM_glimmerT_58793-T1
Valid prediction for CodingQuarry_transcript_43663-T1
Valid prediction for CodingQuarry_transcript_43658-T1
Valid prediction for GlimmerHMM_glimmerT_58787-T1
Valid prediction for pasa_asmbl_38276.p1
Valid prediction for Augustus_model.g38961.t1
Valid prediction for CodingQuarry_transcript_43668-T1
Valid prediction for HiQ_model.g38941.t1
Valid prediction for GlimmerHMM_glimmerT_58795-T1
Valid prediction for HiQ_model.g38947.t1
Valid prediction for Augustus_model.g38960.t1
Valid prediction for CodingQuarry_transcript_43655-T1
Couldn't classify 202888, 203019
Couldn't classify 204119, 204265
Sorry, prediction pasa_asmbl_38551.p1 fails validation.
(GCC)	 AG	202888-203019	GT	AGG
(TTT)	 AG	203851-203946	GT	AGG
(GAG)	 AG	204119-204265	AG	ACA
-recovered pasa_asmbl_38551.p1, internal, 202888, 203019
-recovered pasa_asmbl_38551.p1, internal, 203851, 203946
Valid prediction for snap_scaffold_28-snap.1233-T1
Valid prediction for GlimmerHMM_glimmerT_58786-T1
Valid prediction for GlimmerHMM_glimmerT_58800-T1
Valid prediction for GlimmerHMM_glimmerT_58774-T1
Valid prediction for snap_scaffold_28-snap.1223-T1
Valid prediction for HiQ_model.g38964.t1
Valid prediction for Augustus_model.g38939.t1
Valid prediction for GlimmerHMM_glimmerT_58789-T1
Couldn't classify 155409, 155468
Sorry, prediction pasa_asmbl_38283.p1 fails validation.
(CAA)	 CA	155409-155468	GT	GGG
(GTG)	 AG	155539-155649	GT	AGG
(CAG)	 AG	155831-155910	GT	AGG
(ACT)	 AG	156186-156261	GT	AGG
(AAT)	 AG	156548-156607	AA	AAA
-recovered pasa_asmbl_38283.p1, terminal, 156548, 156607
-recovered pasa_asmbl_38283.p1, internal, 155539, 155649
-recovered pasa_asmbl_38283.p1, internal, 155831, 155910
-recovered pasa_asmbl_38283.p1, internal, 156186, 156261
Valid prediction for Augustus_model.g38958.t1
Couldn't classify 243590, 243689
Sorry, prediction pasa_asmbl_38243.p1 fails validation.
(ATG)	 CA	239779-239835	GT	AGG
(GAC)	 AG	241600-241680	GT	CGG
(ACC)	 AG	242169-242279	GT	AGG
(GAC)	 AG	242734-242845	GT	AGG
(GTC)	 AG	242966-243094	GT	GTG
(TCC)	 AG	243334-243493	GT	AGG
(GAG)	 AG	243590-243689	TG	CTT
-recovered pasa_asmbl_38243.p1, initial, 239779, 239835
-recovered pasa_asmbl_38243.p1, internal, 241600, 241680
-recovered pasa_asmbl_38243.p1, internal, 242169, 242279
-recovered pasa_asmbl_38243.p1, internal, 242734, 242845
-recovered pasa_asmbl_38243.p1, internal, 242966, 243094
-recovered pasa_asmbl_38243.p1, internal, 243334, 243493
Valid prediction for CodingQuarry_transcript_43661-T1
Valid prediction for Augustus_model.g38943.t1
Valid prediction for GlimmerHMM_glimmerT_58788-T1
Valid prediction for GlimmerHMM_glimmerT_58785-T1
Valid prediction for pasa_asmbl_38280.p1
Couldn't classify 119905, 120207
Sorry, prediction pasa_asmbl_38284.p1 fails validation.
(TTG)	 CC	119905-120207	GC	AAG
Valid prediction for HiQ_model.g38950.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31276, rend_intergenic: 26278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45424, rend_intergenic: 41494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47963, rend_intergenic: 45747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122683, rend_intergenic: 120616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124044, rend_intergenic: 122750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207867, rend_intergenic: 202252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231918, rend_intergenic: 228490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238961, rend_intergenic: 232563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 250340
-exon list size: 511


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
1.9    
2.1    
2.3    
2.5    
2.7    
2.9    
3.1    
3.3    
3.5    
3.7    
3.9    
4.1    
4.3    
4.5    
4.7    
4.9    
5.1    
5.3    
5.5    
5.7    
5.8    
6.0    
6.2    
6.4    
6.6    
6.8    
7.0    
7.2    
7.4    
7.6    
7.8    
8.0    
8.2    
8.4    
8.6    
8.8    
9.0    
9.2    
9.4    
9.6    
9.7    
9.9    
10.1    
10.3    
10.5    
10.7    
10.9    
11.1    
11.3    
11.5    
11.7    
11.9    
12.1    
12.3    
12.5    
12.7    
12.9    
13.1    
13.3    
13.5    
13.6    
13.8    
14.0    
14.2    
14.4    
14.6    
14.8    
15.0    
15.2    
15.4    
15.6    
15.8    
16.0    
16.2    
16.4    
16.6    
16.8    
17.0    
17.2    
17.3    
17.5    
17.7    
17.9    
18.1    
18.3    
18.5    
18.7    
18.9    
19.1    
19.3    
19.5    
19.7    
19.9    
20.1    
20.3    
20.5    
20.7    
20.9    
21.1    
21.2    
21.4    
21.6    
21.8    
22.0    
22.2    
22.4    
22.6    
22.8    
23.0    
23.2    
23.4    
23.6    
23.8    
24.0    
24.2    
24.4    
24.6    
24.8    
25.0    
25.1    
25.3    
25.5    
25.7    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.1    
27.3    
27.5    
27.7    
27.9    
28.1    
28.3    
28.5    
28.7    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.4    
31.6    
31.8    
32.0    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.3    
33.5    
33.7    
33.9    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.5    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.2    
40.4    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.7    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.2    
44.4    
44.6    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.2    
46.4    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.0    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.0    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.6    
53.8    
54.0    
54.2    
54.4    
54.6    
54.8    
55.0    
55.2    
55.4    
55.6    
55.8    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.3    
58.5    
58.7    
58.9    
59.1    
59.3    
59.5    
59.6    
59.8    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.8    
62.0    
62.2    
62.4    
62.6    
62.8    
63.0    
63.2    
63.4    
63.5    
63.7    
63.9    
64.1    
64.3    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.1    
66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.9    
73.1    
73.3    
73.5    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.7    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 31276, rend_intergenic: 26278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45424, rend_intergenic: 41494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47963, rend_intergenic: 45747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122683, rend_intergenic: 120616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124044, rend_intergenic: 122750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207867, rend_intergenic: 202252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231918, rend_intergenic: 228490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238961, rend_intergenic: 232563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support