-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_7113420-7350031

-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.g8000.t1
Valid prediction for snap_scaffold_5-snap.1416-T1
Valid prediction for snap_scaffold_5-snap.1444-T1
Valid prediction for snap_scaffold_5-snap.1410-T1
Valid prediction for GlimmerHMM_glimmerT_12152-T1
Valid prediction for GlimmerHMM_glimmerT_12155-T1
Valid prediction for Augustus_model.g8001.t1
Valid prediction for GlimmerHMM_glimmerT_12183-T1
Valid prediction for GlimmerHMM_glimmerT_12175-T1
Valid prediction for snap_scaffold_5-snap.1434-T1
Valid prediction for snap_scaffold_5-snap.1445-T1
Valid prediction for GlimmerHMM_glimmerT_12171-T1
Valid prediction for Augustus_model.g7986.t1
Valid prediction for snap_scaffold_5-snap.1407-T1
Valid prediction for snap_scaffold_5-snap.1443-T1
Valid prediction for GlimmerHMM_glimmerT_12173-T1
Valid prediction for snap_scaffold_5-snap.1409-T1
Valid prediction for GlimmerHMM_glimmerT_12158-T1
Valid prediction for snap_scaffold_5-snap.1418-T1
Valid prediction for CodingQuarry_transcript_52115-T1
Valid prediction for GlimmerHMM_glimmerT_12170-T1
Valid prediction for GlimmerHMM_glimmerT_12181-T1
Valid prediction for GlimmerHMM_glimmerT_12165-T1
Valid prediction for GlimmerHMM_glimmerT_12182-T1
Valid prediction for snap_scaffold_5-snap.1412-T1
Valid prediction for Augustus_model.g7999.t1
Valid prediction for GlimmerHMM_glimmerT_12179-T1
Valid prediction for GlimmerHMM_glimmerT_12164-T1
Valid prediction for Augustus_model.g7996.t1
Valid prediction for Augustus_model.g7994.t1
Valid prediction for snap_scaffold_5-snap.1429-T1
Valid prediction for snap_scaffold_5-snap.1436-T1
Valid prediction for snap_scaffold_5-snap.1423-T1
Valid prediction for snap_scaffold_5-snap.1425-T1
Valid prediction for HiQ_model.g7998.t1
Couldn't classify 203066, 203389
Sorry, prediction pasa_asmbl_45490.p1 fails validation.
(GAG)	 GG	203066-203389	GT	GGG
(GAT)	 AG	204402-204531	GT	AAG
(GTG)	 AG	204721-204784	GT	TAG
(TGA)	 AG	204932-205085	GT	CAG
(CTG)	 AG	205188-205326	GT	TGG
(GTA)	 AG	206658-206932	GG	GAG
-recovered pasa_asmbl_45490.p1, terminal, 206658, 206932
-recovered pasa_asmbl_45490.p1, internal, 204402, 204531
-recovered pasa_asmbl_45490.p1, internal, 204721, 204784
-recovered pasa_asmbl_45490.p1, internal, 204932, 205085
-recovered pasa_asmbl_45490.p1, internal, 205188, 205326
Couldn't classify 200558, 200629
Couldn't classify 202746, 202855
Sorry, prediction pasa_asmbl_45484.p1 fails validation.
(ACC)	 CC	200558-200629	GT	AGG
(AGC)	 AG	201953-202120	GT	AGG
(TTC)	 AG	202270-202353	GT	GGG
(CAG)	 AG	202444-202627	GC	AGG
(GTC)	 AG	202746-202855	GG	GGG
-recovered pasa_asmbl_45484.p1, internal, 201953, 202120
-recovered pasa_asmbl_45484.p1, internal, 202270, 202353
-recovered pasa_asmbl_45484.p1, internal, 202444, 202627
Valid prediction for Augustus_model.g7997.t1
Valid prediction for snap_scaffold_5-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_12176-T1
Valid prediction for snap_scaffold_5-snap.1450-T1
Valid prediction for snap_scaffold_5-snap.1440-T1
Valid prediction for GlimmerHMM_glimmerT_12180-T1
Valid prediction for snap_scaffold_5-snap.1448-T1
Valid prediction for GlimmerHMM_glimmerT_12157-T1
Valid prediction for Augustus_model.g7989.t1
Valid prediction for GlimmerHMM_glimmerT_12162-T1
Valid prediction for GlimmerHMM_glimmerT_12154-T1
Valid prediction for snap_scaffold_5-snap.1424-T1
Valid prediction for snap_scaffold_5-snap.1439-T1
Valid prediction for Augustus_model.g7988.t1
Valid prediction for snap_scaffold_5-snap.1417-T1
Valid prediction for Augustus_model.g7993.t1
Valid prediction for snap_scaffold_5-snap.1414-T1
Valid prediction for snap_scaffold_5-snap.1432-T1
Valid prediction for GlimmerHMM_glimmerT_12153-T1
Valid prediction for snap_scaffold_5-snap.1428-T1
Valid prediction for GlimmerHMM_glimmerT_12156-T1
Couldn't classify 148313, 148471
Couldn't classify 149274, 149456
Sorry, prediction pasa_asmbl_46430.p1 fails validation.
(AAC)	 GG	148313-148471	GT	AGG
(GTG)	 AG	149274-149456	TC	AGT
Valid prediction for HiQ_model.g8002.t1
Valid prediction for Augustus_model.g8005.t1
Valid prediction for Augustus_model.g8006.t1
Valid prediction for snap_scaffold_5-snap.1405-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_5-snap.1437-T1
Valid prediction for Augustus_model.g8003.t1
Valid prediction for snap_scaffold_5-snap.1441-T1
Valid prediction for GlimmerHMM_glimmerT_12168-T1
Valid prediction for GlimmerHMM_glimmerT_12160-T1
Valid prediction for Augustus_model.g7991.t1
Valid prediction for snap_scaffold_5-snap.1413-T1
Couldn't classify 81381, 81489
Couldn't classify 82146, 82202
Couldn't classify 82366, 82520
Sorry, prediction pasa_asmbl_44168.p1 fails validation.
(CAG)	 TT	81381-81489	GT	TGG
(ATG)	 AG	81590-81686	GT	ACG
(GAA)	 AG	81887-82032	GT	TGG
(ATG)	 AG	82146-82202	AT	CTA
(CTG)	 AC	82366-82520	GT	AGG
(GAG)	 AG	82609-82755	GT	AGG
(GTG)	 AG	82864-82935	GT	AGG
(TTC)	 AG	83542-83550	AG	GAA
add_exon() Sorry, pasa_asmbl_44168.p1 81590-81686-initial-1 is invalid.
-recovered pasa_asmbl_44168.p1, initial, 81590, 81686
-recovered pasa_asmbl_44168.p1, terminal, 83542, 83550
-recovered pasa_asmbl_44168.p1, internal, 81590, 81686
-recovered pasa_asmbl_44168.p1, internal, 81887, 82032
-recovered pasa_asmbl_44168.p1, internal, 82609, 82755
-recovered pasa_asmbl_44168.p1, internal, 82864, 82935
Valid prediction for Augustus_model.g7990.t1
Valid prediction for snap_scaffold_5-snap.1446-T1
Valid prediction for snap_scaffold_5-snap.1447-T1
Valid prediction for snap_scaffold_5-snap.1430-T1
Valid prediction for GlimmerHMM_glimmerT_12169-T1
Valid prediction for snap_scaffold_5-snap.1420-T1
Valid prediction for GlimmerHMM_glimmerT_12172-T1
Valid prediction for Augustus_model.g7987.t1
Valid prediction for snap_scaffold_5-snap.1402-T1
Valid prediction for snap_scaffold_5-snap.1435-T1
Valid prediction for snap_scaffold_5-snap.1449-T1
Valid prediction for snap_scaffold_5-snap.1411-T1
Valid prediction for snap_scaffold_5-snap.1415-T1
Valid prediction for GlimmerHMM_glimmerT_12177-T1
Valid prediction for snap_scaffold_5-snap.1427-T1
Valid prediction for snap_scaffold_5-snap.1431-T1
Valid prediction for GlimmerHMM_glimmerT_12167-T1
Valid prediction for snap_scaffold_5-snap.1442-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.1406-T1
Valid prediction for snap_scaffold_5-snap.1452-T1
Valid prediction for GlimmerHMM_glimmerT_12159-T1
Valid prediction for snap_scaffold_5-snap.1433-T1
Valid prediction for snap_scaffold_5-snap.1421-T1
Valid prediction for snap_scaffold_5-snap.1408-T1
Valid prediction for pasa_asmbl_44166.p1
Valid prediction for snap_scaffold_5-snap.1403-T1
Valid prediction for Augustus_model.g7985.t1
Valid prediction for snap_scaffold_5-snap.1438-T1
Valid prediction for snap_scaffold_5-snap.1426-T1
Valid prediction for GlimmerHMM_glimmerT_12163-T1
Valid prediction for GlimmerHMM_glimmerT_12174-T1
Valid prediction for CodingQuarry_transcript_52114-T1
Valid prediction for snap_scaffold_5-snap.1422-T1
Valid prediction for GlimmerHMM_glimmerT_12178-T1
Valid prediction for Augustus_model.g8004.t1
Valid prediction for GlimmerHMM_glimmerT_12166-T1
Valid prediction for Augustus_model.g7992.t1
Valid prediction for GlimmerHMM_glimmerT_12161-T1
Valid prediction for snap_scaffold_5-snap.1451-T1
Valid prediction for Augustus_model.g7995.t1
Valid prediction for snap_scaffold_5-snap.1419-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24192, rend_intergenic: 22421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28977, rend_intergenic: 28590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34932, rend_intergenic: 30454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45563, rend_intergenic: 44406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117721, rend_intergenic: 112115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121329, rend_intergenic: 119182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125451, rend_intergenic: 121865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154001, rend_intergenic: 141950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162050, rend_intergenic: 157424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168236, rend_intergenic: 163394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178603, rend_intergenic: 169413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191457, rend_intergenic: 181581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201695, rend_intergenic: 192206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206932, rend_intergenic: 202411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212144, rend_intergenic: 210463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213028, rend_intergenic: 213020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216333, rend_intergenic: 213182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 236612
-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 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 24192, rend_intergenic: 22421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28977, rend_intergenic: 28590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34932, rend_intergenic: 30454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45563, rend_intergenic: 44406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117721, rend_intergenic: 112115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121329, rend_intergenic: 119182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125451, rend_intergenic: 121865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154001, rend_intergenic: 141950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162050, rend_intergenic: 157424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168236, rend_intergenic: 163394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178603, rend_intergenic: 169413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191457, rend_intergenic: 181581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201695, rend_intergenic: 192206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206932, rend_intergenic: 202411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212144, rend_intergenic: 210463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213028, rend_intergenic: 213020  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216333, rend_intergenic: 213182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support