-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_26/scaffold_26_5300694-5499947

-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_55670-T1
Valid prediction for snap_scaffold_26-snap.1189-T1
Valid prediction for Augustus_model.g36875.t1
Valid prediction for snap_scaffold_26-snap.1200-T1
Valid prediction for GlimmerHMM_glimmerT_55685-T1
Valid prediction for Augustus_model.g36900.t1
Valid prediction for Augustus_model.g36893.t1
Couldn't classify 16713, 16758
Sorry, prediction pasa_asmbl_34979.p1 fails validation.
(ATG)	 AT	13269-13447	GT	TCG
(GGC)	 AG	15170-15269	GT	AGG
(GTG)	 AG	16227-16334	GT	TGG
(GAG)	 AG	16471-16577	GT	GGG
(GCA)	 AG	16713-16758	CC	GGC
-recovered pasa_asmbl_34979.p1, initial, 13269, 13447
-recovered pasa_asmbl_34979.p1, internal, 15170, 15269
-recovered pasa_asmbl_34979.p1, internal, 16227, 16334
-recovered pasa_asmbl_34979.p1, internal, 16471, 16577
Valid prediction for snap_scaffold_26-snap.1193-T1
Valid prediction for Augustus_model.g36881.t1
Valid prediction for Augustus_model.g36891.t1
Valid prediction for GlimmerHMM_glimmerT_55690-T1
Couldn't classify 180270, 180381
Sorry, prediction pasa_asmbl_34996.p1 fails validation.
(TGC)	 CA	180270-180381	GT	GGG
(GTT)	 AG	180860-180940	GT	AGG
(AAT)	 AG	181609-181665	GT	AGG
(CCA)	 AG	181935-181997	GT	AGG
(GCT)	 AG	182103-182257	GT	GGG
(GGT)	 AG	182529-182570	GA	GAG
-recovered pasa_asmbl_34996.p1, terminal, 182529, 182570
-recovered pasa_asmbl_34996.p1, internal, 180860, 180940
-recovered pasa_asmbl_34996.p1, internal, 181609, 181665
-recovered pasa_asmbl_34996.p1, internal, 181935, 181997
-recovered pasa_asmbl_34996.p1, internal, 182103, 182257
Valid prediction for GlimmerHMM_glimmerT_55693-T1
Couldn't classify 155646, 155787
Sorry, prediction pasa_asmbl_34991.p1 fails validation.
(TGT)	 CA	155646-155787	GT	AGG
(GTG)	 AG	156011-156041	GT	CGG
(CGT)	 AG	156162-156260	GT	AGG
(TTG)	 AG	156372-156436	GT	AGG
(AGC)	 AG	156529-156622	GT	AGG
(TGA)	 AG	156755-157175	AA	AAA
add_exon() Sorry, pasa_asmbl_34991.p1 156162-156260-terminal-1 is invalid.
-recovered pasa_asmbl_34991.p1, terminal, 156162, 156260
-recovered pasa_asmbl_34991.p1, terminal, 156755, 157175
-recovered pasa_asmbl_34991.p1, internal, 156011, 156041
-recovered pasa_asmbl_34991.p1, internal, 156162, 156260
-recovered pasa_asmbl_34991.p1, internal, 156372, 156436
-recovered pasa_asmbl_34991.p1, internal, 156529, 156622
Valid prediction for snap_scaffold_26-snap.1208-T1
Couldn't classify 47307, 48554
Sorry, prediction pasa_asmbl_34981.p1 fails validation.
(TGT)	 TG	47307-48554	GG	GAG
Valid prediction for CodingQuarry_transcript_40348-T1
Valid prediction for HiQ_model.g36889.t1
Valid prediction for GlimmerHMM_glimmerT_55698-T1
Valid prediction for snap_scaffold_26-snap.1184-T1
Valid prediction for Augustus_model.g36877.t1
Valid prediction for GlimmerHMM_glimmerT_55679-T1
Valid prediction for GlimmerHMM_glimmerT_55681-T1
Valid prediction for snap_scaffold_26-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_55677-T1
Valid prediction for Augustus_model.g36895.t1
Valid prediction for CodingQuarry_transcript_40345-T1
Valid prediction for snap_scaffold_26-snap.1186-T1
Valid prediction for snap_scaffold_26-snap.1198-T1
Valid prediction for GlimmerHMM_glimmerT_55669-T1
Valid prediction for pasa_asmbl_35000.p1
Valid prediction for GlimmerHMM_glimmerT_55695-T1
Valid prediction for snap_scaffold_26-snap.1207-T1
Valid prediction for HiQ_model.g36896.t1
Valid prediction for Augustus_model.g36887.t1
Valid prediction for snap_scaffold_26-snap.1209-T1
Valid prediction for snap_scaffold_26-snap.1179-T1
Valid prediction for GlimmerHMM_glimmerT_55691-T1
Valid prediction for Augustus_model.g36897.t1
Valid prediction for Augustus_model.g36905.t1
Valid prediction for pasa_asmbl_35329.p1
Valid prediction for snap_scaffold_26-snap.1219-T1
Valid prediction for GlimmerHMM_glimmerT_55687-T1
Valid prediction for Augustus_model.g36879.t1
Couldn't classify 11310, 11390
Sorry, prediction pasa_asmbl_34978.p1 fails validation.
(CAC)	 CC	11310-11390	GT	AGG
(GGT)	 AG	11527-11628	GT	AGG
(GTG)	 AG	11730-11801	GT	AGG
(GGA)	 AG	11931-12032	GG	AAG
-recovered pasa_asmbl_34978.p1, terminal, 11931, 12032
-recovered pasa_asmbl_34978.p1, internal, 11527, 11628
-recovered pasa_asmbl_34978.p1, internal, 11730, 11801
Valid prediction for GlimmerHMM_glimmerT_55668-T1
Valid prediction for GlimmerHMM_glimmerT_55684-T1
Valid prediction for GlimmerHMM_glimmerT_55696-T1
Valid prediction for GlimmerHMM_glimmerT_55699-T1
Couldn't classify 61904, 61987
Sorry, prediction pasa_asmbl_34983.p1 fails validation.
(GAG)	 AA	61904-61987	GT	AGG
(AAA)	 AG	62079-62168	GT	CGG
(TAT)	 AG	62282-62385	GT	CTG
(GCC)	 AG	62469-62546	GT	TGG
(GTA)	 AG	63093-63255	GC	AGG
(GAG)	 AG	63362-63433	GT	CAG
(ATC)	 AG	63529-63651	GT	AGG
(GAG)	 AG	63790-63906	GT	AGG
(GGT)	 AG	64042-64152	GG	GAG
-recovered pasa_asmbl_34983.p1, terminal, 64042, 64152
-recovered pasa_asmbl_34983.p1, internal, 62079, 62168
-recovered pasa_asmbl_34983.p1, internal, 62282, 62385
-recovered pasa_asmbl_34983.p1, internal, 62469, 62546
-recovered pasa_asmbl_34983.p1, internal, 63093, 63255
-recovered pasa_asmbl_34983.p1, internal, 63362, 63433
-recovered pasa_asmbl_34983.p1, internal, 63529, 63651
-recovered pasa_asmbl_34983.p1, internal, 63790, 63906
Valid prediction for HiQ_model.g36883.t1
Valid prediction for GlimmerHMM_glimmerT_55674-T1
Valid prediction for snap_scaffold_26-snap.1178-T1
Valid prediction for CodingQuarry_transcript_40349-T1
Valid prediction for snap_scaffold_26-snap.1221-T1
Valid prediction for snap_scaffold_26-snap.1202-T1
Valid prediction for GlimmerHMM_glimmerT_55665-T1
Valid prediction for GlimmerHMM_glimmerT_55692-T1
Valid prediction for snap_scaffold_26-snap.1183-T1
Couldn't classify 8914, 9048
Couldn't classify 10927, 11046
Sorry, prediction pasa_asmbl_34977.p1 fails validation.
(TTT)	 AG	8914-9048	GT	AGG
(ATT)	 AG	9136-9210	GT	AGG
(GTG)	 AG	9333-9483	GT	AGG
(GTC)	 AG	9639-9835	GT	AGG
(GGC)	 AG	9954-10068	GT	AGG
(CAT)	 AG	10161-10468	GT	AGG
(GTG)	 AG	10588-10827	GT	CGG
(ATG)	 AG	10927-11046	CG	CCC
-recovered pasa_asmbl_34977.p1, internal, 8914, 9048
-recovered pasa_asmbl_34977.p1, internal, 9136, 9210
-recovered pasa_asmbl_34977.p1, internal, 9333, 9483
-recovered pasa_asmbl_34977.p1, internal, 9639, 9835
-recovered pasa_asmbl_34977.p1, internal, 9954, 10068
-recovered pasa_asmbl_34977.p1, internal, 10161, 10468
-recovered pasa_asmbl_34977.p1, internal, 10588, 10827
Valid prediction for HiQ_model.g36902.t1
Valid prediction for CodingQuarry_transcript_40351-T1
Valid prediction for GlimmerHMM_glimmerT_55697-T1
Valid prediction for snap_scaffold_26-snap.1210-T1
Valid prediction for snap_scaffold_26-snap.1216-T1
Valid prediction for snap_scaffold_26-snap.1203-T1
Valid prediction for pasa_asmbl_34990.p1
Valid prediction for Augustus_model.g36894.t1
Valid prediction for Augustus_model.g36899.t1
Valid prediction for snap_scaffold_26-snap.1212-T1
Valid prediction for snap_scaffold_26-snap.1223-T1
Valid prediction for GlimmerHMM_glimmerT_55667-T1
Valid prediction for CodingQuarry_transcript_40350-T1
Valid prediction for GlimmerHMM_glimmerT_55683-T1
Valid prediction for GlimmerHMM_glimmerT_55700-T1
Valid prediction for Augustus_model.g36907.t1
Valid prediction for snap_scaffold_26-snap.1180-T1
Valid prediction for snap_scaffold_26-snap.1195-T1
Valid prediction for HiQ_model.g36903.t1
Valid prediction for snap_scaffold_26-snap.1211-T1
Valid prediction for GlimmerHMM_glimmerT_55676-T1
Valid prediction for Augustus_model.g36876.t1
Valid prediction for snap_scaffold_26-snap.1204-T1
Valid prediction for CodingQuarry_transcript_40343-T1
Valid prediction for snap_scaffold_26-snap.1190-T1
Valid prediction for snap_scaffold_26-snap.1214-T1
Valid prediction for pasa_asmbl_34999.p2
Valid prediction for Augustus_model.g36901.t1
Valid prediction for CodingQuarry_transcript_40346-T1
Valid prediction for snap_scaffold_26-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_55666-T1
Valid prediction for pasa_asmbl_34986.p1

-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 Augustus_model.g36874.t1
Valid prediction for snap_scaffold_26-snap.1222-T1
Valid prediction for snap_scaffold_26-snap.1194-T1
Valid prediction for GlimmerHMM_glimmerT_55688-T1
Valid prediction for snap_scaffold_26-snap.1217-T1
Valid prediction for snap_scaffold_26-snap.1205-T1
Valid prediction for snap_scaffold_26-snap.1213-T1
Valid prediction for snap_scaffold_26-snap.1185-T1
Valid prediction for Augustus_model.g36898.t1
Valid prediction for snap_scaffold_26-snap.1181-T1
Valid prediction for GlimmerHMM_glimmerT_55678-T1
Valid prediction for snap_scaffold_26-snap.1182-T1
Valid prediction for GlimmerHMM_glimmerT_55689-T1
Valid prediction for snap_scaffold_26-snap.1187-T1
Valid prediction for HiQ_model.g36886.t1
Valid prediction for snap_scaffold_26-snap.1177-T1
Valid prediction for Augustus_model.g36882.t1
Valid prediction for Augustus_model.g36890.t1
Valid prediction for GlimmerHMM_glimmerT_55673-T1
Valid prediction for snap_scaffold_26-snap.1215-T1
Valid prediction for Augustus_model.g36878.t1
Valid prediction for snap_scaffold_26-snap.1196-T1
Couldn't classify 1648, 1741
Sorry, prediction pasa_asmbl_35869.p1 fails validation.
(TCG)	 TC	1648-1741	GT	AGG
(AAA)	 AG	1897-1938	GT	AGG
(GTC)	 AG	2113-2252	GT	TGG
(CAC)	 AG	2427-2489	CA	GAC
-recovered pasa_asmbl_35869.p1, terminal, 2427, 2489
-recovered pasa_asmbl_35869.p1, internal, 1897, 1938
-recovered pasa_asmbl_35869.p1, internal, 2113, 2252
Valid prediction for GlimmerHMM_glimmerT_55694-T1
Valid prediction for GlimmerHMM_glimmerT_55682-T1
Valid prediction for pasa_asmbl_35605.p1
Valid prediction for Augustus_model.g36906.t1
Valid prediction for snap_scaffold_26-snap.1192-T1
Valid prediction for snap_scaffold_26-snap.1199-T1
Valid prediction for GlimmerHMM_glimmerT_55675-T1
Valid prediction for Augustus_model.g36892.t1
Valid prediction for snap_scaffold_26-snap.1220-T1
Valid prediction for snap_scaffold_26-snap.1201-T1
Valid prediction for snap_scaffold_26-snap.1176-T1
Valid prediction for Augustus_model.g36880.t1
Valid prediction for snap_scaffold_26-snap.1188-T1
Valid prediction for snap_scaffold_26-snap.1206-T1
Valid prediction for snap_scaffold_26-snap.1197-T1
Valid prediction for snap_scaffold_26-snap.1191-T1
Valid prediction for Augustus_model.g36888.t1
Valid prediction for CodingQuarry_transcript_40353-T1
Valid prediction for Augustus_model.g36885.t1
Valid prediction for GlimmerHMM_glimmerT_55686-T1
Valid prediction for GlimmerHMM_glimmerT_55671-T1
Valid prediction for GlimmerHMM_glimmerT_55680-T1
Valid prediction for GlimmerHMM_glimmerT_55664-T1
Valid prediction for Augustus_model.g36904.t1
Valid prediction for GlimmerHMM_glimmerT_55672-T1
Valid prediction for snap_scaffold_26-snap.1224-T1
Valid prediction for Augustus_model.g36884.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32977, rend_intergenic: 30162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38707, rend_intergenic: 35159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71729, rend_intergenic: 65648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135598, rend_intergenic: 133105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161611, rend_intergenic: 161160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173985, rend_intergenic: 171788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178322, rend_intergenic: 174421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 199254
-exon list size: 495


building trellis

0.2    
0.4    
0.6    
0.8    
1.0    
1.2    
1.4    
1.6    
1.8    
2.0    
2.2    
2.4    
2.6    
2.8    
3.0    
3.2    
3.4    
3.6    
3.8    
4.0    
4.2    
4.4    
4.6    
4.8    
5.0    
5.2    
5.4    
5.6    
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    
8.5    
8.7    
8.9    
9.1    
9.3    
9.5    
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    
13.7    
13.9    
14.1    
14.3    
14.5    
14.7    
14.9    
15.1    
15.3    
15.5    
15.7    
15.9    
16.1    
16.3    
16.5    
16.7    
16.9    
17.1    
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    
21.3    
21.5    
21.7    
21.9    
22.1    
22.3    
22.5    
22.7    
22.9    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.3    
24.5    
24.7    
24.9    
25.2    
25.4    
25.6    
25.8    
26.0    
26.2    
26.4    
26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.6    
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    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.8    
35.0    
35.2    
35.4    
35.6    
35.8    
36.0    
36.2    
36.4    
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    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.7    
44.9    
45.1    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.7    
47.9    
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    
52.1    
52.3    
52.5    
52.7    
52.9    
53.1    
53.3    
53.5    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
54.9    
55.1    
55.3    
55.5    
55.7    
55.9    
56.1    
56.3    
56.5    
56.7    
56.9    
57.1    
57.3    
57.5    
57.7    
57.9    
58.1    
58.4    
58.6    
58.8    
59.0    
59.2    
59.4    
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    
63.6    
63.8    
64.0    
64.2    
64.4    
64.6    
64.8    
65.0    
65.2    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
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    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
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    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
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    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
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    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 32977, rend_intergenic: 30162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38707, rend_intergenic: 35159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71729, rend_intergenic: 65648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135598, rend_intergenic: 133105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161611, rend_intergenic: 161160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173985, rend_intergenic: 171788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178322, rend_intergenic: 174421  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support