-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_5865636-6003720

-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_21-snap.1175-T1
Valid prediction for snap_scaffold_21-snap.1178-T1
Valid prediction for Augustus_model.g31863.t1
Couldn't classify 125745, 125866
Couldn't classify 126362, 126488
Sorry, prediction pasa_asmbl_28957.p1 fails validation.
(AGT)	 TC	125745-125866	GT	AAG
(GGC)	 AG	126046-126207	GT	AGG
(CCA)	 AG	126362-126488	AG	GGA
-recovered pasa_asmbl_28957.p1, internal, 126046, 126207
Valid prediction for GlimmerHMM_glimmerT_47774-T1
Valid prediction for snap_scaffold_21-snap.1174-T1
Valid prediction for snap_scaffold_21-snap.1194-T1
Valid prediction for pasa_asmbl_28594.p1
Valid prediction for snap_scaffold_21-snap.1201-T1
Valid prediction for snap_scaffold_21-snap.1176-T1
Valid prediction for Augustus_model.g31865.t1
Valid prediction for Augustus_model.g31880.t1
Valid prediction for snap_scaffold_21-snap.1203-T1
Valid prediction for snap_scaffold_21-snap.1198-T1
Valid prediction for GlimmerHMM_glimmerT_47768-T1
Valid prediction for GlimmerHMM_glimmerT_47782-T1
Valid prediction for GlimmerHMM_glimmerT_47770-T1
Couldn't classify 130995, 131039
Couldn't classify 133185, 133335
Sorry, prediction pasa_asmbl_28605.p1 fails validation.
(CTG)	 TC	130995-131039	GT	GGG
(ATC)	 AG	131459-131602	GT	AGG
(GAC)	 AG	131707-131875	GT	AGG
(GGG)	 AG	131977-132075	GT	AGG
(GTT)	 AG	132422-132587	GT	AAG
(GGG)	 AG	133185-133335	GT	TGG
-recovered pasa_asmbl_28605.p1, internal, 131459, 131602
-recovered pasa_asmbl_28605.p1, internal, 131707, 131875
-recovered pasa_asmbl_28605.p1, internal, 131977, 132075
-recovered pasa_asmbl_28605.p1, internal, 132422, 132587
-recovered pasa_asmbl_28605.p1, internal, 133185, 133335
Valid prediction for GlimmerHMM_glimmerT_47778-T1
Valid prediction for snap_scaffold_21-snap.1202-T1
Valid prediction for snap_scaffold_21-snap.1184-T1
Valid prediction for snap_scaffold_21-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_47776-T1
Valid prediction for GlimmerHMM_glimmerT_47777-T1
Valid prediction for GlimmerHMM_glimmerT_47761-T1
Valid prediction for GlimmerHMM_glimmerT_47781-T1
Valid prediction for GlimmerHMM_glimmerT_47785-T1
Valid prediction for CodingQuarry_transcript_32561-T1
Valid prediction for Augustus_model.g31871.t1
Valid prediction for Augustus_model.g31874.t1
Valid prediction for Augustus_model.g31873.t1
Valid prediction for snap_scaffold_21-snap.1180-T1
Couldn't classify 102948, 102963
Sorry, prediction pasa_asmbl_28598.p1 fails validation.
(ACC)	 GA	102948-102963	GT	AGG
(AGG)	 AG	104102-104309	GT	AGG
(TGA)	 AG	104562-104680	GT	TGG
(ACG)	 AG	104861-104996	GT	AGG
(GTG)	 AG	105196-105319	GT	GGG
(GAC)	 AG	106005-106154	GT	AGG
(CTG)	 AG	106267-106432	GT	AGG
(GCG)	 AG	106553-106757	GT	AGG
(AAC)	 AG	106873-106941	GT	CAG
(GCT)	 AG	107068-107270	GT	AGG
(GGA)	 AG	107371-107468	GT	GGG
(GGG)	 AG	107747-107963	GT	AGG
(CCA)	 AG	108084-108182	GT	TGG
(GGA)	 AG	108269-108422	GT	AGG
(GAC)	 AG	108548-108716	GT	TGG
(GTG)	 AG	108803-108921	GT	AGG
(TGG)	 AG	109388-109544	GT	AGG
(GAT)	 AG	109699-109899	GT	AGG
(GGG)	 AG	110037-110213	GT	TGG
(TTG)	 AG	110307-110454	GT	CGG
(CCC)	 AG	110614-110704	GT	AGG
(GGG)	 AG	110798-110922	GT	AGG
(TTC)	 AG	111086-111232	GT	AGG
(ATA)	 AG	111353-111443	GT	TGG
(CCG)	 AG	111565-111697	TG	AAT
add_exon() Sorry, pasa_asmbl_28598.p1 111086-111232-terminal-1 is invalid.
-recovered pasa_asmbl_28598.p1, terminal, 111086, 111232
-recovered pasa_asmbl_28598.p1, terminal, 111565, 111697
-recovered pasa_asmbl_28598.p1, internal, 104102, 104309
-recovered pasa_asmbl_28598.p1, internal, 104562, 104680
-recovered pasa_asmbl_28598.p1, internal, 104861, 104996
-recovered pasa_asmbl_28598.p1, internal, 105196, 105319
-recovered pasa_asmbl_28598.p1, internal, 106005, 106154
-recovered pasa_asmbl_28598.p1, internal, 106267, 106432
-recovered pasa_asmbl_28598.p1, internal, 106553, 106757
-recovered pasa_asmbl_28598.p1, internal, 106873, 106941
-recovered pasa_asmbl_28598.p1, internal, 107068, 107270
-recovered pasa_asmbl_28598.p1, internal, 107371, 107468
-recovered pasa_asmbl_28598.p1, internal, 107747, 107963
-recovered pasa_asmbl_28598.p1, internal, 108084, 108182
-recovered pasa_asmbl_28598.p1, internal, 108269, 108422
-recovered pasa_asmbl_28598.p1, internal, 108548, 108716
-recovered pasa_asmbl_28598.p1, internal, 108803, 108921
-recovered pasa_asmbl_28598.p1, internal, 109388, 109544
-recovered pasa_asmbl_28598.p1, internal, 109699, 109899
-recovered pasa_asmbl_28598.p1, internal, 110037, 110213
-recovered pasa_asmbl_28598.p1, internal, 110307, 110454
-recovered pasa_asmbl_28598.p1, internal, 110614, 110704
-recovered pasa_asmbl_28598.p1, internal, 110798, 110922
-recovered pasa_asmbl_28598.p1, internal, 111086, 111232
-recovered pasa_asmbl_28598.p1, internal, 111353, 111443
Valid prediction for GlimmerHMM_glimmerT_47762-T1
Valid prediction for GlimmerHMM_glimmerT_47786-T1
Couldn't classify 127452, 127551
Couldn't classify 127934, 128098
Sorry, prediction pasa_asmbl_28602.p2 fails validation.
(CAG)	 GG	127452-127551	GT	AGG
(CTC)	 AG	127671-127843	GT	GGG
(AGT)	 AG	127934-128098	GG	AGG
-recovered pasa_asmbl_28602.p2, internal, 127671, 127843
Valid prediction for GlimmerHMM_glimmerT_47784-T1
Valid prediction for snap_scaffold_21-snap.1192-T1
Couldn't classify 129837, 130145
Couldn't classify 130680, 130922
Sorry, prediction pasa_asmbl_28604.p1 fails validation.
(AAG)	 AG	129837-130145	GT	AGG
(ATT)	 AG	130258-130358	GT	AGG
(GTT)	 AG	130437-130572	GT	TGG
(TCC)	 AG	130680-130922	GA	CCG
-recovered pasa_asmbl_28604.p1, internal, 129837, 130145
-recovered pasa_asmbl_28604.p1, internal, 130258, 130358
-recovered pasa_asmbl_28604.p1, internal, 130437, 130572
Valid prediction for HiQ_model.g31864.t1
Valid prediction for snap_scaffold_21-snap.1196-T1
Valid prediction for Augustus_model.g31872.t1
Valid prediction for GlimmerHMM_glimmerT_47772-T1
Valid prediction for pasa_asmbl_28595.p1
Valid prediction for Augustus_model.g31877.t1
Valid prediction for snap_scaffold_21-snap.1190-T1
Valid prediction for Augustus_model.g31870.t1
Valid prediction for HiQ_model.g31878.t1
Valid prediction for Augustus_model.g31869.t1
Valid prediction for snap_scaffold_21-snap.1205-T1
Couldn't classify 128749, 128789
Couldn't classify 129493, 129539
Sorry, prediction pasa_asmbl_28603.p1 fails validation.
(ACC)	 CC	128749-128789	GT	AGG
(TCG)	 AG	128895-129069	GT	AGG
(GTG)	 AG	129183-129315	GT	AGG
(TGA)	 AG	129493-129539	GT	CCG
-recovered pasa_asmbl_28603.p1, internal, 128895, 129069
-recovered pasa_asmbl_28603.p1, internal, 129183, 129315
-recovered pasa_asmbl_28603.p1, internal, 129493, 129539
Valid prediction for GlimmerHMM_glimmerT_47771-T1
Valid prediction for snap_scaffold_21-snap.1199-T1
Valid prediction for snap_scaffold_21-snap.1177-T1
Valid prediction for CodingQuarry_transcript_32564-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_21-snap.1191-T1
Valid prediction for GlimmerHMM_glimmerT_47769-T1
Valid prediction for snap_scaffold_21-snap.1197-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.1193-T1
Valid prediction for GlimmerHMM_glimmerT_47764-T1
Valid prediction for GlimmerHMM_glimmerT_47775-T1
Valid prediction for snap_scaffold_21-snap.1188-T1
Valid prediction for GlimmerHMM_glimmerT_47763-T1
Valid prediction for GlimmerHMM_glimmerT_47773-T1
Valid prediction for snap_scaffold_21-snap.1200-T1
Valid prediction for snap_scaffold_21-snap.1189-T1
Valid prediction for GlimmerHMM_glimmerT_47765-T1
Valid prediction for Augustus_model.g31867.t1
Valid prediction for Augustus_model.g31868.t1
Valid prediction for snap_scaffold_21-snap.1187-T1
Valid prediction for snap_scaffold_21-snap.1195-T1
Valid prediction for snap_scaffold_21-snap.1181-T1
Valid prediction for HiQ_model.g31879.t1
Valid prediction for CodingQuarry_transcript_32562-T1
Valid prediction for snap_scaffold_21-snap.1183-T1
Valid prediction for snap_scaffold_21-snap.1204-T1
Valid prediction for Augustus_model.g31875.t1
Valid prediction for snap_scaffold_21-snap.1179-T1
Valid prediction for snap_scaffold_21-snap.1186-T1
Valid prediction for GlimmerHMM_glimmerT_47783-T1
Valid prediction for GlimmerHMM_glimmerT_47780-T1
Valid prediction for snap_scaffold_21-snap.1182-T1
Valid prediction for pasa_asmbl_27710.p1
Valid prediction for Augustus_model.g31876.t1
Couldn't classify 99045, 99101
Couldn't classify 105152, 105250
Sorry, prediction pasa_asmbl_28221.p1 fails validation.
(TAC)	 GC	99045-99101	GT	GGG
(GTG)	 AG	101729-101871	GT	AAG
(CCG)	 AG	101964-102116	GT	AGG
(TCT)	 AG	102272-102461	GT	ACG
(ATT)	 AG	104305-104370	GT	TGG
(TAT)	 AG	105152-105250	GT	TGG
-recovered pasa_asmbl_28221.p1, internal, 101729, 101871
-recovered pasa_asmbl_28221.p1, internal, 101964, 102116
-recovered pasa_asmbl_28221.p1, internal, 102272, 102461
-recovered pasa_asmbl_28221.p1, internal, 104305, 104370
-recovered pasa_asmbl_28221.p1, internal, 105152, 105250
Valid prediction for Augustus_model.g31866.t1
Valid prediction for GlimmerHMM_glimmerT_47766-T1
Valid prediction for GlimmerHMM_glimmerT_47779-T1
Valid prediction for pasa_asmbl_27712.p1
Valid prediction for GlimmerHMM_glimmerT_47767-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25160, rend_intergenic: 22758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33451, rend_intergenic: 28926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37443, rend_intergenic: 36057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64674, rend_intergenic: 58137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66436, rend_intergenic: 65187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68573, rend_intergenic: 66784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79302, rend_intergenic: 71318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92163, rend_intergenic: 88527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135273, rend_intergenic: 132836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138085
-exon list size: 399


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.5    
1.7    
2.0    
2.2    
2.5    
2.7    
3.0    
3.2    
3.5    
3.7    
4.0    
4.2    
4.5    
4.7    
5.0    
5.2    
5.5    
5.7    
6.0    
6.2    
6.5    
6.7    
7.0    
7.2    
7.5    
7.7    
8.0    
8.2    
8.5    
8.7    
9.0    
9.2    
9.5    
9.7    
10.0    
10.2    
10.5    
10.7    
11.0    
11.2    
11.5    
11.7    
12.0    
12.2    
12.5    
12.7    
13.0    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.5    
18.7    
19.0    
19.2    
19.5    
19.7    
20.0    
20.2    
20.4    
20.7    
20.9    
21.2    
21.4    
21.7    
21.9    
22.2    
22.4    
22.7    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.4    
30.7    
30.9    
31.2    
31.4    
31.7    
31.9    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.2    
34.4    
34.7    
34.9    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.1    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.4    
55.6    
55.9    
56.1    
56.4    
56.6    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
61.1    
61.3    
61.6    
61.8    
62.1    
62.3    
62.6    
62.8    
63.1    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.8    
65.1    
65.3    
65.6    
65.8    
66.1    
66.3    
66.6    
66.8    
67.1    
67.3    
67.6    
67.8    
68.1    
68.3    
68.6    
68.8    
69.1    
69.3    
69.6    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.3    
77.6    
77.8    
78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.8    
88.0    
88.3    
88.5    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.3    
95.5    
95.8    
96.0    
96.3    
96.5    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 25160, rend_intergenic: 22758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33451, rend_intergenic: 28926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37443, rend_intergenic: 36057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64674, rend_intergenic: 58137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66436, rend_intergenic: 65187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68573, rend_intergenic: 66784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79302, rend_intergenic: 71318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92163, rend_intergenic: 88527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135273, rend_intergenic: 132836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support