-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_1347364-1521959

-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 CodingQuarry_transcript_46074-T1
Couldn't classify 131870, 132064
Sorry, prediction pasa_asmbl_39855.p1 fails validation.
(GGT)	 GT	131870-132064	GT	AGG
(GAT)	 AG	132468-132563	GT	GAG
(GAG)	 AG	132804-132999	GT	AGG
(GTG)	 AG	133361-133439	GT	GTG
(GGA)	 AG	133687-133801	GT	AGG
(CTG)	 AG	134208-134341	GT	AGG
(ATA)	 AG	134427-134547	GT	AGG
(GAT)	 AG	134913-135037	GT	AAG
(GTA)	 AG	135397-135529	GG	AGG
-recovered pasa_asmbl_39855.p1, terminal, 135397, 135529
-recovered pasa_asmbl_39855.p1, internal, 132468, 132563
-recovered pasa_asmbl_39855.p1, internal, 132804, 132999
-recovered pasa_asmbl_39855.p1, internal, 133361, 133439
-recovered pasa_asmbl_39855.p1, internal, 133687, 133801
-recovered pasa_asmbl_39855.p1, internal, 134208, 134341
-recovered pasa_asmbl_39855.p1, internal, 134427, 134547
-recovered pasa_asmbl_39855.p1, internal, 134913, 135037
Valid prediction for snap_scaffold_3-snap.359-T1
Valid prediction for snap_scaffold_3-snap.364-T1
Valid prediction for snap_scaffold_3-snap.354-T1
Couldn't classify 131426, 131507
Sorry, prediction pasa_asmbl_39852.p1 fails validation.
(ATG)	 AG	129500-129566	GT	TGG
(ATG)	 AG	129852-130012	GT	ACG
(GTT)	 AG	130516-130639	GT	TGG
(AGG)	 AG	131085-131217	GT	TGG
(TAA)	 AG	131426-131507	GT	AGG
-recovered pasa_asmbl_39852.p1, initial, 129500, 129566
add_exon() Sorry, pasa_asmbl_39852.p1 129852-130012-initial-1 is invalid.
-recovered pasa_asmbl_39852.p1, initial, 129852, 130012
-recovered pasa_asmbl_39852.p1, internal, 129500, 129566
-recovered pasa_asmbl_39852.p1, internal, 129852, 130012
-recovered pasa_asmbl_39852.p1, internal, 130516, 130639
-recovered pasa_asmbl_39852.p1, internal, 131085, 131217
-recovered pasa_asmbl_39852.p1, internal, 131426, 131507
Valid prediction for snap_scaffold_3-snap.373-T1
Valid prediction for snap_scaffold_3-snap.347-T1
Valid prediction for GlimmerHMM_glimmerT_6032-T1
Valid prediction for snap_scaffold_3-snap.336-T1
Valid prediction for snap_scaffold_3-snap.342-T1
Valid prediction for Augustus_model.g3934.t1
Valid prediction for snap_scaffold_3-snap.349-T1
Valid prediction for snap_scaffold_3-snap.357-T1
Valid prediction for snap_scaffold_3-snap.339-T1
Valid prediction for GlimmerHMM_glimmerT_6029-T1
Valid prediction for GlimmerHMM_glimmerT_6040-T1
Valid prediction for snap_scaffold_3-snap.346-T1
Valid prediction for GlimmerHMM_glimmerT_6017-T1
Couldn't classify 123566, 123907
Sorry, prediction pasa_asmbl_39851.p1 fails validation.
(CCT)	 TC	123566-123907	AA	GAA
Valid prediction for GlimmerHMM_glimmerT_6024-T1
Valid prediction for Augustus_model.g3928.t1
Valid prediction for GlimmerHMM_glimmerT_6018-T1
Valid prediction for GlimmerHMM_glimmerT_6042-T1
Valid prediction for Augustus_model.g3935.t1
Valid prediction for snap_scaffold_3-snap.345-T1
Valid prediction for pasa_asmbl_39857.p2
Valid prediction for snap_scaffold_3-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_6028-T1
Valid prediction for snap_scaffold_3-snap.370-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6031-T1
Valid prediction for pasa_asmbl_39858.p1
Valid prediction for snap_scaffold_3-snap.372-T1
Couldn't classify 99860, 99991
Sorry, prediction pasa_asmbl_39847.p1 fails validation.
(GAC)	 AG	99860-99991	GT	AGG
(AAG)	 AG	100373-100573	GT	GGG
(AAG)	 AG	101020-101130	GT	AGG
(GCG)	 AG	101725-101875	GT	GGG
(GCA)	 AG	102538-102626	TC	GAT
-recovered pasa_asmbl_39847.p1, terminal, 102538, 102626
-recovered pasa_asmbl_39847.p1, internal, 99860, 99991
-recovered pasa_asmbl_39847.p1, internal, 100373, 100573
-recovered pasa_asmbl_39847.p1, internal, 101020, 101130
-recovered pasa_asmbl_39847.p1, internal, 101725, 101875
Valid prediction for snap_scaffold_3-snap.344-T1
Valid prediction for snap_scaffold_3-snap.334-T1
Valid prediction for snap_scaffold_3-snap.352-T1
Valid prediction for snap_scaffold_3-snap.340-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_6020-T1
Valid prediction for GlimmerHMM_glimmerT_6036-T1
Valid prediction for HiQ_model.g3940.t1
Valid prediction for snap_scaffold_3-snap.369-T1
Valid prediction for Augustus_model.g3938.t1
Valid prediction for CodingQuarry_transcript_46075-T1
Couldn't classify 117490, 117536
Couldn't classify 117718, 118030
Sorry, prediction pasa_asmbl_40889.p1 fails validation.
(GAG)	 TG	117490-117536	GT	ACG
(GAA)	 AG	117718-118030	GA	AGG
Valid prediction for GlimmerHMM_glimmerT_6021-T1
Valid prediction for HiQ_model.g3942.t1
Valid prediction for GlimmerHMM_glimmerT_6038-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_3-snap.363-T1
Valid prediction for Augustus_model.g3933.t1
Valid prediction for snap_scaffold_3-snap.355-T1
Valid prediction for snap_scaffold_3-snap.335-T1
Valid prediction for GlimmerHMM_glimmerT_6030-T1
Valid prediction for snap_scaffold_3-snap.351-T1
Valid prediction for Augustus_model.g3929.t1
Valid prediction for GlimmerHMM_glimmerT_6039-T1
Valid prediction for GlimmerHMM_glimmerT_6016-T1
Valid prediction for GlimmerHMM_glimmerT_6025-T1
Valid prediction for CodingQuarry_transcript_46076-T1
Valid prediction for snap_scaffold_3-snap.366-T1
Valid prediction for GlimmerHMM_glimmerT_6033-T1
Valid prediction for snap_scaffold_3-snap.343-T1
Valid prediction for Augustus_model.g3926.t1
Valid prediction for snap_scaffold_3-snap.341-T1
Valid prediction for GlimmerHMM_glimmerT_6019-T1
Valid prediction for snap_scaffold_3-snap.333-T1
Valid prediction for snap_scaffold_3-snap.367-T1
Valid prediction for Augustus_model.g3941.t1
Valid prediction for snap_scaffold_3-snap.356-T1
Valid prediction for Augustus_model.g3932.t1
Valid prediction for GlimmerHMM_glimmerT_6034-T1
Valid prediction for HiQ_model.g3943.t1
Valid prediction for GlimmerHMM_glimmerT_6035-T1
Valid prediction for snap_scaffold_3-snap.371-T1
Valid prediction for snap_scaffold_3-snap.353-T1
Valid prediction for Augustus_model.g3930.t1
Valid prediction for GlimmerHMM_glimmerT_6026-T1
Valid prediction for snap_scaffold_3-snap.362-T1
Valid prediction for snap_scaffold_3-snap.350-T1
Valid prediction for GlimmerHMM_glimmerT_6015-T1
Valid prediction for snap_scaffold_3-snap.338-T1
Valid prediction for snap_scaffold_3-snap.348-T1
Valid prediction for HiQ_model.g3939.t1
Valid prediction for snap_scaffold_3-snap.368-T1
Valid prediction for snap_scaffold_3-snap.337-T1
Couldn't classify 83865, 83873
Sorry, prediction pasa_asmbl_38706.p1 fails validation.
(CAC)	 AG	83865-83873	GT	TGG
(GCT)	 AG	84036-84093	GT	AGG
(GGA)	 AG	84439-84525	GT	AGG
(GCG)	 AG	84787-84918	GT	TGG
(ACG)	 AG	85512-85684	GT	GAG
-recovered pasa_asmbl_38706.p1, terminal, 85512, 85684
-recovered pasa_asmbl_38706.p1, internal, 83865, 83873
-recovered pasa_asmbl_38706.p1, internal, 84036, 84093
-recovered pasa_asmbl_38706.p1, internal, 84439, 84525
-recovered pasa_asmbl_38706.p1, internal, 84787, 84918
-recovered pasa_asmbl_38706.p1, internal, 85512, 85684
Valid prediction for GlimmerHMM_glimmerT_6023-T1
Valid prediction for GlimmerHMM_glimmerT_6022-T1
Valid prediction for snap_scaffold_3-snap.361-T1
Couldn't classify 21185, 21352
Couldn't classify 22595, 22654
Sorry, prediction pasa_asmbl_38711.p1 fails validation.
(CTG)	 CT	21185-21352	GT	AGG
(GTG)	 AG	22076-22273	GT	TGG
(AGC)	 AG	22595-22654	AT	AGA
-recovered pasa_asmbl_38711.p1, internal, 22076, 22273
Couldn't classify 26152, 26330
Sorry, prediction pasa_asmbl_38710.p1 fails validation.
(TGG)	 CC	26152-26330	GT	GGG
(CTT)	 AG	26550-26676	GT	AGG
(AAG)	 AG	27056-27154	GT	CAG
(CTG)	 AG	27574-27642	GT	AGG
(ACC)	 AG	28194-28440	GT	CAG
(ATA)	 AG	29006-29071	GT	AGG
(CTC)	 AG	29186-29272	GT	TGG
(AGG)	 AG	29833-29933	GT	AGG
(AGA)	 AG	30140-30589	CA	GAC
-recovered pasa_asmbl_38710.p1, terminal, 30140, 30589
-recovered pasa_asmbl_38710.p1, internal, 26550, 26676
-recovered pasa_asmbl_38710.p1, internal, 27056, 27154
-recovered pasa_asmbl_38710.p1, internal, 27574, 27642
-recovered pasa_asmbl_38710.p1, internal, 28194, 28440
-recovered pasa_asmbl_38710.p1, internal, 29006, 29071
-recovered pasa_asmbl_38710.p1, internal, 29186, 29272
-recovered pasa_asmbl_38710.p1, internal, 29833, 29933
Valid prediction for Augustus_model.g3937.t1
Valid prediction for HiQ_model.g3936.t1
Valid prediction for Augustus_model.g3924.t1
Valid prediction for Augustus_model.g3925.t1
Valid prediction for GlimmerHMM_glimmerT_6037-T1
Valid prediction for Augustus_model.g3927.t1
Valid prediction for CodingQuarry_transcript_46073-T1
Valid prediction for snap_scaffold_3-snap.358-T1
Valid prediction for GlimmerHMM_glimmerT_6041-T1
Valid prediction for GlimmerHMM_glimmerT_6027-T1
Valid prediction for snap_scaffold_3-snap.360-T1
Couldn't classify 53740, 53756
Sorry, prediction pasa_asmbl_38707.p1 fails validation.
(CGG)	 TG	53740-53756	GT	AGG
(GTT)	 AG	54051-54667	GT	AGG
(GTG)	 AG	54962-55245	GG	GAG
add_exon() Sorry, pasa_asmbl_38707.p1 54051-54667-terminal-2 is invalid.
-recovered pasa_asmbl_38707.p1, terminal, 54051, 54667
-recovered pasa_asmbl_38707.p1, terminal, 54962, 55245
-recovered pasa_asmbl_38707.p1, internal, 54051, 54667
Valid prediction for Augustus_model.g3931.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13835, rend_intergenic: 8172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21999, rend_intergenic: 19809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23587, rend_intergenic: 22059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34909, rend_intergenic: 30895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41460, rend_intergenic: 37959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70004, rend_intergenic: 68591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78953, rend_intergenic: 75347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83417, rend_intergenic: 80052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87891, rend_intergenic: 83710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97995, rend_intergenic: 96794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102626, rend_intergenic: 98748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118039, rend_intergenic: 106150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138763, rend_intergenic: 131246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150004, rend_intergenic: 144008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174596
-exon list size: 391


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.1    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.9    
6.1    
6.4    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.7    
8.9    
9.2    
9.4    
9.7    
9.9    
10.2    
10.4    
10.7    
10.9    
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    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.8    
17.0    
17.3    
17.6    
17.8    
18.1    
18.3    
18.6    
18.8    
19.1    
19.3    
19.6    
19.8    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.2    
23.4    
23.7    
23.9    
24.2    
24.4    
24.7    
24.9    
25.2    
25.4    
25.7    
26.0    
26.2    
26.5    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.9    
36.1    
36.4    
36.6    
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    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
51.1    
51.4    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.7    
53.9    
54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.8    
59.0    
59.3    
59.5    
59.8    
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    
63.4    
63.6    
63.9    
64.1    
64.4    
64.6    
64.9    
65.1    
65.4    
65.6    
65.9    
66.2    
66.4    
66.7    
66.9    
67.2    
67.4    
67.7    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.5    
72.8    
73.0    
73.3    
73.5    
73.8    
74.0    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
75.8    
76.1    
76.3    
76.6    
76.8    
77.1    
77.4    
77.6    
77.9    
78.1    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.2    
80.4    
80.7    
80.9    
81.2    
81.4    
81.7    
81.9    
82.2    
82.4    
82.7    
83.0    
83.2    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
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    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.1    
91.3    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
96.9    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 13835, rend_intergenic: 8172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21999, rend_intergenic: 19809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23587, rend_intergenic: 22059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34909, rend_intergenic: 30895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41460, rend_intergenic: 37959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70004, rend_intergenic: 68591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78953, rend_intergenic: 75347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83417, rend_intergenic: 80052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87891, rend_intergenic: 83710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97995, rend_intergenic: 96794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102626, rend_intergenic: 98748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118039, rend_intergenic: 106150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138763, rend_intergenic: 131246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150004, rend_intergenic: 144008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support