-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_4874559-4980899

-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_10-snap.1087-T1
Valid prediction for snap_scaffold_10-snap.1070-T1
Valid prediction for GlimmerHMM_glimmerT_24681-T1
Valid prediction for snap_scaffold_10-snap.1072-T1
Valid prediction for snap_scaffold_10-snap.1078-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g16423.t1
Valid prediction for Augustus_model.g16433.t1
Valid prediction for Augustus_model.g16427.t1
Couldn't classify 88499, 88697
Sorry, prediction pasa_asmbl_3137.p1 fails validation.
(ATG)	 TG	87261-87289	GT	CAG
(ATC)	 AG	87511-87657	GT	CGG
(GAA)	 AG	88499-88697	CG	ACC
-recovered pasa_asmbl_3137.p1, initial, 87261, 87289
-recovered pasa_asmbl_3137.p1, internal, 87511, 87657
Valid prediction for snap_scaffold_10-snap.1069-T1
Valid prediction for Augustus_model.g16428.t1
Couldn't classify 55841, 55921
Couldn't classify 57128, 57192
Sorry, prediction pasa_asmbl_3135.p1 fails validation.
(GAG)	 CA	55841-55921	GT	AGG
(TCT)	 AG	56042-56187	GT	GGG
(GGG)	 AG	56397-56562	GT	AGG
(CAC)	 AG	56788-57007	GT	AGG
(CTG)	 AG	57128-57192	GA	AGG
-recovered pasa_asmbl_3135.p1, internal, 56042, 56187
-recovered pasa_asmbl_3135.p1, internal, 56397, 56562
-recovered pasa_asmbl_3135.p1, internal, 56788, 57007
Valid prediction for CodingQuarry_transcript_5383-T1
Valid prediction for GlimmerHMM_glimmerT_24686-T1
Couldn't classify 40390, 40546
Couldn't classify 41201, 41361
Sorry, prediction pasa_asmbl_3133.p1 fails validation.
(AGC)	 GC	40390-40546	GT	AGG
(GCT)	 AG	41201-41361	GA	GAG
Valid prediction for snap_scaffold_10-snap.1080-T1
Valid prediction for GlimmerHMM_glimmerT_24683-T1
Couldn't classify 22795, 22836
Sorry, prediction pasa_asmbl_3130.p1 fails validation.
(ACT)	 AG	22795-22836	GT	CGG
(GTT)	 AG	23231-23488	CC	GAC
-recovered pasa_asmbl_3130.p1, terminal, 23231, 23488
-recovered pasa_asmbl_3130.p1, internal, 22795, 22836
Valid prediction for snap_scaffold_10-snap.1084-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Couldn't classify 53733, 53775
Couldn't classify 54897, 54992
Sorry, prediction pasa_asmbl_3134.p1 fails validation.
(GTC)	 CC	53733-53775	GT	CTG
(ATG)	 AG	53887-54008	GT	TGG
(CAC)	 AG	54159-54250	GT	GAG
(CTT)	 AG	54607-54685	GT	AGG
(GTG)	 AG	54897-54992	GA	CCG
add_exon() Sorry, pasa_asmbl_3134.p1 53887-54008-initial-1 is invalid.
-recovered pasa_asmbl_3134.p1, initial, 53887, 54008
-recovered pasa_asmbl_3134.p1, internal, 53887, 54008
-recovered pasa_asmbl_3134.p1, internal, 54159, 54250
-recovered pasa_asmbl_3134.p1, internal, 54607, 54685
Valid prediction for Augustus_model.g16434.t1
Valid prediction for snap_scaffold_10-snap.1076-T1
Valid prediction for CodingQuarry_transcript_5385-T1
Valid prediction for CodingQuarry_transcript_5384-T1
Valid prediction for Augustus_model.g16426.t1
Valid prediction for GlimmerHMM_glimmerT_24680-T1
Valid prediction for Augustus_model.g16420.t1
Valid prediction for snap_scaffold_10-snap.1090-T1
Valid prediction for snap_scaffold_10-snap.1067-T1
Valid prediction for Augustus_model.g16421.t1
Valid prediction for GlimmerHMM_glimmerT_24693-T1
Valid prediction for GlimmerHMM_glimmerT_24684-T1
Valid prediction for snap_scaffold_10-snap.1092-T1
Valid prediction for snap_scaffold_10-snap.1074-T1
Valid prediction for GlimmerHMM_glimmerT_24688-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_10-snap.1082-T1
Valid prediction for GlimmerHMM_glimmerT_24689-T1
Valid prediction for snap_scaffold_10-snap.1088-T1
Valid prediction for snap_scaffold_10-snap.1086-T1
Valid prediction for snap_scaffold_10-snap.1091-T1
Valid prediction for Augustus_model.g16429.t1
Valid prediction for Augustus_model.g16431.t1
Valid prediction for GlimmerHMM_glimmerT_24694-T1
Valid prediction for GlimmerHMM_glimmerT_24682-T1
Valid prediction for snap_scaffold_10-snap.1083-T1
Valid prediction for GlimmerHMM_glimmerT_24685-T1
Valid prediction for GlimmerHMM_glimmerT_24690-T1
Valid prediction for GlimmerHMM_glimmerT_24687-T1
Valid prediction for pasa_asmbl_5084.p1
Valid prediction for snap_scaffold_10-snap.1075-T1
Valid prediction for snap_scaffold_10-snap.1068-T1
Valid prediction for GlimmerHMM_glimmerT_24691-T1
Couldn't classify 66978, 67397
Couldn't classify 69465, 69683
Sorry, prediction CodingQuarry_transcript_5388-T1 fails validation.
(ATG)	 AG	66978-67397	CT	ACC
(CTT)	 AC	69465-69683	AC	GAA
Valid prediction for snap_scaffold_10-snap.1089-T1
Valid prediction for Augustus_model.g16430.t1
Valid prediction for GlimmerHMM_glimmerT_24692-T1
Valid prediction for Augustus_model.g16435.t1
Valid prediction for snap_scaffold_10-snap.1093-T1
Valid prediction for snap_scaffold_10-snap.1073-T1
Valid prediction for snap_scaffold_10-snap.1079-T1
Couldn't classify 25605, 25623
Couldn't classify 27647, 27721
Sorry, prediction pasa_asmbl_4324.p1 fails validation.
(AAC)	 AC	25605-25623	GT	CGG
(GGG)	 AG	25806-25890	GT	AGG
(AGT)	 AG	26010-26045	GT	AGG
(CAG)	 AG	26152-26285	GT	TGG
(GTC)	 AG	26484-26607	GT	GGG
(GTT)	 AG	27324-27468	GT	TGG
(GAA)	 AG	27647-27721	CC	GGC
-recovered pasa_asmbl_4324.p1, internal, 25806, 25890
-recovered pasa_asmbl_4324.p1, internal, 26010, 26045
-recovered pasa_asmbl_4324.p1, internal, 26152, 26285
-recovered pasa_asmbl_4324.p1, internal, 26484, 26607
-recovered pasa_asmbl_4324.p1, internal, 27324, 27468
Valid prediction for HiQ_model.g16422.t1
Valid prediction for snap_scaffold_10-snap.1081-T1
Valid prediction for Augustus_model.g16432.t1
Valid prediction for snap_scaffold_10-snap.1085-T1
Valid prediction for snap_scaffold_10-snap.1077-T1
Valid prediction for Augustus_model.g16424.t1
Valid prediction for snap_scaffold_10-snap.1071-T1
Valid prediction for Augustus_model.g16425.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5976, rend_intergenic: 2303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7171, rend_intergenic: 6192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18318, rend_intergenic: 9622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23488, rend_intergenic: 23371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29432, rend_intergenic: 24004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31866, rend_intergenic: 30265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34952, rend_intergenic: 32751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36246, rend_intergenic: 35052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39349, rend_intergenic: 36659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60326, rend_intergenic: 41179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66402, rend_intergenic: 64992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74458, rend_intergenic: 69526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80864, rend_intergenic: 74478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85393, rend_intergenic: 82962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99623, rend_intergenic: 85625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104616, rend_intergenic: 100377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 106341
-exon list size: 347


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 5976, rend_intergenic: 2303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7171, rend_intergenic: 6192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18318, rend_intergenic: 9622  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23488, rend_intergenic: 23371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29432, rend_intergenic: 24004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31866, rend_intergenic: 30265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34952, rend_intergenic: 32751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36246, rend_intergenic: 35052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39349, rend_intergenic: 36659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60326, rend_intergenic: 41179  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66402, rend_intergenic: 64992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74458, rend_intergenic: 69526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80864, rend_intergenic: 74478  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85393, rend_intergenic: 82962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99623, rend_intergenic: 85625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104616, rend_intergenic: 100377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support