-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_19515102-19756009

-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_4-snap.4035-T1
Valid prediction for snap_scaffold_4-snap.4052-T1
Valid prediction for GlimmerHMM_glimmerT_11284-T1
Valid prediction for GlimmerHMM_glimmerT_11293-T1
Valid prediction for snap_scaffold_4-snap.4019-T1
Valid prediction for snap_scaffold_4-snap.4050-T1
Valid prediction for snap_scaffold_4-snap.4061-T1
Valid prediction for snap_scaffold_4-snap.4044-T1
Valid prediction for snap_scaffold_4-snap.4046-T1
Valid prediction for snap_scaffold_4-snap.4039-T1
Valid prediction for CodingQuarry_transcript_49407-T1
Valid prediction for snap_scaffold_4-snap.4015-T1
Couldn't classify 164097, 164188
Sorry, prediction pasa_asmbl_42156.p1 fails validation.
(CTT)	 AA	164097-164188	GT	AGG
(GAT)	 AG	164593-164764	GT	TGG
(GTG)	 AG	164872-165009	GT	AGG
(GTG)	 AG	165099-165266	GT	TGG
(GTC)	 AG	165639-166373	TA	GAT
-recovered pasa_asmbl_42156.p1, terminal, 165639, 166373
-recovered pasa_asmbl_42156.p1, internal, 164593, 164764
-recovered pasa_asmbl_42156.p1, internal, 164872, 165009
-recovered pasa_asmbl_42156.p1, internal, 165099, 165266
Valid prediction for snap_scaffold_4-snap.4028-T1
Valid prediction for snap_scaffold_4-snap.4021-T1
Valid prediction for snap_scaffold_4-snap.4054-T1
Valid prediction for pasa_asmbl_42154.p1
Valid prediction for GlimmerHMM_glimmerT_11276-T1
Valid prediction for GlimmerHMM_glimmerT_11268-T1
Valid prediction for snap_scaffold_4-snap.4055-T1
Valid prediction for GlimmerHMM_glimmerT_11285-T1
Valid prediction for snap_scaffold_4-snap.4057-T1
Valid prediction for GlimmerHMM_glimmerT_11287-T1
Valid prediction for snap_scaffold_4-snap.4058-T1
Valid prediction for GlimmerHMM_glimmerT_11280-T1
Valid prediction for GlimmerHMM_glimmerT_11292-T1
Valid prediction for GlimmerHMM_glimmerT_11282-T1
Valid prediction for pasa_asmbl_42158.p1
Valid prediction for snap_scaffold_4-snap.4062-T1
Valid prediction for snap_scaffold_4-snap.4041-T1
Valid prediction for GlimmerHMM_glimmerT_11288-T1
Couldn't classify 163776, 163777
Sorry, prediction CodingQuarry_transcript_49413-T1 fails validation.
(ATG)	 CT	163776-163777	GT	ATG
(GAT)	 AG	164593-164764	GT	TGG
(GTG)	 AG	164872-165009	GT	AGG
(GTG)	 AG	165099-165266	GT	TGG
(GTC)	 AG	165639-166373	TA	GAT
-recovered CodingQuarry_transcript_49413-T1, terminal, 165639, 166373
-recovered CodingQuarry_transcript_49413-T1, internal, 164593, 164764
-recovered CodingQuarry_transcript_49413-T1, internal, 164872, 165009
-recovered CodingQuarry_transcript_49413-T1, internal, 165099, 165266
Valid prediction for GlimmerHMM_glimmerT_11286-T1
Valid prediction for GlimmerHMM_glimmerT_11272-T1
Valid prediction for GlimmerHMM_glimmerT_11290-T1
Valid prediction for snap_scaffold_4-snap.4036-T1
Valid prediction for snap_scaffold_4-snap.4048-T1
Valid prediction for snap_scaffold_4-snap.4034-T1
Valid prediction for snap_scaffold_4-snap.4047-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.4043-T1
Valid prediction for snap_scaffold_4-snap.4025-T1
Valid prediction for snap_scaffold_4-snap.4027-T1
Valid prediction for CodingQuarry_transcript_49417-T1
Valid prediction for CodingQuarry_transcript_49414-T1
Valid prediction for snap_scaffold_4-snap.4049-T1
Valid prediction for snap_scaffold_4-snap.4023-T1
Valid prediction for CodingQuarry_transcript_49406-T1
Valid prediction for CodingQuarry_transcript_49416-T1
Valid prediction for snap_scaffold_4-snap.4042-T1
Valid prediction for snap_scaffold_4-snap.4018-T1
Valid prediction for snap_scaffold_4-snap.4031-T1
Valid prediction for snap_scaffold_4-snap.4032-T1
Valid prediction for snap_scaffold_4-snap.4033-T1
Valid prediction for GlimmerHMM_glimmerT_11266-T1
Valid prediction for pasa_asmbl_42152.p1
Valid prediction for pasa_asmbl_42160.p1
Valid prediction for CodingQuarry_transcript_49404-T1
Valid prediction for snap_scaffold_4-snap.4040-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 GlimmerHMM_glimmerT_11281-T1
Valid prediction for snap_scaffold_4-snap.4030-T1
Valid prediction for GlimmerHMM_glimmerT_11289-T1
Valid prediction for CodingQuarry_transcript_49403-T1
Valid prediction for GlimmerHMM_glimmerT_11274-T1
Valid prediction for snap_scaffold_4-snap.4020-T1
Couldn't classify 33953, 34035
Sorry, prediction pasa_asmbl_43487.p1 fails validation.
(CAG)	 CA	33953-34035	GT	AGG
(GAT)	 AG	34606-34776	GT	AGG
(GAC)	 AG	37746-37863	GT	GGG
(ATC)	 AG	38433-38613	GT	AGG
(GTG)	 AG	38704-38843	GT	AGG
(ATC)	 AG	39094-39192	GT	AGG
(GTG)	 AG	39433-39567	GT	TGG
(AAG)	 AG	39854-40000	CT	GAC
-recovered pasa_asmbl_43487.p1, terminal, 39854, 40000
-recovered pasa_asmbl_43487.p1, internal, 34606, 34776
-recovered pasa_asmbl_43487.p1, internal, 37746, 37863
-recovered pasa_asmbl_43487.p1, internal, 38433, 38613
-recovered pasa_asmbl_43487.p1, internal, 38704, 38843
-recovered pasa_asmbl_43487.p1, internal, 39094, 39192
-recovered pasa_asmbl_43487.p1, internal, 39433, 39567
Valid prediction for GlimmerHMM_glimmerT_11283-T1
Valid prediction for CodingQuarry_transcript_49411-T1
Valid prediction for GlimmerHMM_glimmerT_11277-T1
Valid prediction for snap_scaffold_4-snap.4026-T1
Valid prediction for CodingQuarry_transcript_49412-T1
Valid prediction for GlimmerHMM_glimmerT_11271-T1
Valid prediction for GlimmerHMM_glimmerT_11291-T1
Valid prediction for GlimmerHMM_glimmerT_11278-T1
Valid prediction for GlimmerHMM_glimmerT_11270-T1
Valid prediction for pasa_asmbl_43463.p3
Valid prediction for GlimmerHMM_glimmerT_11273-T1
Valid prediction for snap_scaffold_4-snap.4024-T1
Valid prediction for snap_scaffold_4-snap.4022-T1
Valid prediction for pasa_asmbl_43444.p1
Valid prediction for snap_scaffold_4-snap.4017-T1
Couldn't classify 31184, 31349
Sorry, prediction pasa_asmbl_43488.p1 fails validation.
(ATG)	 GC	28894-29032	GT	TGG
(ATG)	 AG	29363-29531	GT	GGG
(GTG)	 AG	31184-31349	GG	GAG
-recovered pasa_asmbl_43488.p1, initial, 28894, 29032
add_exon() Sorry, pasa_asmbl_43488.p1 29363-29531-initial-1 is invalid.
-recovered pasa_asmbl_43488.p1, initial, 29363, 29531
-recovered pasa_asmbl_43488.p1, internal, 29363, 29531
Valid prediction for CodingQuarry_transcript_49415-T1
Couldn't classify 147660, 147834
Sorry, prediction pasa_asmbl_43472.p1 fails validation.
(GTT)	 GT	147660-147834	GT	AGG
(TGG)	 AG	149425-149588	GT	AGG
(TTC)	 AG	150278-150481	TT	GAT
-recovered pasa_asmbl_43472.p1, terminal, 150278, 150481
-recovered pasa_asmbl_43472.p1, internal, 149425, 149588
Valid prediction for snap_scaffold_4-snap.4059-T1
Couldn't classify 206358, 206496
Couldn't classify 208378, 208482
Sorry, prediction pasa_asmbl_43451.p1 fails validation.
(GTA)	 CA	206358-206496	GT	TGG
(CGC)	 AG	207308-207463	GT	AGG
(GTG)	 AG	207594-207715	GT	AGG
(GAC)	 AG	207997-208104	GT	AGG
(GGC)	 AG	208378-208482	AG	AGA
-recovered pasa_asmbl_43451.p1, internal, 207308, 207463
-recovered pasa_asmbl_43451.p1, internal, 207594, 207715
-recovered pasa_asmbl_43451.p1, internal, 207997, 208104
Valid prediction for snap_scaffold_4-snap.4016-T1
Valid prediction for GlimmerHMM_glimmerT_11269-T1
Valid prediction for CodingQuarry_transcript_49408-T1
Valid prediction for pasa_asmbl_43454.p1
Valid prediction for CodingQuarry_transcript_49410-T1
Valid prediction for snap_scaffold_4-snap.4029-T1
Valid prediction for GlimmerHMM_glimmerT_11275-T1
Valid prediction for snap_scaffold_4-snap.4056-T1
Valid prediction for snap_scaffold_4-snap.4045-T1
Valid prediction for snap_scaffold_4-snap.4060-T1
Valid prediction for snap_scaffold_4-snap.4038-T1
Valid prediction for snap_scaffold_4-snap.4037-T1
Valid prediction for GlimmerHMM_glimmerT_11279-T1
Valid prediction for snap_scaffold_4-snap.4051-T1
Valid prediction for GlimmerHMM_glimmerT_11267-T1
Couldn't classify 213048, 213177
Sorry, prediction pasa_asmbl_43448.p2 fails validation.
(CTG)	 GC	213048-213177	GT	TGG
(GAA)	 AG	215055-215141	GT	GCG
(TAA)	 AG	215891-216006	GG	GAG
-recovered pasa_asmbl_43448.p2, terminal, 215891, 216006
-recovered pasa_asmbl_43448.p2, internal, 215055, 215141
Valid prediction for CodingQuarry_transcript_49409-T1
Valid prediction for snap_scaffold_4-snap.4053-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21735, rend_intergenic: 12907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23933, rend_intergenic: 22781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47471, rend_intergenic: 24491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50430, rend_intergenic: 47724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51764, rend_intergenic: 50561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63989, rend_intergenic: 55220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72440, rend_intergenic: 64903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77291, rend_intergenic: 73838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93538, rend_intergenic: 78402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127857, rend_intergenic: 118351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163240, rend_intergenic: 129418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166373, rend_intergenic: 165600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178155, rend_intergenic: 166927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182697, rend_intergenic: 179838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196032, rend_intergenic: 185809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207012, rend_intergenic: 199156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223576, rend_intergenic: 208130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240908
-exon list size: 370


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.2    
2.4    
2.7    
3.0    
3.2    
3.5    
3.8    
4.0    
4.3    
4.6    
4.8    
5.1    
5.4    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.5    
7.8    
8.1    
8.3    
8.6    
8.9    
9.1    
9.4    
9.7    
9.9    
10.2    
10.5    
10.8    
11.0    
11.3    
11.6    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.2    
14.5    
14.8    
15.1    
15.3    
15.6    
15.9    
16.1    
16.4    
16.7    
16.9    
17.2    
17.5    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.6    
22.8    
23.1    
23.4    
23.7    
23.9    
24.2    
24.5    
24.7    
25.0    
25.3    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.4    
27.7    
28.0    
28.2    
28.5    
28.8    
29.0    
29.3    
29.6    
29.8    
30.1    
30.4    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.1    
34.4    
34.7    
34.9    
35.2    
35.5    
35.8    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.4    
38.7    
39.0    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.1    
41.4    
41.7    
41.9    
42.2    
42.5    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.2    
46.5    
46.8    
47.0    
47.3    
47.6    
47.8    
48.1    
48.4    
48.7    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.3    
51.6    
51.9    
52.2    
52.4    
52.7    
53.0    
53.2    
53.5    
53.8    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.5    
57.8    
58.1    
58.3    
58.6    
58.9    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.0    
61.3    
61.6    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.4    
63.7    
64.0    
64.2    
64.5    
64.8    
65.1    
65.3    
65.6    
65.9    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.6    
69.9    
70.2    
70.4    
70.7    
71.0    
71.2    
71.5    
71.8    
72.0    
72.3    
72.6    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.7    
75.0    
75.3    
75.5    
75.8    
76.1    
76.3    
76.6    
76.9    
77.2    
77.4    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.5    
82.8    
83.1    
83.3    
83.6    
83.9    
84.1    
84.4    
84.7    
84.9    
85.2    
85.5    
85.8    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.4    
88.7    
89.0    
89.2    
89.5    
89.8    
90.1    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
91.9    
92.2    
92.5    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.6    
94.9    
95.2    
95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.0    
97.3    
97.6    
97.8    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 21735, rend_intergenic: 12907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23933, rend_intergenic: 22781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47471, rend_intergenic: 24491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50430, rend_intergenic: 47724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51764, rend_intergenic: 50561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63989, rend_intergenic: 55220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72440, rend_intergenic: 64903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77291, rend_intergenic: 73838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93538, rend_intergenic: 78402  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127857, rend_intergenic: 118351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163240, rend_intergenic: 129418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166373, rend_intergenic: 165600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178155, rend_intergenic: 166927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182697, rend_intergenic: 179838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196032, rend_intergenic: 185809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207012, rend_intergenic: 199156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223576, rend_intergenic: 208130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support