-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_19204306-19373802

-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 HiQ_model.g7363.t1
Couldn't classify 37780, 37869
Couldn't classify 40372, 40380
Sorry, prediction pasa_asmbl_42131.p1 fails validation.
(TCA)	 AC	37780-37869	GT	AGG
(GTT)	 AG	38672-38797	GT	CGG
(GTG)	 AG	39231-39434	GT	ACG
(AAG)	 AG	39807-39977	GT	AGG
(GTC)	 AG	40372-40380	GG	AAG
-recovered pasa_asmbl_42131.p1, internal, 38672, 38797
-recovered pasa_asmbl_42131.p1, internal, 39231, 39434
-recovered pasa_asmbl_42131.p1, internal, 39807, 39977
Valid prediction for GlimmerHMM_glimmerT_11223-T1
Valid prediction for GlimmerHMM_glimmerT_11237-T1
Valid prediction for GlimmerHMM_glimmerT_11230-T1
Couldn't classify 158198, 158299
Couldn't classify 161929, 162018
Sorry, prediction pasa_asmbl_42135.p1 fails validation.
(TGG)	 CT	158198-158299	GT	GCG
(AAG)	 AG	158888-159013	GT	CTG
(AGG)	 AG	159283-159325	GT	AGG
(GTC)	 AG	159686-159767	GT	AGG
(ACA)	 AG	160036-160080	GT	CGG
(GTT)	 AG	160331-160383	GT	ATG
(CGG)	 AG	160490-160607	GT	AGG
(GGG)	 AG	161427-161514	GT	TGG
(GAT)	 AG	161929-162018	TG	GGT
-recovered pasa_asmbl_42135.p1, internal, 158888, 159013
-recovered pasa_asmbl_42135.p1, internal, 159283, 159325
-recovered pasa_asmbl_42135.p1, internal, 159686, 159767
-recovered pasa_asmbl_42135.p1, internal, 160036, 160080
-recovered pasa_asmbl_42135.p1, internal, 160331, 160383
-recovered pasa_asmbl_42135.p1, internal, 160490, 160607
-recovered pasa_asmbl_42135.p1, internal, 161427, 161514
Valid prediction for Augustus_model.g7372.t1
Valid prediction for GlimmerHMM_glimmerT_11218-T1
Valid prediction for snap_scaffold_4-snap.3965-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3948-T1
Valid prediction for snap_scaffold_4-snap.3951-T1
Valid prediction for CodingQuarry_transcript_49391-T1
Valid prediction for snap_scaffold_4-snap.3974-T1
Couldn't classify 47078, 47202
Couldn't classify 49046, 49063
Sorry, prediction pasa_asmbl_42170.p1 fails validation.
(GCC)	 AG	47078-47202	GT	CTG
(GGT)	 AG	48367-48523	GT	CAG
(GAG)	 AG	49046-49063	GT	ACG
-recovered pasa_asmbl_42170.p1, internal, 47078, 47202
-recovered pasa_asmbl_42170.p1, internal, 48367, 48523
-recovered pasa_asmbl_42170.p1, internal, 49046, 49063
Valid prediction for snap_scaffold_4-snap.3947-T1
Couldn't classify 73313, 73990
Sorry, prediction pasa_asmbl_42133.p1 fails validation.
(ATG)	 AA	73313-73990	AG	GGA
Valid prediction for snap_scaffold_4-snap.3962-T1
Valid prediction for snap_scaffold_4-snap.3956-T1
Valid prediction for snap_scaffold_4-snap.3954-T1
Valid prediction for Augustus_model.g7368.t1
Valid prediction for snap_scaffold_4-snap.3959-T1
Valid prediction for snap_scaffold_4-snap.3970-T1
Valid prediction for Augustus_model.g7377.t1
Valid prediction for snap_scaffold_4-snap.3981-T1
Valid prediction for snap_scaffold_4-snap.3964-T1
Valid prediction for snap_scaffold_4-snap.3952-T1
Valid prediction for GlimmerHMM_glimmerT_11242-T1
Valid prediction for GlimmerHMM_glimmerT_11234-T1
Valid prediction for snap_scaffold_4-snap.3966-T1
Valid prediction for pasa_asmbl_42129.p1
Couldn't classify 49214, 49243
Sorry, prediction pasa_asmbl_42132.p1 fails validation.
(AGG)	 AG	49214-49243	GT	TGG
(ATG)	 AG	49974-50180	GT	AGG
(AAG)	 AG	50414-50560	GT	GGG
(GTG)	 AG	51744-51992	TG	AGT
-recovered pasa_asmbl_42132.p1, initial, 49974, 50180
-recovered pasa_asmbl_42132.p1, terminal, 51744, 51992
-recovered pasa_asmbl_42132.p1, internal, 49214, 49243
-recovered pasa_asmbl_42132.p1, internal, 49974, 50180
-recovered pasa_asmbl_42132.p1, internal, 50414, 50560
Valid prediction for Augustus_model.g7365.t1
Valid prediction for GlimmerHMM_glimmerT_11236-T1
Valid prediction for Augustus_model.g7371.t1
Valid prediction for snap_scaffold_4-snap.3969-T1
Valid prediction for GlimmerHMM_glimmerT_11217-T1
Valid prediction for snap_scaffold_4-snap.3972-T1
Valid prediction for GlimmerHMM_glimmerT_11225-T1
Valid prediction for snap_scaffold_4-snap.3977-T1
Valid prediction for snap_scaffold_4-snap.3960-T1
Valid prediction for Augustus_model.g7373.t1
Valid prediction for snap_scaffold_4-snap.3978-T1
Valid prediction for GlimmerHMM_glimmerT_11222-T1
Valid prediction for GlimmerHMM_glimmerT_11219-T1
Valid prediction for snap_scaffold_4-snap.3968-T1
Valid prediction for GlimmerHMM_glimmerT_11238-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: -)Couldn't classify 36629, 37327
Sorry, prediction pasa_asmbl_43427.p1 fails validation.
(ATG)	 GG	36629-37327	TC	GGT
Valid prediction for snap_scaffold_4-snap.3950-T1
Valid prediction for snap_scaffold_4-snap.3979-T1
Valid prediction for HiQ_model.g7378.t1
Valid prediction for snap_scaffold_4-snap.3971-T1
Valid prediction for Augustus_model.g7362.t1
Couldn't classify 102233, 102351
Couldn't classify 103842, 104175
Sorry, prediction pasa_asmbl_43416.p1 fails validation.
(GAT)	 GA	102233-102351	GT	AGG
(GTA)	 AG	103842-104175	GA	AGG
Valid prediction for snap_scaffold_4-snap.3973-T1
Valid prediction for Augustus_model.g7364.t1
Valid prediction for GlimmerHMM_glimmerT_11220-T1
Valid prediction for snap_scaffold_4-snap.3976-T1
Valid prediction for snap_scaffold_4-snap.3961-T1
Valid prediction for GlimmerHMM_glimmerT_11239-T1
Valid prediction for Augustus_model.g7370.t1
Couldn't classify 97422, 97559
Sorry, prediction pasa_asmbl_43419.p1 fails validation.
(CCA)	 AG	97422-97559	GT	AGG
(GCT)	 AG	98559-98676	GT	TGG
(ATA)	 AG	98907-98969	GT	AGG
(GGA)	 AG	99148-99221	GA	GAG
-recovered pasa_asmbl_43419.p1, terminal, 99148, 99221
-recovered pasa_asmbl_43419.p1, internal, 97422, 97559
-recovered pasa_asmbl_43419.p1, internal, 98559, 98676
-recovered pasa_asmbl_43419.p1, internal, 98907, 98969
Valid prediction for CodingQuarry_transcript_49394-T1
Valid prediction for CodingQuarry_transcript_49392-T1
Valid prediction for GlimmerHMM_glimmerT_11224-T1
Couldn't classify 23593, 23618
Couldn't classify 25770, 25934
Sorry, prediction pasa_asmbl_43432.p1 fails validation.
(CTA)	 CT	23593-23618	GT	AGG
(TTC)	 AG	25328-25466	GT	AGG
(TTT)	 AG	25770-25934	GT	CTG
-recovered pasa_asmbl_43432.p1, internal, 25328, 25466
-recovered pasa_asmbl_43432.p1, internal, 25770, 25934
Valid prediction for snap_scaffold_4-snap.3949-T1
Valid prediction for CodingQuarry_transcript_49393-T1
Valid prediction for GlimmerHMM_glimmerT_11241-T1
Couldn't classify 165335, 165664
Sorry, prediction pasa_asmbl_43413.p1 fails validation.
(GTG)	 AG	165335-165664	GT	TGG
-recovered pasa_asmbl_43413.p1, internal, 165335, 165664
Valid prediction for CodingQuarry_transcript_49396-T1
Valid prediction for pasa_asmbl_43415.p1
Valid prediction for Augustus_model.g7375.t1
Valid prediction for GlimmerHMM_glimmerT_11232-T1
Valid prediction for snap_scaffold_4-snap.3953-T1
Valid prediction for Augustus_model.g7374.t1
Couldn't classify 26368, 26456
Couldn't classify 32176, 32224
Sorry, prediction pasa_asmbl_43430.p1 fails validation.
(CGC)	 GC	26368-26456	GT	AGG
(GTC)	 AG	26636-26765	GT	AGG
(GAG)	 AG	26843-26894	GT	GGG
(TGA)	 AG	27134-27228	GT	AGG
(CAT)	 AG	27325-27429	GT	AGG
(ATC)	 AG	28648-28783	GT	AGG
(GTT)	 AG	29114-29205	GT	CTG
(TCG)	 AG	29410-29561	GT	TGG
(GTG)	 AG	29748-29824	GT	TGG
(AGT)	 AG	29989-30074	GT	AGG
(AGG)	 AG	30271-30381	GT	AGG
(ATC)	 AG	30691-30805	GT	CGG
(GCT)	 AG	31174-31273	GT	ACG
(GCA)	 AG	31773-32042	GT	AGG
(GAG)	 AG	32176-32224	CC	AGC
-recovered pasa_asmbl_43430.p1, internal, 26636, 26765
-recovered pasa_asmbl_43430.p1, internal, 26843, 26894
-recovered pasa_asmbl_43430.p1, internal, 27134, 27228
-recovered pasa_asmbl_43430.p1, internal, 27325, 27429
-recovered pasa_asmbl_43430.p1, internal, 28648, 28783
-recovered pasa_asmbl_43430.p1, internal, 29114, 29205
-recovered pasa_asmbl_43430.p1, internal, 29410, 29561
-recovered pasa_asmbl_43430.p1, internal, 29748, 29824
-recovered pasa_asmbl_43430.p1, internal, 29989, 30074
-recovered pasa_asmbl_43430.p1, internal, 30271, 30381
-recovered pasa_asmbl_43430.p1, internal, 30691, 30805
-recovered pasa_asmbl_43430.p1, internal, 31174, 31273
-recovered pasa_asmbl_43430.p1, internal, 31773, 32042
Valid prediction for Augustus_model.g7366.t1
Valid prediction for pasa_asmbl_43433.p1
Valid prediction for Augustus_model.g7369.t1
Valid prediction for GlimmerHMM_glimmerT_11228-T1
Valid prediction for GlimmerHMM_glimmerT_11235-T1
Valid prediction for HiQ_model.g7367.t1
Valid prediction for GlimmerHMM_glimmerT_11227-T1
Couldn't classify 165917, 166216
Sorry, prediction pasa_asmbl_43412.p2 fails validation.
(GAG)	 GT	165917-166216	GG	GAG
Valid prediction for snap_scaffold_4-snap.3980-T1
Valid prediction for GlimmerHMM_glimmerT_11226-T1
Valid prediction for Augustus_model.g7376.t1
Valid prediction for snap_scaffold_4-snap.3975-T1
Valid prediction for GlimmerHMM_glimmerT_11229-T1
Valid prediction for snap_scaffold_4-snap.3955-T1
Valid prediction for GlimmerHMM_glimmerT_11231-T1
Valid prediction for GlimmerHMM_glimmerT_11233-T1
Valid prediction for snap_scaffold_4-snap.3958-T1
Valid prediction for GlimmerHMM_glimmerT_11243-T1
Valid prediction for GlimmerHMM_glimmerT_11240-T1
Valid prediction for GlimmerHMM_glimmerT_11221-T1
Valid prediction for GlimmerHMM_glimmerT_11216-T1
Valid prediction for snap_scaffold_4-snap.3963-T1
Valid prediction for CodingQuarry_transcript_49395-T1
Valid prediction for snap_scaffold_4-snap.3957-T1
Valid prediction for snap_scaffold_4-snap.3967-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13218, rend_intergenic: 10001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27457, rend_intergenic: 16661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30396, rend_intergenic: 29129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43073, rend_intergenic: 32134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51992, rend_intergenic: 43185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61862, rend_intergenic: 55129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65576, rend_intergenic: 63078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75339, rend_intergenic: 73409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83923, rend_intergenic: 75902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87533, rend_intergenic: 86460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102506, rend_intergenic: 88790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126223, rend_intergenic: 107853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135831, rend_intergenic: 134812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144142, rend_intergenic: 137173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155891, rend_intergenic: 149843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167711, rend_intergenic: 156892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169497
-exon list size: 444


building trellis

0.2    
0.4    
0.7    
0.9    
1.1    
1.3    
1.6    
1.8    
2.0    
2.2    
2.5    
2.7    
2.9    
3.1    
3.4    
3.6    
3.8    
4.0    
4.3    
4.5    
4.7    
4.9    
5.2    
5.4    
5.6    
5.8    
6.1    
6.3    
6.5    
6.7    
7.0    
7.2    
7.4    
7.6    
7.8    
8.1    
8.3    
8.5    
8.7    
9.0    
9.2    
9.4    
9.6    
9.9    
10.1    
10.3    
10.5    
10.8    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.3    
12.6    
12.8    
13.0    
13.2    
13.5    
13.7    
13.9    
14.1    
14.3    
14.6    
14.8    
15.0    
15.2    
15.5    
15.7    
15.9    
16.1    
16.4    
16.6    
16.8    
17.0    
17.3    
17.5    
17.7    
17.9    
18.2    
18.4    
18.6    
18.8    
19.1    
19.3    
19.5    
19.7    
20.0    
20.2    
20.4    
20.6    
20.9    
21.1    
21.3    
21.5    
21.7    
22.0    
22.2    
22.4    
22.6    
22.9    
23.1    
23.3    
23.5    
23.8    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
26.2    
26.5    
26.7    
26.9    
27.1    
27.4    
27.6    
27.8    
28.0    
28.3    
28.5    
28.7    
28.9    
29.1    
29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.2    
31.4    
31.6    
31.8    
32.1    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.5    
34.8    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.2    
39.5    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.0    
41.3    
41.5    
41.7    
41.9    
42.2    
42.4    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.7    
46.0    
46.2    
46.4    
46.6    
46.9    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.4    
48.7    
48.9    
49.1    
49.3    
49.6    
49.8    
50.0    
50.2    
50.4    
50.7    
50.9    
51.1    
51.3    
51.6    
51.8    
52.0    
52.2    
52.5    
52.7    
52.9    
53.1    
53.4    
53.6    
53.8    
54.0    
54.3    
54.5    
54.7    
54.9    
55.2    
55.4    
55.6    
55.8    
56.1    
56.3    
56.5    
56.7    
57.0    
57.2    
57.4    
57.6    
57.8    
58.1    
58.3    
58.5    
58.7    
59.0    
59.2    
59.4    
59.6    
59.9    
60.1    
60.3    
60.5    
60.8    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.3    
62.6    
62.8    
63.0    
63.2    
63.5    
63.7    
63.9    
64.1    
64.3    
64.6    
64.8    
65.0    
65.2    
65.5    
65.7    
65.9    
66.1    
66.4    
66.6    
66.8    
67.0    
67.3    
67.5    
67.7    
67.9    
68.2    
68.4    
68.6    
68.8    
69.1    
69.3    
69.5    
69.7    
70.0    
70.2    
70.4    
70.6    
70.9    
71.1    
71.3    
71.5    
71.7    
72.0    
72.2    
72.4    
72.6    
72.9    
73.1    
73.3    
73.5    
73.8    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.2    
76.5    
76.7    
76.9    
77.1    
77.4    
77.6    
77.8    
78.0    
78.3    
78.5    
78.7    
78.9    
79.1    
79.4    
79.6    
79.8    
80.0    
80.3    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.1    
82.3    
82.5    
82.7    
83.0    
83.2    
83.4    
83.6    
83.9    
84.1    
84.3    
84.5    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 13218, rend_intergenic: 10001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27457, rend_intergenic: 16661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30396, rend_intergenic: 29129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43073, rend_intergenic: 32134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51992, rend_intergenic: 43185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61862, rend_intergenic: 55129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65576, rend_intergenic: 63078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75339, rend_intergenic: 73409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83923, rend_intergenic: 75902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87533, rend_intergenic: 86460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102506, rend_intergenic: 88790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126223, rend_intergenic: 107853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135831, rend_intergenic: 134812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144142, rend_intergenic: 137173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155891, rend_intergenic: 149843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167711, rend_intergenic: 156892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support