-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_9634690-9810845

-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 GlimmerHMM_glimmerT_59418-T1
Valid prediction for pasa_asmbl_37801.p1
Valid prediction for GlimmerHMM_glimmerT_59397-T1
Valid prediction for GlimmerHMM_glimmerT_59404-T1
Valid prediction for snap_scaffold_28-snap.2166-T1
Couldn't classify 134671, 134752
Sorry, prediction pasa_asmbl_37804.p1 fails validation.
(GCT)	 CA	134671-134752	GT	AGG
(GTC)	 AG	134966-135125	GT	AGG
(GAA)	 AG	135407-135523	GT	AAG
(GTT)	 AG	135952-136118	GT	GGG
(GTC)	 AG	136313-136518	GT	TGG
(GAT)	 AG	136643-136789	GT	AGG
(GTG)	 AG	137001-137639	TC	GAT
-recovered pasa_asmbl_37804.p1, terminal, 137001, 137639
-recovered pasa_asmbl_37804.p1, internal, 134966, 135125
-recovered pasa_asmbl_37804.p1, internal, 135407, 135523
-recovered pasa_asmbl_37804.p1, internal, 135952, 136118
-recovered pasa_asmbl_37804.p1, internal, 136313, 136518
-recovered pasa_asmbl_37804.p1, internal, 136643, 136789
Valid prediction for snap_scaffold_28-snap.2155-T1
Valid prediction for snap_scaffold_28-snap.2184-T1
Valid prediction for snap_scaffold_28-snap.2169-T1
Couldn't classify 6399, 6549
Couldn't classify 7736, 7743
Sorry, prediction pasa_asmbl_37797.p1 fails validation.
(GAT)	 CC	6399-6549	GT	CAG
(GTA)	 AG	6637-6737	GT	AGG
(GCC)	 AG	7285-7486	GT	AGG
(GTA)	 AG	7736-7743	TG	GCT
-recovered pasa_asmbl_37797.p1, internal, 6637, 6737
-recovered pasa_asmbl_37797.p1, internal, 7285, 7486
Valid prediction for GlimmerHMM_glimmerT_59412-T1
Valid prediction for snap_scaffold_28-snap.2157-T1
Couldn't classify 172040, 173419
Sorry, prediction pasa_asmbl_37811.p1 fails validation.
(GCA)	 CA	172040-173419	AC	GAA
Valid prediction for GlimmerHMM_glimmerT_59400-T1
Valid prediction for GlimmerHMM_glimmerT_59411-T1
Valid prediction for Augustus_model.g39363.t1
Valid prediction for GlimmerHMM_glimmerT_59409-T1
Valid prediction for CodingQuarry_transcript_43769-T1
Valid prediction for Augustus_model.g39365.t1
Valid prediction for snap_scaffold_28-snap.2181-T1
Couldn't classify 139525, 139545
Couldn't classify 142042, 142158
Sorry, prediction pasa_asmbl_37805.p1 fails validation.
(GGT)	 GA	139525-139545	GT	AGG
(TTT)	 AG	139762-139803	GT	GGG
(GAT)	 AG	139907-139957	GT	CTG
(ACT)	 AG	140097-140184	GT	GGG
(GCA)	 AG	141668-141762	GT	GAG
(ACG)	 AG	142042-142158	AG	TGA
-recovered pasa_asmbl_37805.p1, internal, 139762, 139803
-recovered pasa_asmbl_37805.p1, internal, 139907, 139957
-recovered pasa_asmbl_37805.p1, internal, 140097, 140184
-recovered pasa_asmbl_37805.p1, internal, 141668, 141762
Valid prediction for snap_scaffold_28-snap.2171-T1
Valid prediction for snap_scaffold_28-snap.2154-T1
Valid prediction for HiQ_model.g39364.t1
Valid prediction for snap_scaffold_28-snap.2168-T1
Valid prediction for snap_scaffold_28-snap.2187-T1
Valid prediction for GlimmerHMM_glimmerT_59410-T1
Valid prediction for snap_scaffold_28-snap.2179-T1
Valid prediction for GlimmerHMM_glimmerT_59396-T1
Valid prediction for HiQ_model.g39361.t1
Valid prediction for GlimmerHMM_glimmerT_59395-T1
Couldn't classify 158866, 158935
Couldn't classify 164543, 164548
Sorry, prediction pasa_asmbl_37808.p1 fails validation.
(CTG)	 AC	158866-158935	GT	AGG
(CGG)	 AG	159032-159174	GC	AGG
(GTG)	 AG	159488-159609	GT	AAG
(ATA)	 AG	160217-160298	GT	GGG
(GCG)	 AG	160973-161105	GT	CAG
(GAT)	 AG	161346-161449	GT	TTG
(AGC)	 AG	161632-161711	GT	AGG
(GAT)	 AG	163833-163972	GT	AGG
(CAC)	 AG	164140-164303	GT	AGG
(TAC)	 AG	164543-164548	CA	AGC
-recovered pasa_asmbl_37808.p1, internal, 159032, 159174
-recovered pasa_asmbl_37808.p1, internal, 159488, 159609
-recovered pasa_asmbl_37808.p1, internal, 160217, 160298
-recovered pasa_asmbl_37808.p1, internal, 160973, 161105
-recovered pasa_asmbl_37808.p1, internal, 161346, 161449
-recovered pasa_asmbl_37808.p1, internal, 161632, 161711
-recovered pasa_asmbl_37808.p1, internal, 163833, 163972
-recovered pasa_asmbl_37808.p1, internal, 164140, 164303
Valid prediction for Augustus_model.g39356.t1
Valid prediction for GlimmerHMM_glimmerT_59399-T1
Valid prediction for GlimmerHMM_glimmerT_59416-T1
Valid prediction for Augustus_model.g39366.t1
Valid prediction for GlimmerHMM_glimmerT_59394-T1
Valid prediction for snap_scaffold_28-snap.2161-T1
Couldn't classify 133054, 133217
Couldn't classify 133607, 133760
Sorry, prediction pasa_asmbl_37823.p1 fails validation.
(GGC)	 CG	133054-133217	GT	CGG
(GAT)	 AG	133607-133760	AT	GGA
Valid prediction for GlimmerHMM_glimmerT_59405-T1
Valid prediction for snap_scaffold_28-snap.2185-T1
Valid prediction for Augustus_model.g39359.t1
Valid prediction for pasa_asmbl_37806.p1
Valid prediction for snap_scaffold_28-snap.2163-T1
Couldn't classify 351, 510
Sorry, prediction pasa_asmbl_37875.p1 fails validation.
(TAC)	 CG	351-510	GT	AGG
(GTA)	 AG	760-947	GT	AGG
(GTG)	 AG	1149-1427	AG	AGA
-recovered pasa_asmbl_37875.p1, terminal, 1149, 1427
-recovered pasa_asmbl_37875.p1, internal, 760, 947
Valid prediction for snap_scaffold_28-snap.2186-T1
Valid prediction for Augustus_model.g39362.t1
Valid prediction for CodingQuarry_transcript_43770-T1
Valid prediction for snap_scaffold_28-snap.2160-T1
Valid prediction for GlimmerHMM_glimmerT_59414-T1
Valid prediction for GlimmerHMM_glimmerT_59413-T1
Valid prediction for HiQ_model.g39357.t1
Couldn't classify 174247, 174291
Couldn't classify 174316, 174516
Sorry, prediction CodingQuarry_transcript_43771-T1 fails validation.
(ATG)	 TT	174247-174291	AT	ACA
(ATC)	 AC	174316-174516	CT	GAC

-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 HiQ_model.g39360.t1
Valid prediction for snap_scaffold_28-snap.2162-T1
Valid prediction for snap_scaffold_28-snap.2174-T1
Valid prediction for GlimmerHMM_glimmerT_59402-T1
Valid prediction for GlimmerHMM_glimmerT_59407-T1
Valid prediction for GlimmerHMM_glimmerT_59398-T1
Valid prediction for snap_scaffold_28-snap.2175-T1
Couldn't classify 167706, 168038
Sorry, prediction pasa_asmbl_37799.p1 fails validation.
(ATG)	 AC	167706-168038	AG	GGA
Valid prediction for CodingQuarry_transcript_43768-T1
Valid prediction for GlimmerHMM_glimmerT_59417-T1
Valid prediction for snap_scaffold_28-snap.2165-T1
Valid prediction for snap_scaffold_28-snap.2182-T1
Valid prediction for snap_scaffold_28-snap.2156-T1
Valid prediction for GlimmerHMM_glimmerT_59403-T1
Valid prediction for snap_scaffold_28-snap.2159-T1
Valid prediction for GlimmerHMM_glimmerT_59415-T1
Valid prediction for GlimmerHMM_glimmerT_59408-T1
Valid prediction for Augustus_model.g39358.t1
Valid prediction for snap_scaffold_28-snap.2173-T1
Valid prediction for GlimmerHMM_glimmerT_59406-T1
Valid prediction for snap_scaffold_28-snap.2167-T1
Valid prediction for snap_scaffold_28-snap.2164-T1
Valid prediction for snap_scaffold_28-snap.2158-T1
Couldn't classify 138128, 138261
Sorry, prediction pasa_asmbl_38530.p1 fails validation.
(ATG)	 AT	134087-134198	GT	TGG
(GGC)	 AG	135186-135372	GT	AGG
(GGA)	 AG	135598-135683	GT	AGG
(GCA)	 AG	135785-135874	GT	AGG
(TGC)	 AG	135989-136057	GT	AGG
(CCG)	 AG	136520-136677	GT	AGG
(GAG)	 AG	137020-137174	GT	AAG
(GTT)	 AG	137342-137493	GT	AGG
(GTC)	 AG	137743-137958	GT	TGG
(GTG)	 AG	138128-138261	GG	ATG
-recovered pasa_asmbl_38530.p1, initial, 134087, 134198
-recovered pasa_asmbl_38530.p1, internal, 135186, 135372
-recovered pasa_asmbl_38530.p1, internal, 135598, 135683
-recovered pasa_asmbl_38530.p1, internal, 135785, 135874
-recovered pasa_asmbl_38530.p1, internal, 135989, 136057
-recovered pasa_asmbl_38530.p1, internal, 136520, 136677
-recovered pasa_asmbl_38530.p1, internal, 137020, 137174
-recovered pasa_asmbl_38530.p1, internal, 137342, 137493
-recovered pasa_asmbl_38530.p1, internal, 137743, 137958
Valid prediction for snap_scaffold_28-snap.2177-T1
Valid prediction for snap_scaffold_28-snap.2180-T1
Valid prediction for snap_scaffold_28-snap.2170-T1
Valid prediction for snap_scaffold_28-snap.2178-T1
Valid prediction for snap_scaffold_28-snap.2176-T1
Valid prediction for snap_scaffold_28-snap.2183-T1
Couldn't classify 138265, 138363
Sorry, prediction pasa_asmbl_38527.p1 fails validation.
(AGG)	 GC	138265-138363	GT	AGG
(GGT)	 AG	138456-138661	GT	AGG
(CTG)	 AG	141149-141152	CT	GAC
-recovered pasa_asmbl_38527.p1, terminal, 141149, 141152
-recovered pasa_asmbl_38527.p1, internal, 138456, 138661
Valid prediction for GlimmerHMM_glimmerT_59401-T1
Valid prediction for snap_scaffold_28-snap.2172-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 33464, rend_intergenic: 29557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61851, rend_intergenic: 59909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71667, rend_intergenic: 69268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78367, rend_intergenic: 77694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92353, rend_intergenic: 78491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137639, rend_intergenic: 92436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145073, rend_intergenic: 140313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160774, rend_intergenic: 158185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176156
-exon list size: 392


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
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    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
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    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
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    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
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    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
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    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
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    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 33464, rend_intergenic: 29557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61851, rend_intergenic: 59909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71667, rend_intergenic: 69268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78367, rend_intergenic: 77694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92353, rend_intergenic: 78491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137639, rend_intergenic: 92436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145073, rend_intergenic: 140313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160774, rend_intergenic: 158185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support