-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_1-173184

-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_8599-T1
Valid prediction for snap_scaffold_4-snap.32-T1
Valid prediction for GlimmerHMM_glimmerT_8597-T1
Valid prediction for snap_scaffold_4-snap.17-T1
Valid prediction for snap_scaffold_4-snap.26-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g5591.t1
Valid prediction for CodingQuarry_transcript_48863-T1
Valid prediction for snap_scaffold_4-snap.13-T1
Valid prediction for Augustus_model.g5590.t1
Valid prediction for GlimmerHMM_glimmerT_8570-T1
Valid prediction for Augustus_model.g5588.t1
Valid prediction for snap_scaffold_4-snap.31-T1
Valid prediction for GlimmerHMM_glimmerT_8583-T1
Valid prediction for snap_scaffold_4-snap.15-T1
Valid prediction for snap_scaffold_4-snap.20-T1
Valid prediction for snap_scaffold_4-snap.8-T1
Valid prediction for snap_scaffold_4-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_8578-T1
Valid prediction for snap_scaffold_4-snap.29-T1
Valid prediction for snap_scaffold_4-snap.5-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8575-T1
Couldn't classify 158, 252
Sorry, prediction snap_scaffold_4-snap.1-T1 fails validation.
(CGT)	 AG	158-252	GT	ACG
(GGG)	 AG	852-967	GT	CTG
(GTA)	 AG	3612-3794	GT	TGG
(TCT)	 AG	9305-9740	GT	AGG
(TAC)	 AG	9843-10005	GT	ATG
(ACG)	 AG	13254-13280	GT	AAG
(CAG)	 AG	15327-15452	GT	ACG
(GGT)	 AG	15507-15700	GT	GTG
(GTC)	 AG	16356-16518	GT	CTG
(AGA)	 AG	19433-19773	GT	AAG
(ACG)	 AG	21366-21460	GT	TGG
(ACA)	 AG	21765-21905	GT	CGG
(ACC)	 AG	22791-22887	GT	TGG
(TTT)	 AG	23787-23875	GT	CGG
(CCG)	 AG	24063-24355	GT	CGG
(GTA)	 AG	24389-24491	GT	GAG
(AAA)	 AG	24662-24678	GT	TTG
(GCT)	 AG	25291-25380	GT	GAG
(GAC)	 AG	27363-27447	GT	AGG
(CGT)	 AG	38462-38565	AG	AAA
-recovered snap_scaffold_4-snap.1-T1, terminal, 38462, 38565
-recovered snap_scaffold_4-snap.1-T1, internal, 158, 252
-recovered snap_scaffold_4-snap.1-T1, internal, 852, 967
-recovered snap_scaffold_4-snap.1-T1, internal, 3612, 3794
-recovered snap_scaffold_4-snap.1-T1, internal, 9305, 9740
-recovered snap_scaffold_4-snap.1-T1, internal, 9843, 10005
-recovered snap_scaffold_4-snap.1-T1, internal, 13254, 13280
-recovered snap_scaffold_4-snap.1-T1, internal, 15327, 15452
-recovered snap_scaffold_4-snap.1-T1, internal, 15507, 15700
-recovered snap_scaffold_4-snap.1-T1, internal, 16356, 16518
-recovered snap_scaffold_4-snap.1-T1, internal, 19433, 19773
-recovered snap_scaffold_4-snap.1-T1, internal, 21366, 21460
-recovered snap_scaffold_4-snap.1-T1, internal, 21765, 21905
-recovered snap_scaffold_4-snap.1-T1, internal, 22791, 22887
-recovered snap_scaffold_4-snap.1-T1, internal, 23787, 23875
-recovered snap_scaffold_4-snap.1-T1, internal, 24063, 24355
-recovered snap_scaffold_4-snap.1-T1, internal, 24389, 24491
-recovered snap_scaffold_4-snap.1-T1, internal, 24662, 24678
-recovered snap_scaffold_4-snap.1-T1, internal, 25291, 25380
-recovered snap_scaffold_4-snap.1-T1, internal, 27363, 27447
Valid prediction for snap_scaffold_4-snap.19-T1
Couldn't classify 154360, 154592
Sorry, prediction pasa_asmbl_41086.p1 fails validation.
(ATG)	 TC	153713-153847	GT	TGG
(CAC)	 AG	154001-154199	GT	GGG
(GGG)	 AG	154360-154592	TA	CGT
-recovered pasa_asmbl_41086.p1, initial, 153713, 153847
-recovered pasa_asmbl_41086.p1, internal, 154001, 154199
Valid prediction for GlimmerHMM_glimmerT_8595-T1
Valid prediction for GlimmerHMM_glimmerT_8580-T1
Valid prediction for snap_scaffold_4-snap.11-T1
Valid prediction for GlimmerHMM_glimmerT_8600-T1
Valid prediction for GlimmerHMM_glimmerT_8596-T1
Valid prediction for snap_scaffold_4-snap.22-T1
Valid prediction for Augustus_model.g5586.t1
Valid prediction for GlimmerHMM_glimmerT_8572-T1
Valid prediction for GlimmerHMM_glimmerT_8592-T1
Valid prediction for snap_scaffold_4-snap.28-T1
Valid prediction for snap_scaffold_4-snap.25-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.34-T1
Valid prediction for GlimmerHMM_glimmerT_8588-T1
Couldn't classify 83897, 84070
Couldn't classify 87576, 87712
Sorry, prediction pasa_asmbl_42214.p1 fails validation.
(GGA)	 CA	83897-84070	GT	GGG
(GAG)	 AG	86769-86943	GT	AGG
(GCA)	 AG	87576-87712	AA	ACA
-recovered pasa_asmbl_42214.p1, internal, 86769, 86943
Valid prediction for Augustus_model.g5596.t1
Valid prediction for HiQ_model.g5595.t1
Valid prediction for GlimmerHMM_glimmerT_8598-T1
Couldn't classify 157977, 158155
Sorry, prediction pasa_asmbl_41088.p1 fails validation.
(TGC)	 GA	157977-158155	GT	AGG
(TGA)	 AG	158277-158349	GT	AGG
(AAG)	 AG	158691-158850	GT	ACG
(GAT)	 AG	158960-159039	GA	AGG
-recovered pasa_asmbl_41088.p1, terminal, 158960, 159039
-recovered pasa_asmbl_41088.p1, internal, 158277, 158349
-recovered pasa_asmbl_41088.p1, internal, 158691, 158850
Valid prediction for GlimmerHMM_glimmerT_8585-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_8590-T1
Valid prediction for GlimmerHMM_glimmerT_8594-T1
Valid prediction for GlimmerHMM_glimmerT_8591-T1
Valid prediction for GlimmerHMM_glimmerT_8581-T1
Couldn't classify 64840, 64962
Sorry, prediction pasa_asmbl_42301.p1 fails validation.
(CAG)	 GT	64840-64962	GT	GTG
(GAC)	 AG	65300-65445	GT	ATG
(AGT)	 AG	67497-67575	GT	AGG
(GGG)	 AG	68170-68299	GT	AGG
(ATC)	 AG	68411-68605	GT	TGG
(AAT)	 AG	68762-68784	TG	GAT
-recovered pasa_asmbl_42301.p1, terminal, 68762, 68784
-recovered pasa_asmbl_42301.p1, internal, 65300, 65445
-recovered pasa_asmbl_42301.p1, internal, 67497, 67575
-recovered pasa_asmbl_42301.p1, internal, 68170, 68299
-recovered pasa_asmbl_42301.p1, internal, 68411, 68605
Valid prediction for snap_scaffold_4-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_8584-T1
Valid prediction for GlimmerHMM_glimmerT_8574-T1
Valid prediction for GlimmerHMM_glimmerT_8589-T1
Valid prediction for GlimmerHMM_glimmerT_8579-T1
Valid prediction for snap_scaffold_4-snap.36-T1
Valid prediction for snap_scaffold_4-snap.6-T1
Valid prediction for GlimmerHMM_glimmerT_8587-T1
Valid prediction for GlimmerHMM_glimmerT_8573-T1
Valid prediction for GlimmerHMM_glimmerT_8571-T1
Couldn't classify 132878, 133006
Sorry, prediction pasa_asmbl_42296.p1 fails validation.
(ATG)	 TC	129423-129482	GT	AGG
(CCC)	 AG	129617-129678	GT	GAG
(TGA)	 AG	129807-129909	GT	AGG
(GAG)	 AG	130446-130565	GT	AGG
(AAA)	 AG	131619-131712	GT	AGG
(TCC)	 AG	131795-131925	GT	AGG
(CAA)	 AG	132878-133006	GG	CTG
-recovered pasa_asmbl_42296.p1, initial, 129423, 129482
-recovered pasa_asmbl_42296.p1, internal, 129617, 129678
-recovered pasa_asmbl_42296.p1, internal, 129807, 129909
-recovered pasa_asmbl_42296.p1, internal, 130446, 130565
-recovered pasa_asmbl_42296.p1, internal, 131619, 131712
-recovered pasa_asmbl_42296.p1, internal, 131795, 131925
Valid prediction for snap_scaffold_4-snap.12-T1
Valid prediction for snap_scaffold_4-snap.14-T1
Valid prediction for snap_scaffold_4-snap.24-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_48860-T1
Valid prediction for GlimmerHMM_glimmerT_8582-T1
Valid prediction for Augustus_model.g5593.t1
Valid prediction for snap_scaffold_4-snap.10-T1
Couldn't classify 67519, 67576
Couldn't classify 68172, 68227
Sorry, prediction CodingQuarry_transcript_48861-T1 fails validation.
(ATG)	 TC	67519-67576	TA	GGT
(GGT)	 GG	68172-68227	CC	GAC
Couldn't classify 56177, 56273
Couldn't classify 57658, 57834
Sorry, prediction pasa_asmbl_42306.p1 fails validation.
(TAC)	 GG	56177-56273	GT	GAG
(CGT)	 AG	56876-57032	GT	CGG
(GAA)	 AG	57301-57439	GT	GTG
(GAG)	 AG	57658-57834	TG	TGT
-recovered pasa_asmbl_42306.p1, internal, 56876, 57032
-recovered pasa_asmbl_42306.p1, internal, 57301, 57439
Valid prediction for snap_scaffold_4-snap.21-T1
Valid prediction for snap_scaffold_4-snap.18-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.16-T1
Valid prediction for snap_scaffold_4-snap.2-T1
Valid prediction for Augustus_model.g5587.t1
Valid prediction for snap_scaffold_4-snap.4-T1
Valid prediction for snap_scaffold_4-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_8586-T1
Valid prediction for GlimmerHMM_glimmerT_8569-T1
Valid prediction for snap_scaffold_4-snap.23-T1
Valid prediction for GlimmerHMM_glimmerT_8593-T1
Valid prediction for Augustus_model.g5592.t1
Couldn't classify 53364, 53420
Sorry, prediction pasa_asmbl_42307.p1 fails validation.
(ATG)	 AC	52324-52610	GT	AAG
(TCA)	 AG	53105-53204	GT	AGG
(GCA)	 AG	53364-53420	GT	TGG
-recovered pasa_asmbl_42307.p1, initial, 52324, 52610
-recovered pasa_asmbl_42307.p1, internal, 53105, 53204
-recovered pasa_asmbl_42307.p1, internal, 53364, 53420
Valid prediction for GlimmerHMM_glimmerT_8576-T1
Valid prediction for GlimmerHMM_glimmerT_8577-T1
Valid prediction for Augustus_model.g5594.t1
Valid prediction for snap_scaffold_4-snap.30-T1
Couldn't classify 77399, 77769
Sorry, prediction pasa_asmbl_42297.p1 fails validation.
(ATG)	 TA	76738-76849	GT	AGG
(ACG)	 AG	76990-77085	GT	AGG
(TTT)	 AG	77399-77769	GC	GGG
-recovered pasa_asmbl_42297.p1, initial, 76738, 76849
-recovered pasa_asmbl_42297.p1, internal, 76990, 77085
-recovered pasa_asmbl_42297.p1, internal, 77399, 77769
Valid prediction for HiQ_model.g5589.t1
Valid prediction for snap_scaffold_4-snap.3-T1
Valid prediction for snap_scaffold_4-snap.7-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 45095, rend_intergenic: 45092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38565, rend_intergenic: 180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40140, rend_intergenic: 38742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41548, rend_intergenic: 40140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52176, rend_intergenic: 47090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76156, rend_intergenic: 61823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77187, rend_intergenic: 76235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83784, rend_intergenic: 81089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91182, rend_intergenic: 87572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104778, rend_intergenic: 104401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108418, rend_intergenic: 104842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120861, rend_intergenic: 115352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126469, rend_intergenic: 122901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132496, rend_intergenic: 128987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137016, rend_intergenic: 133755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168403, rend_intergenic: 163620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173184
-exon list size: 337


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
2.9    
3.2    
3.5    
3.8    
4.1    
4.4    
4.7    
5.0    
5.3    
5.6    
5.9    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.8    
9.1    
9.4    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.8    
12.1    
12.4    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.7    
15.0    
15.3    
15.6    
15.9    
16.2    
16.5    
16.8    
17.1    
17.4    
17.7    
18.0    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.4    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.4    
22.7    
23.0    
23.3    
23.6    
23.9    
24.2    
24.5    
24.8    
25.1    
25.4    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.3    
33.6    
33.9    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.1    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.1    
45.4    
45.7    
46.0    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
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    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
54.0    
54.3    
54.6    
54.9    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
61.9    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.1    
66.4    
66.7    
67.0    
67.3    
67.6    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.6    
74.9    
75.2    
75.5    
75.8    
76.1    
76.4    
76.7    
77.0    
77.3    
77.6    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.6    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
82.0    
82.3    
82.6    
82.9    
83.2    
83.5    
83.8    
84.1    
84.4    
84.7    
85.0    
85.3    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.6    
87.9    
88.2    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.1    
94.4    
94.7    
95.0    
95.3    
95.6    
95.9    
96.2    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 31 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 45095, rend_intergenic: 45092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38565, rend_intergenic: 180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40140, rend_intergenic: 38742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41548, rend_intergenic: 40140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52176, rend_intergenic: 47090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76156, rend_intergenic: 61823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77187, rend_intergenic: 76235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83784, rend_intergenic: 81089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91182, rend_intergenic: 87572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104778, rend_intergenic: 104401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108418, rend_intergenic: 104842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120861, rend_intergenic: 115352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126469, rend_intergenic: 122901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132496, rend_intergenic: 128987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137016, rend_intergenic: 133755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168403, rend_intergenic: 163620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support