-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_3377085-3587246

-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_40055-T1
Valid prediction for pasa_asmbl_18727.p1
Valid prediction for snap_scaffold_17-snap.754-T1
Valid prediction for Augustus_model.g26669.t1
Valid prediction for Augustus_model.g26672.t1
Valid prediction for GlimmerHMM_glimmerT_40048-T1
Valid prediction for GlimmerHMM_glimmerT_40058-T1
Valid prediction for CodingQuarry_transcript_21931-T1
Valid prediction for snap_scaffold_17-snap.713-T1
Valid prediction for snap_scaffold_17-snap.737-T1
Valid prediction for snap_scaffold_17-snap.720-T1
Valid prediction for snap_scaffold_17-snap.726-T1
Valid prediction for CodingQuarry_transcript_21927-T1
Valid prediction for GlimmerHMM_glimmerT_40035-T1
Valid prediction for Augustus_model.g26666.t1
Valid prediction for snap_scaffold_17-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_40054-T1
Valid prediction for CodingQuarry_transcript_21928-T1
Valid prediction for HiQ_model.g26671.t1
Valid prediction for GlimmerHMM_glimmerT_40037-T1
Valid prediction for snap_scaffold_17-snap.752-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 37064, 37161
Sorry, prediction pasa_asmbl_18724.p1 fails validation.
(ATG)	 AA	31071-31157	GT	ATG
(ATT)	 AG	33561-33585	GT	TGG
(ATG)	 AG	34658-34766	GT	GAG
(TAA)	 AG	36701-36726	GT	TGG
(AAT)	 AG	37064-37161	GT	AGG
-recovered pasa_asmbl_18724.p1, initial, 31071, 31157
add_exon() Sorry, pasa_asmbl_18724.p1 34658-34766-initial-1 is invalid.
-recovered pasa_asmbl_18724.p1, initial, 34658, 34766
-recovered pasa_asmbl_18724.p1, internal, 33561, 33585
-recovered pasa_asmbl_18724.p1, internal, 34658, 34766
-recovered pasa_asmbl_18724.p1, internal, 36701, 36726
-recovered pasa_asmbl_18724.p1, internal, 37064, 37161
Valid prediction for snap_scaffold_17-snap.743-T1
Valid prediction for Augustus_model.g26668.t1
Couldn't classify 15008, 15094
Sorry, prediction pasa_asmbl_18722.p1 fails validation.
(ATG)	 AC	13174-13265	GT	TGG
(CAT)	 AG	13432-13617	GT	CTG
(ATA)	 AG	13832-13923	GT	AGG
(GAG)	 AG	14035-14153	GT	AGG
(GTT)	 AG	14697-14867	GT	AGG
(GTG)	 AG	15008-15094	AC	ACA
-recovered pasa_asmbl_18722.p1, initial, 13174, 13265
-recovered pasa_asmbl_18722.p1, internal, 13432, 13617
-recovered pasa_asmbl_18722.p1, internal, 13832, 13923
-recovered pasa_asmbl_18722.p1, internal, 14035, 14153
-recovered pasa_asmbl_18722.p1, internal, 14697, 14867
Valid prediction for GlimmerHMM_glimmerT_40033-T1
Valid prediction for HiQ_model.g26663.t1
Valid prediction for snap_scaffold_17-snap.716-T1
Valid prediction for snap_scaffold_17-snap.711-T1
Valid prediction for GlimmerHMM_glimmerT_40053-T1
Valid prediction for HiQ_model.g26665.t1
Valid prediction for snap_scaffold_17-snap.735-T1
Valid prediction for Augustus_model.g26677.t1
Valid prediction for Augustus_model.g26680.t1
Valid prediction for Augustus_model.g26661.t1
Valid prediction for snap_scaffold_17-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_40052-T1
Valid prediction for snap_scaffold_17-snap.727-T1
Valid prediction for pasa_asmbl_18721.p1
Couldn't classify 46618, 46741
Sorry, prediction pasa_asmbl_18725.p1 fails validation.
(AGA)	 CC	46618-46741	GT	AGG
(GTG)	 AG	47067-47143	GT	AGG
(GAG)	 AG	47517-47570	GT	CAG
(CAC)	 AG	49317-49429	GT	CAG
(TGT)	 AG	50052-50129	GT	AAG
(TCA)	 AG	50727-50818	GT	AGG
(CTT)	 AG	51410-51438	AA	GAA
-recovered pasa_asmbl_18725.p1, terminal, 51410, 51438
-recovered pasa_asmbl_18725.p1, internal, 47067, 47143
-recovered pasa_asmbl_18725.p1, internal, 47517, 47570
-recovered pasa_asmbl_18725.p1, internal, 49317, 49429
-recovered pasa_asmbl_18725.p1, internal, 50052, 50129
-recovered pasa_asmbl_18725.p1, internal, 50727, 50818
Valid prediction for Augustus_model.g26676.t1
Valid prediction for GlimmerHMM_glimmerT_40042-T1
Valid prediction for GlimmerHMM_glimmerT_40038-T1
Valid prediction for snap_scaffold_17-snap.742-T1
Valid prediction for snap_scaffold_17-snap.745-T1
Valid prediction for GlimmerHMM_glimmerT_40051-T1
Valid prediction for snap_scaffold_17-snap.747-T1
Valid prediction for snap_scaffold_17-snap.715-T1
Valid prediction for GlimmerHMM_glimmerT_40043-T1
Valid prediction for snap_scaffold_17-snap.739-T1
Valid prediction for GlimmerHMM_glimmerT_40057-T1
Valid prediction for GlimmerHMM_glimmerT_40040-T1
Valid prediction for snap_scaffold_17-snap.728-T1
Valid prediction for snap_scaffold_17-snap.730-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 149913, 150062
Couldn't classify 152717, 152794
Sorry, prediction pasa_asmbl_17819.p1 fails validation.
(GCT)	 TA	149913-150062	GT	CGG
(CCT)	 AG	151601-151707	GT	TGG
(CAG)	 AG	151981-152104	GT	TGG
(GGC)	 AG	152717-152794	GT	AGG
-recovered pasa_asmbl_17819.p1, internal, 151601, 151707
-recovered pasa_asmbl_17819.p1, internal, 151981, 152104
-recovered pasa_asmbl_17819.p1, internal, 152717, 152794
Valid prediction for GlimmerHMM_glimmerT_40056-T1
Valid prediction for snap_scaffold_17-snap.733-T1
Valid prediction for GlimmerHMM_glimmerT_40059-T1
Valid prediction for snap_scaffold_17-snap.741-T1
Valid prediction for snap_scaffold_17-snap.717-T1
Valid prediction for GlimmerHMM_glimmerT_40039-T1
Valid prediction for snap_scaffold_17-snap.738-T1
Valid prediction for snap_scaffold_17-snap.732-T1
Valid prediction for snap_scaffold_17-snap.755-T1
Valid prediction for snap_scaffold_17-snap.722-T1
Valid prediction for snap_scaffold_17-snap.751-T1
Valid prediction for snap_scaffold_17-snap.721-T1
Valid prediction for GlimmerHMM_glimmerT_40044-T1
Valid prediction for snap_scaffold_17-snap.723-T1
Valid prediction for Augustus_model.g26670.t1
Valid prediction for snap_scaffold_17-snap.719-T1
Valid prediction for GlimmerHMM_glimmerT_40045-T1
Valid prediction for GlimmerHMM_glimmerT_40041-T1
Valid prediction for GlimmerHMM_glimmerT_40047-T1
Valid prediction for snap_scaffold_17-snap.736-T1
Valid prediction for snap_scaffold_17-snap.729-T1
Valid prediction for Augustus_model.g26675.t1
Valid prediction for GlimmerHMM_glimmerT_40049-T1
Valid prediction for snap_scaffold_17-snap.750-T1
Valid prediction for pasa_asmbl_17812.p1
Valid prediction for GlimmerHMM_glimmerT_40034-T1
Couldn't classify 186511, 186666
Sorry, prediction pasa_asmbl_17814.p2 fails validation.
(ATC)	 AG	186511-186666	GT	AGG
(ATC)	 AG	188406-188591	TC	GAT
-recovered pasa_asmbl_17814.p2, terminal, 188406, 188591
-recovered pasa_asmbl_17814.p2, internal, 186511, 186666
Valid prediction for GlimmerHMM_glimmerT_40036-T1
Valid prediction for GlimmerHMM_glimmerT_40050-T1
Couldn't classify 99947, 99977
Couldn't classify 104014, 104103
Sorry, prediction pasa_asmbl_18486.p1 fails validation.
(CCC)	 CG	99947-99977	GT	ACG
(TAA)	 AG	101150-101391	GT	TGG
(AAT)	 AG	104014-104103	GT	AGG
-recovered pasa_asmbl_18486.p1, internal, 101150, 101391
-recovered pasa_asmbl_18486.p1, internal, 104014, 104103
Valid prediction for snap_scaffold_17-snap.731-T1
Valid prediction for GlimmerHMM_glimmerT_40046-T1
Valid prediction for snap_scaffold_17-snap.753-T1
Valid prediction for snap_scaffold_17-snap.740-T1
Valid prediction for snap_scaffold_17-snap.712-T1
Valid prediction for Augustus_model.g26678.t1
Valid prediction for CodingQuarry_transcript_21929-T1
Valid prediction for snap_scaffold_17-snap.734-T1
Valid prediction for snap_scaffold_17-snap.724-T1
Valid prediction for Augustus_model.g26667.t1
Valid prediction for CodingQuarry_transcript_21930-T1
Valid prediction for Augustus_model.g26679.t1
Valid prediction for snap_scaffold_17-snap.718-T1
Valid prediction for snap_scaffold_17-snap.757-T1
Valid prediction for Augustus_model.g26673.t1
Valid prediction for snap_scaffold_17-snap.714-T1
Valid prediction for HiQ_model.g26662.t1
Valid prediction for snap_scaffold_17-snap.749-T1
Valid prediction for CodingQuarry_transcript_21926-T1
Valid prediction for GlimmerHMM_glimmerT_40060-T1
Valid prediction for Augustus_model.g26674.t1
Valid prediction for snap_scaffold_17-snap.746-T1
Valid prediction for snap_scaffold_17-snap.744-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g26664.t1
Valid prediction for pasa_asmbl_17811.p1
Valid prediction for snap_scaffold_17-snap.725-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40165, rend_intergenic: 38889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49433, rend_intergenic: 40523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81199, rend_intergenic: 80325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106140, rend_intergenic: 103058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111630, rend_intergenic: 109406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117150, rend_intergenic: 115322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123897, rend_intergenic: 117501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133492, rend_intergenic: 124292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139726, rend_intergenic: 137012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152945, rend_intergenic: 148430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167110, rend_intergenic: 154524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173230, rend_intergenic: 167444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210162
-exon list size: 330


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
26.2    
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    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
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    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
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    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
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    
73.8    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 40165, rend_intergenic: 38889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49433, rend_intergenic: 40523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81199, rend_intergenic: 80325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106140, rend_intergenic: 103058  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111630, rend_intergenic: 109406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117150, rend_intergenic: 115322  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123897, rend_intergenic: 117501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133492, rend_intergenic: 124292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139726, rend_intergenic: 137012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152945, rend_intergenic: 148430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167110, rend_intergenic: 154524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173230, rend_intergenic: 167444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support