-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_12193191-12317206

-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_41198-T1
Valid prediction for GlimmerHMM_glimmerT_41202-T1
Valid prediction for CodingQuarry_transcript_22206-T1
Valid prediction for GlimmerHMM_glimmerT_41194-T1
Valid prediction for GlimmerHMM_glimmerT_41186-T1
Valid prediction for snap_scaffold_17-snap.2494-T1
Valid prediction for snap_scaffold_17-snap.2488-T1
Valid prediction for snap_scaffold_17-snap.2500-T1
Valid prediction for GlimmerHMM_glimmerT_41201-T1
Valid prediction for GlimmerHMM_glimmerT_41196-T1
Valid prediction for CodingQuarry_transcript_22208-T1
Valid prediction for snap_scaffold_17-snap.2496-T1
Valid prediction for snap_scaffold_17-snap.2492-T1
Valid prediction for snap_scaffold_17-snap.2490-T1
Valid prediction for GlimmerHMM_glimmerT_41185-T1
Valid prediction for GlimmerHMM_glimmerT_41205-T1
Valid prediction for snap_scaffold_17-snap.2483-T1
Couldn't classify 13579, 13902
Sorry, prediction pasa_asmbl_19281.p2 fails validation.
(ATG)	 GC	13579-13902	GG	GGG
Valid prediction for CodingQuarry_transcript_22207-T1
Valid prediction for snap_scaffold_17-snap.2487-T1
Valid prediction for CodingQuarry_transcript_22209-T1
Valid prediction for HiQ_model.g27469.t1
Valid prediction for snap_scaffold_17-snap.2502-T1
Valid prediction for snap_scaffold_17-snap.2474-T1
Valid prediction for GlimmerHMM_glimmerT_41204-T1
Valid prediction for GlimmerHMM_glimmerT_41197-T1
Valid prediction for snap_scaffold_17-snap.2503-T1
Valid prediction for snap_scaffold_17-snap.2505-T1
Valid prediction for Augustus_model.g27470.t1
Valid prediction for Augustus_model.g27477.t1
Valid prediction for snap_scaffold_17-snap.2477-T1
Valid prediction for pasa_asmbl_19276.p1
Valid prediction for snap_scaffold_17-snap.2480-T1
Valid prediction for GlimmerHMM_glimmerT_41184-T1
Valid prediction for snap_scaffold_17-snap.2475-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 snap_scaffold_17-snap.2501-T1
Valid prediction for GlimmerHMM_glimmerT_41189-T1
Valid prediction for snap_scaffold_17-snap.2499-T1
Valid prediction for CodingQuarry_transcript_22212-T1
Valid prediction for HiQ_model.g27473.t1
Valid prediction for snap_scaffold_17-snap.2504-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 102356, 102439
Sorry, prediction pasa_asmbl_18317.p1 fails validation.
(GCC)	 AA	102356-102439	GT	AGG
(GTA)	 AG	102830-102931	GT	AGG
(GTG)	 AG	103111-103167	GT	AGG
(CTG)	 AG	103261-103327	GT	AGG
(CTG)	 AG	103416-103510	GT	ACG
(ATG)	 AG	104033-104104	GT	TGG
(TTC)	 AG	104586-104677	GT	AGG
(GAA)	 AG	105343-105418	GT	AGG
(GAA)	 AG	105586-105705	TT	GAT
-recovered pasa_asmbl_18317.p1, initial, 104033, 104104
-recovered pasa_asmbl_18317.p1, terminal, 105586, 105705
-recovered pasa_asmbl_18317.p1, internal, 102830, 102931
-recovered pasa_asmbl_18317.p1, internal, 103111, 103167
-recovered pasa_asmbl_18317.p1, internal, 103261, 103327
-recovered pasa_asmbl_18317.p1, internal, 103416, 103510
-recovered pasa_asmbl_18317.p1, internal, 104033, 104104
-recovered pasa_asmbl_18317.p1, internal, 104586, 104677
-recovered pasa_asmbl_18317.p1, internal, 105343, 105418
Valid prediction for snap_scaffold_17-snap.2498-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 101034, 101153
Sorry, prediction pasa_asmbl_18474.p1 fails validation.
(GAA)	 TG	101034-101153	GT	AGG
(CAC)	 AG	101260-101556	GA	AGG
-recovered pasa_asmbl_18474.p1, terminal, 101260, 101556
Valid prediction for snap_scaffold_17-snap.2495-T1
Valid prediction for snap_scaffold_17-snap.2484-T1
Valid prediction for snap_scaffold_17-snap.2478-T1
Valid prediction for Augustus_model.g27474.t1
Valid prediction for Augustus_model.g27476.t1
Valid prediction for pasa_asmbl_18322.p1
Valid prediction for snap_scaffold_17-snap.2476-T1
Valid prediction for snap_scaffold_17-snap.2497-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g27471.t1
Valid prediction for snap_scaffold_17-snap.2479-T1
Valid prediction for snap_scaffold_17-snap.2482-T1
Valid prediction for GlimmerHMM_glimmerT_41203-T1
Couldn't classify 97481, 97769
Sorry, prediction pasa_asmbl_18320.p1 fails validation.
(ATG)	 GA	92152-92308	GT	AGG
(GCT)	 AG	92456-92574	GT	AGG
(AAC)	 AG	92962-93069	GT	AGG
(GCC)	 AG	93733-93846	GT	AGG
(GTG)	 AG	94218-94394	GT	TGG
(TGC)	 AG	95542-95677	GT	AGG
(AGG)	 AG	95876-96081	GT	AGG
(GTG)	 AG	96367-96516	GT	AGG
(GCG)	 AG	97178-97299	GT	GGG
(GTA)	 AG	97481-97769	GG	GGG
-recovered pasa_asmbl_18320.p1, initial, 92152, 92308
-recovered pasa_asmbl_18320.p1, internal, 92456, 92574
-recovered pasa_asmbl_18320.p1, internal, 92962, 93069
-recovered pasa_asmbl_18320.p1, internal, 93733, 93846
-recovered pasa_asmbl_18320.p1, internal, 94218, 94394
-recovered pasa_asmbl_18320.p1, internal, 95542, 95677
-recovered pasa_asmbl_18320.p1, internal, 95876, 96081
-recovered pasa_asmbl_18320.p1, internal, 96367, 96516
-recovered pasa_asmbl_18320.p1, internal, 97178, 97299
Valid prediction for snap_scaffold_17-snap.2486-T1
Valid prediction for Augustus_model.g27478.t1
Valid prediction for snap_scaffold_17-snap.2489-T1
Valid prediction for snap_scaffold_17-snap.2481-T1
Valid prediction for Augustus_model.g27472.t1
Valid prediction for snap_scaffold_17-snap.2493-T1
Valid prediction for GlimmerHMM_glimmerT_41195-T1
Valid prediction for GlimmerHMM_glimmerT_41190-T1
Valid prediction for snap_scaffold_17-snap.2485-T1
Valid prediction for Augustus_model.g27475.t1
Valid prediction for GlimmerHMM_glimmerT_41187-T1
Valid prediction for GlimmerHMM_glimmerT_41193-T1
Valid prediction for GlimmerHMM_glimmerT_41192-T1
Valid prediction for GlimmerHMM_glimmerT_41188-T1
Valid prediction for GlimmerHMM_glimmerT_41191-T1
Valid prediction for GlimmerHMM_glimmerT_41200-T1
Valid prediction for CodingQuarry_transcript_22213-T1
Valid prediction for snap_scaffold_17-snap.2491-T1
Valid prediction for snap_scaffold_17-snap.2506-T1
Valid prediction for CodingQuarry_transcript_22210-T1
Valid prediction for GlimmerHMM_glimmerT_41199-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14594, rend_intergenic: 11206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31089, rend_intergenic: 25927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40579, rend_intergenic: 38856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48294, rend_intergenic: 44674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50447, rend_intergenic: 48895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53550, rend_intergenic: 52258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58516, rend_intergenic: 53664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75948, rend_intergenic: 73091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108669, rend_intergenic: 106754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119080, rend_intergenic: 111979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 124016
-exon list size: 253


building trellis

0.4    
0.8    
1.2    
1.6    
2.0    
2.4    
2.7    
3.1    
3.5    
3.9    
4.3    
4.7    
5.1    
5.5    
5.9    
6.3    
6.7    
7.1    
7.5    
7.8    
8.2    
8.6    
9.0    
9.4    
9.8    
10.2    
10.6    
11.0    
11.4    
11.8    
12.2    
12.5    
12.9    
13.3    
13.7    
14.1    
14.5    
14.9    
15.3    
15.7    
16.1    
16.5    
16.9    
17.3    
17.6    
18.0    
18.4    
18.8    
19.2    
19.6    
20.0    
20.4    
20.8    
21.2    
21.6    
22.0    
22.4    
22.7    
23.1    
23.5    
23.9    
24.3    
24.7    
25.1    
25.5    
25.9    
26.3    
26.7    
27.1    
27.5    
27.8    
28.2    
28.6    
29.0    
29.4    
29.8    
30.2    
30.6    
31.0    
31.4    
31.8    
32.2    
32.5    
32.9    
33.3    
33.7    
34.1    
34.5    
34.9    
35.3    
35.7    
36.1    
36.5    
36.9    
37.3    
37.6    
38.0    
38.4    
38.8    
39.2    
39.6    
40.0    
40.4    
40.8    
41.2    
41.6    
42.0    
42.4    
42.7    
43.1    
43.5    
43.9    
44.3    
44.7    
45.1    
45.5    
45.9    
46.3    
46.7    
47.1    
47.5    
47.8    
48.2    
48.6    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.4    
51.8    
52.2    
52.5    
52.9    
53.3    
53.7    
54.1    
54.5    
54.9    
55.3    
55.7    
56.1    
56.5    
56.9    
57.3    
57.6    
58.0    
58.4    
58.8    
59.2    
59.6    
60.0    
60.4    
60.8    
61.2    
61.6    
62.0    
62.4    
62.7    
63.1    
63.5    
63.9    
64.3    
64.7    
65.1    
65.5    
65.9    
66.3    
66.7    
67.1    
67.5    
67.8    
68.2    
68.6    
69.0    
69.4    
69.8    
70.2    
70.6    
71.0    
71.4    
71.8    
72.2    
72.5    
72.9    
73.3    
73.7    
74.1    
74.5    
74.9    
75.3    
75.7    
76.1    
76.5    
76.9    
77.3    
77.6    
78.0    
78.4    
78.8    
79.2    
79.6    
80.0    
80.4    
80.8    
81.2    
81.6    
82.0    
82.4    
82.7    
83.1    
83.5    
83.9    
84.3    
84.7    
85.1    
85.5    
85.9    
86.3    
86.7    
87.1    
87.5    
87.8    
88.2    
88.6    
89.0    
89.4    
89.8    
90.2    
90.6    
91.0    
91.4    
91.8    
92.2    
92.5    
92.9    
93.3    
93.7    
94.1    
94.5    
94.9    
95.3    
95.7    
96.1    
96.5    
96.9    
97.3    
97.6    
98.0    
98.4    
98.8    
99.2    
99.6    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 14594, rend_intergenic: 11206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31089, rend_intergenic: 25927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40579, rend_intergenic: 38856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48294, rend_intergenic: 44674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50447, rend_intergenic: 48895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53550, rend_intergenic: 52258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58516, rend_intergenic: 53664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75948, rend_intergenic: 73091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108669, rend_intergenic: 106754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119080, rend_intergenic: 111979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 110894 - 124016
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support