-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_9795464-10002315

-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_59433-T1
Valid prediction for snap_scaffold_28-snap.2222-T1
Valid prediction for snap_scaffold_28-snap.2224-T1
Valid prediction for Augustus_model.g39366.t1
Valid prediction for snap_scaffold_28-snap.2205-T1
Valid prediction for snap_scaffold_28-snap.2214-T1
Couldn't classify 11266, 12645
Sorry, prediction pasa_asmbl_37811.p1 fails validation.
(GCA)	 CA	11266-12645	AC	GAA
Valid prediction for snap_scaffold_28-snap.2207-T1
Valid prediction for GlimmerHMM_glimmerT_59432-T1
Valid prediction for snap_scaffold_28-snap.2186-T1
Valid prediction for GlimmerHMM_glimmerT_59425-T1
Valid prediction for GlimmerHMM_glimmerT_59434-T1
Valid prediction for snap_scaffold_28-snap.2215-T1
Valid prediction for snap_scaffold_28-snap.2198-T1
Valid prediction for snap_scaffold_28-snap.2190-T1
Valid prediction for snap_scaffold_28-snap.2203-T1
Couldn't classify 13473, 13517
Couldn't classify 13542, 13742
Sorry, prediction CodingQuarry_transcript_43771-T1 fails validation.
(ATG)	 TT	13473-13517	AT	ACA
(ATC)	 AC	13542-13742	CT	GAC
Valid prediction for Augustus_model.g39369.t1
Valid prediction for snap_scaffold_28-snap.2209-T1
Valid prediction for GlimmerHMM_glimmerT_59428-T1
Valid prediction for snap_scaffold_28-snap.2187-T1
Valid prediction for snap_scaffold_28-snap.2197-T1
Valid prediction for GlimmerHMM_glimmerT_59426-T1
Valid prediction for GlimmerHMM_glimmerT_59427-T1
Valid prediction for snap_scaffold_28-snap.2195-T1
Valid prediction for snap_scaffold_28-snap.2202-T1
Valid prediction for GlimmerHMM_glimmerT_59424-T1
Valid prediction for snap_scaffold_28-snap.2220-T1
Valid prediction for snap_scaffold_28-snap.2185-T1
Valid prediction for snap_scaffold_28-snap.2218-T1
Valid prediction for Augustus_model.g39374.t1
Valid prediction for snap_scaffold_28-snap.2226-T1
Valid prediction for GlimmerHMM_glimmerT_59422-T1
Valid prediction for GlimmerHMM_glimmerT_59421-T1
Valid prediction for snap_scaffold_28-snap.2193-T1
Valid prediction for snap_scaffold_28-snap.2206-T1
Valid prediction for snap_scaffold_28-snap.2212-T1
Valid prediction for Augustus_model.g39373.t1
Valid prediction for snap_scaffold_28-snap.2211-T1
Valid prediction for GlimmerHMM_glimmerT_59430-T1
Valid prediction for snap_scaffold_28-snap.2200-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_59431-T1
Valid prediction for snap_scaffold_28-snap.2216-T1
Valid prediction for snap_scaffold_28-snap.2208-T1
Couldn't classify 190233, 190424
Sorry, prediction pasa_asmbl_38532.p1 fails validation.
(TAC)	 AG	190233-190424	GT	AGG
(GTA)	 AG	190639-190729	GT	AGG
(GCC)	 AG	191080-191222	GA	AGG
-recovered pasa_asmbl_38532.p1, terminal, 191080, 191222
-recovered pasa_asmbl_38532.p1, internal, 190233, 190424
-recovered pasa_asmbl_38532.p1, internal, 190639, 190729
Couldn't classify 188596, 188751
Sorry, prediction pasa_asmbl_38533.p1 fails validation.
(ATG)	 AA	187291-187351	GT	AGG
(TGC)	 AG	187789-188011	GT	AGG
(CAT)	 AG	188280-188442	GT	AGG
(GTG)	 AG	188596-188751	GT	ACG
-recovered pasa_asmbl_38533.p1, initial, 187291, 187351
-recovered pasa_asmbl_38533.p1, internal, 187789, 188011
-recovered pasa_asmbl_38533.p1, internal, 188280, 188442
-recovered pasa_asmbl_38533.p1, internal, 188596, 188751
Valid prediction for GlimmerHMM_glimmerT_59423-T1
Valid prediction for snap_scaffold_28-snap.2219-T1
Valid prediction for GlimmerHMM_glimmerT_59420-T1
Valid prediction for snap_scaffold_28-snap.2196-T1
Valid prediction for snap_scaffold_28-snap.2189-T1
Valid prediction for snap_scaffold_28-snap.2225-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.2210-T1
Valid prediction for Augustus_model.g39371.t1
Couldn't classify 48249, 48322
Couldn't classify 52339, 52374
Sorry, prediction pasa_asmbl_38535.p1 fails validation.
(AGC)	 CC	48249-48322	GT	AGG
(TTA)	 AG	48559-48640	GT	AGG
(GCC)	 AG	50183-50287	GT	AGG
(GCA)	 AG	50401-50469	GT	AGG
(CTT)	 AG	50689-50769	GT	CAG
(ATC)	 AG	52339-52374	GA	TGG
-recovered pasa_asmbl_38535.p1, internal, 48559, 48640
-recovered pasa_asmbl_38535.p1, internal, 50183, 50287
-recovered pasa_asmbl_38535.p1, internal, 50401, 50469
-recovered pasa_asmbl_38535.p1, internal, 50689, 50769
Valid prediction for snap_scaffold_28-snap.2217-T1
Valid prediction for snap_scaffold_28-snap.2204-T1
Valid prediction for snap_scaffold_28-snap.2191-T1
Valid prediction for snap_scaffold_28-snap.2221-T1
Valid prediction for Augustus_model.g39368.t1
Valid prediction for Augustus_model.g39370.t1
Valid prediction for GlimmerHMM_glimmerT_59419-T1
Valid prediction for snap_scaffold_28-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_59429-T1
Valid prediction for snap_scaffold_28-snap.2213-T1
Valid prediction for Augustus_model.g39367.t1
Valid prediction for snap_scaffold_28-snap.2223-T1
Valid prediction for snap_scaffold_28-snap.2201-T1
Valid prediction for snap_scaffold_28-snap.2188-T1
Valid prediction for snap_scaffold_28-snap.2194-T1
Valid prediction for snap_scaffold_28-snap.2192-T1
Valid prediction for Augustus_model.g39372.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31550, rend_intergenic: 23588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48207, rend_intergenic: 42563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61809, rend_intergenic: 59285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67055, rend_intergenic: 65834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75438, rend_intergenic: 70223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81256, rend_intergenic: 77593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100534, rend_intergenic: 90400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125003, rend_intergenic: 116698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146775, rend_intergenic: 136174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170621, rend_intergenic: 168647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176042, rend_intergenic: 174589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198152, rend_intergenic: 196331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206852
-exon list size: 237


building trellis

0.4    
0.8    
1.3    
1.7    
2.1    
2.5    
2.9    
3.3    
3.8    
4.2    
4.6    
5.0    
5.4    
5.9    
6.3    
6.7    
7.1    
7.5    
7.9    
8.4    
8.8    
9.2    
9.6    
10.0    
10.5    
10.9    
11.3    
11.7    
12.1    
12.6    
13.0    
13.4    
13.8    
14.2    
14.6    
15.1    
15.5    
15.9    
16.3    
16.7    
17.2    
17.6    
18.0    
18.4    
18.8    
19.2    
19.7    
20.1    
20.5    
20.9    
21.3    
21.8    
22.2    
22.6    
23.0    
23.4    
23.8    
24.3    
24.7    
25.1    
25.5    
25.9    
26.4    
26.8    
27.2    
27.6    
28.0    
28.5    
28.9    
29.3    
29.7    
30.1    
30.5    
31.0    
31.4    
31.8    
32.2    
32.6    
33.1    
33.5    
33.9    
34.3    
34.7    
35.1    
35.6    
36.0    
36.4    
36.8    
37.2    
37.7    
38.1    
38.5    
38.9    
39.3    
39.7    
40.2    
40.6    
41.0    
41.4    
41.8    
42.3    
42.7    
43.1    
43.5    
43.9    
44.4    
44.8    
45.2    
45.6    
46.0    
46.4    
46.9    
47.3    
47.7    
48.1    
48.5    
49.0    
49.4    
49.8    
50.2    
50.6    
51.0    
51.5    
51.9    
52.3    
52.7    
53.1    
53.6    
54.0    
54.4    
54.8    
55.2    
55.6    
56.1    
56.5    
56.9    
57.3    
57.7    
58.2    
58.6    
59.0    
59.4    
59.8    
60.3    
60.7    
61.1    
61.5    
61.9    
62.3    
62.8    
63.2    
63.6    
64.0    
64.4    
64.9    
65.3    
65.7    
66.1    
66.5    
66.9    
67.4    
67.8    
68.2    
68.6    
69.0    
69.5    
69.9    
70.3    
70.7    
71.1    
71.5    
72.0    
72.4    
72.8    
73.2    
73.6    
74.1    
74.5    
74.9    
75.3    
75.7    
76.2    
76.6    
77.0    
77.4    
77.8    
78.2    
78.7    
79.1    
79.5    
79.9    
80.3    
80.8    
81.2    
81.6    
82.0    
82.4    
82.8    
83.3    
83.7    
84.1    
84.5    
84.9    
85.4    
85.8    
86.2    
86.6    
87.0    
87.4    
87.9    
88.3    
88.7    
89.1    
89.5    
90.0    
90.4    
90.8    
91.2    
91.6    
92.1    
92.5    
92.9    
93.3    
93.7    
94.1    
94.6    
95.0    
95.4    
95.8    
96.2    
96.7    
97.1    
97.5    
97.9    
98.3    
98.7    
99.2    
99.6    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 31550, rend_intergenic: 23588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48207, rend_intergenic: 42563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61809, rend_intergenic: 59285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67055, rend_intergenic: 65834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75438, rend_intergenic: 70223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81256, rend_intergenic: 77593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100534, rend_intergenic: 90400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125003, rend_intergenic: 116698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146775, rend_intergenic: 136174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170621, rend_intergenic: 168647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176042, rend_intergenic: 174589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198152, rend_intergenic: 196331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support