-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_11793260-11996694

-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 snap_scaffold_2-snap.2251-T1
Valid prediction for Augustus_model.g3085.t1
Valid prediction for snap_scaffold_2-snap.2247-T1
Valid prediction for Augustus_model.g3081.t1
Valid prediction for snap_scaffold_2-snap.2280-T1
Couldn't classify 106892, 107470
Couldn't classify 110957, 111040
Sorry, prediction pasa_asmbl_24782.p1 fails validation.
(GCC)	 GG	106892-107470	GT	GCG
(GGA)	 AG	107610-107669	GT	GGG
(CTG)	 AG	107849-107919	GT	TTG
(TCT)	 AG	108071-108140	GT	GTG
(GTT)	 AG	108255-108321	GT	AGG
(ATG)	 AG	108433-108530	GT	AGG
(CCC)	 AG	108657-108734	GT	AGG
(GGG)	 AG	108913-109013	GT	AAG
(GCA)	 AG	109743-109832	GT	AGG
(CCT)	 AG	110060-110105	GT	AGG
(GAC)	 AG	110328-110469	GT	GGG
(ACT)	 AG	110563-110705	GT	AGG
(TAC)	 AG	110957-111040	GC	AGG
add_exon() Sorry, pasa_asmbl_24782.p1 108433-108530-initial-1 is invalid.
-recovered pasa_asmbl_24782.p1, initial, 108433, 108530
-recovered pasa_asmbl_24782.p1, internal, 107610, 107669
-recovered pasa_asmbl_24782.p1, internal, 107849, 107919
-recovered pasa_asmbl_24782.p1, internal, 108071, 108140
-recovered pasa_asmbl_24782.p1, internal, 108255, 108321
-recovered pasa_asmbl_24782.p1, internal, 108433, 108530
-recovered pasa_asmbl_24782.p1, internal, 108657, 108734
-recovered pasa_asmbl_24782.p1, internal, 108913, 109013
-recovered pasa_asmbl_24782.p1, internal, 109743, 109832
-recovered pasa_asmbl_24782.p1, internal, 110060, 110105
-recovered pasa_asmbl_24782.p1, internal, 110328, 110469
-recovered pasa_asmbl_24782.p1, internal, 110563, 110705
-recovered pasa_asmbl_24782.p1, internal, 110957, 111040
Valid prediction for snap_scaffold_2-snap.2252-T1
Valid prediction for snap_scaffold_2-snap.2258-T1
Valid prediction for HiQ_model.g3084.t1
Valid prediction for snap_scaffold_2-snap.2267-T1
Valid prediction for GlimmerHMM_glimmerT_4579-T1
Valid prediction for Augustus_model.g3086.t1
Valid prediction for HiQ_model.g3071.t1
Valid prediction for snap_scaffold_2-snap.2266-T1
Valid prediction for snap_scaffold_2-snap.2253-T1
Valid prediction for snap_scaffold_2-snap.2261-T1
Valid prediction for snap_scaffold_2-snap.2278-T1
Couldn't classify 105882, 106200
Couldn't classify 106734, 106750
Sorry, prediction pasa_asmbl_24781.p1 fails validation.
(GGA)	 TG	105882-106200	GT	AGG
(ATT)	 AG	106734-106750	CC	ACC
Valid prediction for GlimmerHMM_glimmerT_4573-T1
Valid prediction for GlimmerHMM_glimmerT_4566-T1
Valid prediction for snap_scaffold_2-snap.2259-T1
Valid prediction for snap_scaffold_2-snap.2270-T1
Valid prediction for GlimmerHMM_glimmerT_4586-T1
Valid prediction for Augustus_model.g3089.t1
Couldn't classify 1905, 2069
Sorry, prediction pasa_asmbl_24774.p1 fails validation.
(CCA)	 GC	1905-2069	GT	ACG
(CGT)	 AG	2442-2609	GG	GAG
-recovered pasa_asmbl_24774.p1, terminal, 2442, 2609
Valid prediction for snap_scaffold_2-snap.2256-T1
Valid prediction for snap_scaffold_2-snap.2263-T1
Valid prediction for snap_scaffold_2-snap.2275-T1
Valid prediction for GlimmerHMM_glimmerT_4568-T1
Valid prediction for Augustus_model.g3080.t1
Valid prediction for snap_scaffold_2-snap.2257-T1
Valid prediction for GlimmerHMM_glimmerT_4565-T1
Valid prediction for GlimmerHMM_glimmerT_4564-T1
Valid prediction for snap_scaffold_2-snap.2277-T1
Valid prediction for snap_scaffold_2-snap.2254-T1
Valid prediction for snap_scaffold_2-snap.2272-T1
Valid prediction for snap_scaffold_2-snap.2262-T1
Valid prediction for GlimmerHMM_glimmerT_4580-T1
Valid prediction for snap_scaffold_2-snap.2273-T1
Valid prediction for GlimmerHMM_glimmerT_4584-T1
Valid prediction for GlimmerHMM_glimmerT_4569-T1
Valid prediction for Augustus_model.g3074.t1
Valid prediction for Augustus_model.g3088.t1
Valid prediction for GlimmerHMM_glimmerT_4570-T1
Valid prediction for GlimmerHMM_glimmerT_4575-T1
Valid prediction for GlimmerHMM_glimmerT_4574-T1
Valid prediction for Augustus_model.g3073.t1
Valid prediction for GlimmerHMM_glimmerT_4582-T1
Couldn't classify 111489, 111854
Sorry, prediction pasa_asmbl_24784.p1 fails validation.
(ATA)	 GC	111489-111854	GA	AGG
Valid prediction for snap_scaffold_2-snap.2268-T1
Valid prediction for GlimmerHMM_glimmerT_4578-T1
Valid prediction for snap_scaffold_2-snap.2264-T1
Valid prediction for GlimmerHMM_glimmerT_4581-T1
Valid prediction for snap_scaffold_2-snap.2265-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_4571-T1
Valid prediction for GlimmerHMM_glimmerT_4577-T1
Valid prediction for snap_scaffold_2-snap.2249-T1
Valid prediction for Augustus_model.g3090.t1
Valid prediction for snap_scaffold_2-snap.2250-T1
Valid prediction for Augustus_model.g3087.t1
Valid prediction for GlimmerHMM_glimmerT_4583-T1
Valid prediction for Augustus_model.g3072.t1
Valid prediction for Augustus_model.g3077.t1
Valid prediction for Augustus_model.g3079.t1
Valid prediction for Augustus_model.g3076.t1
Valid prediction for GlimmerHMM_glimmerT_4588-T1
Valid prediction for GlimmerHMM_glimmerT_4576-T1
Valid prediction for Augustus_model.g3083.t1
Valid prediction for Augustus_model.g3082.t1
Valid prediction for snap_scaffold_2-snap.2279-T1
Valid prediction for Augustus_model.g3075.t1
Valid prediction for snap_scaffold_2-snap.2274-T1
Valid prediction for GlimmerHMM_glimmerT_4587-T1
Valid prediction for Augustus_model.g3078.t1
Valid prediction for GlimmerHMM_glimmerT_4567-T1
Valid prediction for GlimmerHMM_glimmerT_4585-T1
Valid prediction for snap_scaffold_2-snap.2248-T1
Couldn't classify 176615, 176684
Sorry, prediction pasa_asmbl_23460.p1 fails validation.
(GTC)	 AG	176615-176684	GT	AGG
(AGC)	 AG	177158-177328	GT	GGG
(GGC)	 AG	177543-177714	GT	CAG
(GCA)	 AG	177881-178181	GT	TGG
(GGC)	 AG	178318-178412	GT	AAG
(GTG)	 AG	178497-178638	GT	AGG
(TCT)	 AG	178804-178944	GT	AGG
(GAC)	 AG	179091-179218	GT	AGG
(GGT)	 AG	179303-179369	GT	AGG
(GCT)	 AG	179551-179664	GT	GGG
(ATC)	 AG	179926-180041	GT	AGG
(ACA)	 AG	180328-180445	GT	AGG
(GTG)	 AG	180744-180899	GT	CGG
(ACT)	 AG	181078-181347	GG	GAG
add_exon() Sorry, pasa_asmbl_23460.p1 179091-179218-terminal-2 is invalid.
-recovered pasa_asmbl_23460.p1, terminal, 179091, 179218
-recovered pasa_asmbl_23460.p1, terminal, 181078, 181347
-recovered pasa_asmbl_23460.p1, internal, 176615, 176684
-recovered pasa_asmbl_23460.p1, internal, 177158, 177328
-recovered pasa_asmbl_23460.p1, internal, 177543, 177714
-recovered pasa_asmbl_23460.p1, internal, 177881, 178181
-recovered pasa_asmbl_23460.p1, internal, 178318, 178412
-recovered pasa_asmbl_23460.p1, internal, 178497, 178638
-recovered pasa_asmbl_23460.p1, internal, 178804, 178944
-recovered pasa_asmbl_23460.p1, internal, 179091, 179218
-recovered pasa_asmbl_23460.p1, internal, 179303, 179369
-recovered pasa_asmbl_23460.p1, internal, 179551, 179664
-recovered pasa_asmbl_23460.p1, internal, 179926, 180041
-recovered pasa_asmbl_23460.p1, internal, 180328, 180445
-recovered pasa_asmbl_23460.p1, internal, 180744, 180899
Valid prediction for snap_scaffold_2-snap.2255-T1
Valid prediction for GlimmerHMM_glimmerT_4589-T1
Couldn't classify 138077, 138167
Sorry, prediction pasa_asmbl_23462.p1 fails validation.
(AGA)	 CC	138077-138167	GT	AGG
(GTG)	 AG	140209-140381	GT	AGG
(GGT)	 AG	142612-142824	GT	TTG
(GTG)	 AG	144732-144832	GT	AAG
(CAC)	 AG	147760-147863	GT	AGG
(TGA)	 AG	148162-148279	GT	AGG
(GGA)	 AG	148430-148609	GT	AGG
(GCC)	 AG	149867-149994	GT	CGG
(GCA)	 AG	151441-151569	GT	AGG
(AGT)	 AG	152448-153163	CG	AGC
add_exon() Sorry, pasa_asmbl_23462.p1 151441-151569-terminal-1 is invalid.
-recovered pasa_asmbl_23462.p1, terminal, 151441, 151569
-recovered pasa_asmbl_23462.p1, terminal, 152448, 153163
-recovered pasa_asmbl_23462.p1, internal, 140209, 140381
-recovered pasa_asmbl_23462.p1, internal, 142612, 142824
-recovered pasa_asmbl_23462.p1, internal, 144732, 144832
-recovered pasa_asmbl_23462.p1, internal, 147760, 147863
-recovered pasa_asmbl_23462.p1, internal, 148162, 148279
-recovered pasa_asmbl_23462.p1, internal, 148430, 148609
-recovered pasa_asmbl_23462.p1, internal, 149867, 149994
-recovered pasa_asmbl_23462.p1, internal, 151441, 151569
Valid prediction for snap_scaffold_2-snap.2269-T1
Valid prediction for GlimmerHMM_glimmerT_4572-T1
Valid prediction for snap_scaffold_2-snap.2260-T1
Valid prediction for snap_scaffold_2-snap.2271-T1
Valid prediction for snap_scaffold_2-snap.2276-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51985, rend_intergenic: 50273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62014, rend_intergenic: 53070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65145, rend_intergenic: 62539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99669, rend_intergenic: 80572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125154, rend_intergenic: 119218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126079, rend_intergenic: 126054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147922, rend_intergenic: 145398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157069, rend_intergenic: 155452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203435
-exon list size: 354


building trellis

0.3    
0.6    
0.8    
1.1    
1.4    
1.7    
2.0    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
3.9    
4.2    
4.5    
4.8    
5.1    
5.3    
5.6    
5.9    
6.2    
6.5    
6.7    
7.0    
7.3    
7.6    
7.9    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.8    
10.1    
10.4    
10.7    
11.0    
11.2    
11.5    
11.8    
12.1    
12.4    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.1    
17.4    
17.7    
18.0    
18.3    
18.5    
18.8    
19.1    
19.4    
19.7    
19.9    
20.2    
20.5    
20.8    
21.1    
21.3    
21.6    
21.9    
22.2    
22.5    
22.8    
23.0    
23.3    
23.6    
23.9    
24.2    
24.4    
24.7    
25.0    
25.3    
25.6    
25.8    
26.1    
26.4    
26.7    
27.0    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.3    
30.6    
30.9    
31.2    
31.5    
31.7    
32.0    
32.3    
32.6    
32.9    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.8    
35.1    
35.4    
35.7    
36.0    
36.2    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.8    
39.0    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
42.1    
42.4    
42.7    
43.0    
43.3    
43.5    
43.8    
44.1    
44.4    
44.7    
44.9    
45.2    
45.5    
45.8    
46.1    
46.3    
46.6    
46.9    
47.2    
47.5    
47.8    
48.0    
48.3    
48.6    
48.9    
49.2    
49.4    
49.7    
50.0    
50.3    
50.6    
50.8    
51.1    
51.4    
51.7    
52.0    
52.2    
52.5    
52.8    
53.1    
53.4    
53.7    
53.9    
54.2    
54.5    
54.8    
55.1    
55.3    
55.6    
55.9    
56.2    
56.5    
56.7    
57.0    
57.3    
57.6    
57.9    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
60.4    
60.7    
61.0    
61.2    
61.5    
61.8    
62.1    
62.4    
62.6    
62.9    
63.2    
63.5    
63.8    
64.0    
64.3    
64.6    
64.9    
65.2    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.1    
67.4    
67.7    
68.0    
68.3    
68.5    
68.8    
69.1    
69.4    
69.7    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.0    
73.3    
73.6    
73.9    
74.2    
74.4    
74.7    
75.0    
75.3    
75.6    
75.8    
76.1    
76.4    
76.7    
77.0    
77.2    
77.5    
77.8    
78.1    
78.4    
78.7    
78.9    
79.2    
79.5    
79.8    
80.1    
80.3    
80.6    
80.9    
81.2    
81.5    
81.7    
82.0    
82.3    
82.6    
82.9    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.6    
87.9    
88.2    
88.5    
88.8    
89.0    
89.3    
89.6    
89.9    
90.2    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.1    
92.4    
92.7    
93.0    
93.3    
93.5    
93.8    
94.1    
94.4    
94.7    
94.9    
95.2    
95.5    
95.8    
96.1    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.0    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 51985, rend_intergenic: 50273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62014, rend_intergenic: 53070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65145, rend_intergenic: 62539  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99669, rend_intergenic: 80572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125154, rend_intergenic: 119218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126079, rend_intergenic: 126054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147922, rend_intergenic: 145398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157069, rend_intergenic: 155452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support