-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_12041226-12186204

-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_22996-T1
Valid prediction for HiQ_model.g15336.t1
Valid prediction for snap_scaffold_9-snap.2365-T1
Couldn't classify 140469, 140531
Sorry, prediction pasa_asmbl_54419.p1 fails validation.
(CTG)	 AA	140469-140531	GT	ATG
(AAA)	 AG	140645-140785	GT	AGG
(TAC)	 AG	141011-141092	GT	TGG
(GCT)	 AG	141268-141361	GT	AGG
(GTC)	 AG	141572-141713	GT	AGG
(ATC)	 AG	141895-142002	GT	AGG
(ATC)	 AG	142384-142449	GT	AGG
(GTG)	 AG	142679-142765	GT	AGG
(GCC)	 AG	142929-143249	AG	AGA
-recovered pasa_asmbl_54419.p1, terminal, 142929, 143249
-recovered pasa_asmbl_54419.p1, internal, 140645, 140785
-recovered pasa_asmbl_54419.p1, internal, 141011, 141092
-recovered pasa_asmbl_54419.p1, internal, 141268, 141361
-recovered pasa_asmbl_54419.p1, internal, 141572, 141713
-recovered pasa_asmbl_54419.p1, internal, 141895, 142002
-recovered pasa_asmbl_54419.p1, internal, 142384, 142449
-recovered pasa_asmbl_54419.p1, internal, 142679, 142765
Valid prediction for snap_scaffold_9-snap.2373-T1
Valid prediction for GlimmerHMM_glimmerT_23007-T1
Valid prediction for GlimmerHMM_glimmerT_22982-T1
Valid prediction for GlimmerHMM_glimmerT_22983-T1
Couldn't classify 120006, 120308
Sorry, prediction pasa_asmbl_54681.p1 fails validation.
(AAG)	 AC	120006-120308	CT	ACC
Valid prediction for Augustus_model.g15345.t1
Valid prediction for CodingQuarry_transcript_62358-T1
Valid prediction for snap_scaffold_9-snap.2363-T1
Valid prediction for GlimmerHMM_glimmerT_22984-T1
Valid prediction for snap_scaffold_9-snap.2381-T1
Valid prediction for snap_scaffold_9-snap.2393-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_22997-T1
Valid prediction for CodingQuarry_transcript_62357-T1
Valid prediction for GlimmerHMM_glimmerT_22992-T1
Valid prediction for Augustus_model.g15341.t1
Valid prediction for snap_scaffold_9-snap.2386-T1
Valid prediction for snap_scaffold_9-snap.2391-T1
Valid prediction for snap_scaffold_9-snap.2385-T1
Valid prediction for snap_scaffold_9-snap.2396-T1
Valid prediction for HiQ_model.g15334.t1
Valid prediction for snap_scaffold_9-snap.2397-T1
Valid prediction for snap_scaffold_9-snap.2377-T1
Valid prediction for Augustus_model.g15342.t1
Couldn't classify 138611, 138835
Sorry, prediction pasa_asmbl_54417.p2 fails validation.
(ATG)	 TG	138182-138358	GT	CGG
(CAG)	 AG	138611-138835	AC	ACA
-recovered pasa_asmbl_54417.p2, initial, 138182, 138358
Valid prediction for snap_scaffold_9-snap.2362-T1
Valid prediction for GlimmerHMM_glimmerT_22999-T1
Valid prediction for HiQ_model.g15335.t1
Valid prediction for snap_scaffold_9-snap.2387-T1
Valid prediction for snap_scaffold_9-snap.2378-T1
Valid prediction for GlimmerHMM_glimmerT_23006-T1
Valid prediction for Augustus_model.g15331.t1
Valid prediction for snap_scaffold_9-snap.2372-T1
Valid prediction for Augustus_model.g15338.t1
Valid prediction for GlimmerHMM_glimmerT_23003-T1
Valid prediction for snap_scaffold_9-snap.2370-T1
Valid prediction for snap_scaffold_9-snap.2380-T1
Valid prediction for GlimmerHMM_glimmerT_22993-T1
Valid prediction for GlimmerHMM_glimmerT_22994-T1
Valid prediction for pasa_asmbl_54408.p1
Valid prediction for GlimmerHMM_glimmerT_22990-T1
Valid prediction for CodingQuarry_transcript_62359-T1
Valid prediction for Augustus_model.g15325.t1
Valid prediction for GlimmerHMM_glimmerT_23002-T1
Valid prediction for pasa_asmbl_54409.p1
Valid prediction for snap_scaffold_9-snap.2390-T1
Valid prediction for snap_scaffold_9-snap.2376-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_9-snap.2392-T1
Valid prediction for GlimmerHMM_glimmerT_22986-T1
Valid prediction for GlimmerHMM_glimmerT_23001-T1
Valid prediction for pasa_asmbl_55345.p1
Valid prediction for snap_scaffold_9-snap.2395-T1
Valid prediction for snap_scaffold_9-snap.2383-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2389-T1
Valid prediction for GlimmerHMM_glimmerT_23005-T1
Valid prediction for snap_scaffold_9-snap.2369-T1
Valid prediction for Augustus_model.g15327.t1
Valid prediction for GlimmerHMM_glimmerT_22985-T1
Valid prediction for CodingQuarry_transcript_62354-T1
Valid prediction for snap_scaffold_9-snap.2388-T1
Valid prediction for HiQ_model.g15337.t1
Valid prediction for CodingQuarry_transcript_62362-T1
Valid prediction for GlimmerHMM_glimmerT_23000-T1
Valid prediction for snap_scaffold_9-snap.2371-T1
Valid prediction for snap_scaffold_9-snap.2364-T1
Valid prediction for CodingQuarry_transcript_62352-T1
Valid prediction for snap_scaffold_9-snap.2374-T1
Valid prediction for HiQ_model.g15333.t1
Valid prediction for CodingQuarry_transcript_62356-T1
Valid prediction for GlimmerHMM_glimmerT_22989-T1
Valid prediction for snap_scaffold_9-snap.2368-T1
Valid prediction for Augustus_model.g15332.t1
Valid prediction for snap_scaffold_9-snap.2379-T1
Valid prediction for pasa_asmbl_55353.p1
Valid prediction for Augustus_model.g15344.t1
Valid prediction for Augustus_model.g15339.t1
Valid prediction for CodingQuarry_transcript_62353-T1
Valid prediction for GlimmerHMM_glimmerT_22995-T1
Valid prediction for GlimmerHMM_glimmerT_22987-T1
Valid prediction for snap_scaffold_9-snap.2382-T1
Valid prediction for Augustus_model.g15328.t1
Valid prediction for GlimmerHMM_glimmerT_22998-T1
Valid prediction for CodingQuarry_transcript_62360-T1
Valid prediction for HiQ_model.g15326.t1
Valid prediction for GlimmerHMM_glimmerT_23004-T1
Valid prediction for GlimmerHMM_glimmerT_22991-T1
Couldn't classify 28088, 28213
Sorry, prediction pasa_asmbl_55357.p1 fails validation.
(CAA)	 GG	28088-28213	GT	TGG
(CCA)	 AG	28321-28375	GT	AGG
(TGT)	 AG	28742-28805	GT	AGG
(GAA)	 AG	29004-29109	GT	GGG
(GGC)	 AG	29210-29257	GT	TTG
(GAA)	 AG	29386-29494	GT	AGG
(GTT)	 AG	29785-29830	GT	AGG
(GTC)	 AG	29964-30051	GT	AGG
(GTG)	 AG	30139-30251	GT	AGG
(AGT)	 AG	30335-30428	GT	AGG
(ATC)	 AG	30524-30616	GT	CGG
(GTG)	 AG	30770-30835	GT	AGG
(GAG)	 AG	30965-31105	TA	GAT
-recovered pasa_asmbl_55357.p1, terminal, 30965, 31105
-recovered pasa_asmbl_55357.p1, internal, 28321, 28375
-recovered pasa_asmbl_55357.p1, internal, 28742, 28805
-recovered pasa_asmbl_55357.p1, internal, 29004, 29109
-recovered pasa_asmbl_55357.p1, internal, 29210, 29257
-recovered pasa_asmbl_55357.p1, internal, 29386, 29494
-recovered pasa_asmbl_55357.p1, internal, 29785, 29830
-recovered pasa_asmbl_55357.p1, internal, 29964, 30051
-recovered pasa_asmbl_55357.p1, internal, 30139, 30251
-recovered pasa_asmbl_55357.p1, internal, 30335, 30428
-recovered pasa_asmbl_55357.p1, internal, 30524, 30616
-recovered pasa_asmbl_55357.p1, internal, 30770, 30835
Valid prediction for snap_scaffold_9-snap.2394-T1
Valid prediction for Augustus_model.g15330.t1
Valid prediction for GlimmerHMM_glimmerT_22988-T1
Valid prediction for HiQ_model.g15340.t1
Valid prediction for pasa_asmbl_55355.p1
Valid prediction for snap_scaffold_9-snap.2367-T1
Valid prediction for CodingQuarry_transcript_62361-T1
Valid prediction for pasa_asmbl_55349.p1
Valid prediction for snap_scaffold_9-snap.2384-T1
Valid prediction for CodingQuarry_transcript_62355-T1
Valid prediction for Augustus_model.g15329.t1
Valid prediction for snap_scaffold_9-snap.2375-T1
Valid prediction for snap_scaffold_9-snap.2361-T1
Valid prediction for snap_scaffold_9-snap.2366-T1
Valid prediction for Augustus_model.g15343.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8546, rend_intergenic: 7390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15374, rend_intergenic: 10463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21712, rend_intergenic: 19805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43313, rend_intergenic: 39441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50335, rend_intergenic: 47824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64323, rend_intergenic: 51962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86296, rend_intergenic: 79142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103677, rend_intergenic: 100887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111718, rend_intergenic: 109036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128579, rend_intergenic: 124947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132497, rend_intergenic: 128924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 144979
-exon list size: 355


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    
3.6    
3.9    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.9    
6.2    
6.4    
6.7    
7.0    
7.3    
7.6    
7.8    
8.1    
8.4    
8.7    
9.0    
9.2    
9.5    
9.8    
10.1    
10.4    
10.6    
10.9    
11.2    
11.5    
11.8    
12.0    
12.3    
12.6    
12.9    
13.2    
13.4    
13.7    
14.0    
14.3    
14.6    
14.8    
15.1    
15.4    
15.7    
16.0    
16.2    
16.5    
16.8    
17.1    
17.4    
17.6    
17.9    
18.2    
18.5    
18.8    
19.0    
19.3    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.3    
21.6    
21.8    
22.1    
22.4    
22.7    
23.0    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.3    
26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.9    
29.1    
29.4    
29.7    
30.0    
30.3    
30.5    
30.8    
31.1    
31.4    
31.7    
31.9    
32.2    
32.5    
32.8    
33.1    
33.3    
33.6    
33.9    
34.2    
34.5    
34.7    
35.0    
35.3    
35.6    
35.9    
36.1    
36.4    
36.7    
37.0    
37.3    
37.5    
37.8    
38.1    
38.4    
38.7    
38.9    
39.2    
39.5    
39.8    
40.1    
40.3    
40.6    
40.9    
41.2    
41.5    
41.7    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.3    
44.5    
44.8    
45.1    
45.4    
45.7    
45.9    
46.2    
46.5    
46.8    
47.1    
47.3    
47.6    
47.9    
48.2    
48.5    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.5    
51.8    
52.1    
52.4    
52.7    
52.9    
53.2    
53.5    
53.8    
54.1    
54.3    
54.6    
54.9    
55.2    
55.5    
55.7    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.3    
58.5    
58.8    
59.1    
59.4    
59.7    
59.9    
60.2    
60.5    
60.8    
61.1    
61.3    
61.6    
61.9    
62.2    
62.5    
62.7    
63.0    
63.3    
63.6    
63.9    
64.1    
64.4    
64.7    
65.0    
65.3    
65.5    
65.8    
66.1    
66.4    
66.7    
66.9    
67.2    
67.5    
67.8    
68.1    
68.3    
68.6    
68.9    
69.2    
69.5    
69.7    
70.0    
70.3    
70.6    
70.9    
71.1    
71.4    
71.7    
72.0    
72.3    
72.5    
72.8    
73.1    
73.4    
73.7    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.0    
77.3    
77.6    
77.9    
78.2    
78.4    
78.7    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.7    
81.0    
81.2    
81.5    
81.8    
82.1    
82.4    
82.6    
82.9    
83.2    
83.5    
83.8    
84.0    
84.3    
84.6    
84.9    
85.2    
85.4    
85.7    
86.0    
86.3    
86.6    
86.8    
87.1    
87.4    
87.7    
88.0    
88.2    
88.5    
88.8    
89.1    
89.4    
89.6    
89.9    
90.2    
90.5    
90.8    
91.0    
91.3    
91.6    
91.9    
92.2    
92.4    
92.7    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.1    
96.4    
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 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 8546, rend_intergenic: 7390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15374, rend_intergenic: 10463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21712, rend_intergenic: 19805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43313, rend_intergenic: 39441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50335, rend_intergenic: 47824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64323, rend_intergenic: 51962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86296, rend_intergenic: 79142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103677, rend_intergenic: 100887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111718, rend_intergenic: 109036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128579, rend_intergenic: 124947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132497, rend_intergenic: 128924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support