-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_13051001-13234270

-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: +)Couldn't classify 128649, 128778
Couldn't classify 133077, 133108
Sorry, prediction pasa_asmbl_16747.p2 fails validation.
(CTG)	 AT	128649-128778	GT	AGG
(CTC)	 AG	130580-130690	GT	AGG
(GTC)	 AG	131460-131510	GT	AGG
(CAT)	 AG	133077-133108	GC	GGG
-recovered pasa_asmbl_16747.p2, internal, 130580, 130690
-recovered pasa_asmbl_16747.p2, internal, 131460, 131510
-recovered pasa_asmbl_16747.p2, internal, 133077, 133108
Valid prediction for snap_scaffold_16-snap.2479-T1
Valid prediction for snap_scaffold_16-snap.2480-T1
Valid prediction for snap_scaffold_16-snap.2487-T1
Valid prediction for GlimmerHMM_glimmerT_39302-T1
Valid prediction for CodingQuarry_transcript_20118-T1
Valid prediction for snap_scaffold_16-snap.2506-T1
Valid prediction for Augustus_model.g26225.t1
Valid prediction for snap_scaffold_16-snap.2482-T1
Valid prediction for snap_scaffold_16-snap.2477-T1
Valid prediction for snap_scaffold_16-snap.2489-T1
Valid prediction for snap_scaffold_16-snap.2475-T1
Valid prediction for GlimmerHMM_glimmerT_39309-T1
Valid prediction for Augustus_model.g26229.t1
Valid prediction for Augustus_model.g26230.t1
Valid prediction for snap_scaffold_16-snap.2515-T1
Valid prediction for snap_scaffold_16-snap.2503-T1
Valid prediction for snap_scaffold_16-snap.2504-T1
Valid prediction for snap_scaffold_16-snap.2474-T1
Valid prediction for GlimmerHMM_glimmerT_39306-T1
Couldn't classify 162530, 162568
Couldn't classify 163085, 163312
Sorry, prediction CodingQuarry_transcript_20119-T1 fails validation.
(ATG)	 TT	162530-162568	AT	ACA
(ACG)	 AC	163085-163312	GT	AGG
(GTG)	 AG	163534-163736	GT	AAG
(GTG)	 AG	164098-164336	GT	AGG
(GCC)	 AG	164541-164763	GT	AAG
(GGA)	 AG	165096-165328	GT	GGG
(ACT)	 AG	165664-165830	GT	CGG
(GGT)	 AG	167821-167886	GA	GAG
-recovered CodingQuarry_transcript_20119-T1, terminal, 167821, 167886
-recovered CodingQuarry_transcript_20119-T1, internal, 163534, 163736
-recovered CodingQuarry_transcript_20119-T1, internal, 164098, 164336
-recovered CodingQuarry_transcript_20119-T1, internal, 164541, 164763
-recovered CodingQuarry_transcript_20119-T1, internal, 165096, 165328
-recovered CodingQuarry_transcript_20119-T1, internal, 165664, 165830
Valid prediction for snap_scaffold_16-snap.2485-T1
Valid prediction for pasa_asmbl_16651.p1
Valid prediction for CodingQuarry_transcript_20117-T1
Valid prediction for GlimmerHMM_glimmerT_39297-T1
Valid prediction for GlimmerHMM_glimmerT_39298-T1
Valid prediction for snap_scaffold_16-snap.2501-T1
Valid prediction for GlimmerHMM_glimmerT_39292-T1
Valid prediction for snap_scaffold_16-snap.2490-T1
Valid prediction for GlimmerHMM_glimmerT_39294-T1
Valid prediction for snap_scaffold_16-snap.2509-T1
Valid prediction for GlimmerHMM_glimmerT_39305-T1
Valid prediction for snap_scaffold_16-snap.2507-T1
Valid prediction for Augustus_model.g26226.t1
Valid prediction for snap_scaffold_16-snap.2498-T1
Valid prediction for snap_scaffold_16-snap.2497-T1
Valid prediction for Augustus_model.g26227.t1
Couldn't classify 133607, 133846
Sorry, prediction pasa_asmbl_16646.p1 fails validation.
(GTC)	 GT	133607-133846	GT	AGG
(GTG)	 AG	133983-134079	GT	AGG
(ATC)	 AG	134191-134244	GT	CCG
(CTG)	 AG	134539-134825	GG	GAG
-recovered pasa_asmbl_16646.p1, terminal, 134539, 134825
-recovered pasa_asmbl_16646.p1, internal, 133983, 134079
-recovered pasa_asmbl_16646.p1, internal, 134191, 134244
Valid prediction for Augustus_model.g26224.t1
Valid prediction for GlimmerHMM_glimmerT_39312-T1
Valid prediction for snap_scaffold_16-snap.2493-T1
Valid prediction for HiQ_model.g26231.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 Augustus_model.g26222.t1
Valid prediction for snap_scaffold_16-snap.2473-T1
Valid prediction for GlimmerHMM_glimmerT_39307-T1
Valid prediction for snap_scaffold_16-snap.2483-T1
Valid prediction for snap_scaffold_16-snap.2484-T1
Valid prediction for Augustus_model.g26221.t1
Valid prediction for Augustus_model.g26223.t1
Valid prediction for snap_scaffold_16-snap.2508-T1
Valid prediction for GlimmerHMM_glimmerT_39301-T1
Valid prediction for GlimmerHMM_glimmerT_39308-T1
Valid prediction for GlimmerHMM_glimmerT_39293-T1
Valid prediction for snap_scaffold_16-snap.2502-T1
Valid prediction for snap_scaffold_16-snap.2511-T1
Valid prediction for snap_scaffold_16-snap.2478-T1
Valid prediction for snap_scaffold_16-snap.2492-T1
Valid prediction for snap_scaffold_16-snap.2499-T1
Valid prediction for snap_scaffold_16-snap.2486-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g26232.t1
Valid prediction for GlimmerHMM_glimmerT_39311-T1
Valid prediction for snap_scaffold_16-snap.2495-T1
Valid prediction for snap_scaffold_16-snap.2488-T1
Valid prediction for snap_scaffold_16-snap.2476-T1
Valid prediction for snap_scaffold_16-snap.2481-T1
Valid prediction for GlimmerHMM_glimmerT_39296-T1
Valid prediction for snap_scaffold_16-snap.2510-T1
Valid prediction for snap_scaffold_16-snap.2491-T1
Valid prediction for snap_scaffold_16-snap.2512-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.2505-T1
Valid prediction for GlimmerHMM_glimmerT_39310-T1
Valid prediction for GlimmerHMM_glimmerT_39299-T1
Valid prediction for Augustus_model.g26228.t1
Valid prediction for GlimmerHMM_glimmerT_39303-T1
Valid prediction for snap_scaffold_16-snap.2513-T1
Valid prediction for snap_scaffold_16-snap.2494-T1
Valid prediction for snap_scaffold_16-snap.2500-T1
Valid prediction for snap_scaffold_16-snap.2514-T1
Valid prediction for GlimmerHMM_glimmerT_39300-T1
Valid prediction for snap_scaffold_16-snap.2496-T1
Valid prediction for GlimmerHMM_glimmerT_39304-T1
Valid prediction for GlimmerHMM_glimmerT_39295-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7568, rend_intergenic: 3716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14340, rend_intergenic: 8942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20013, rend_intergenic: 15741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27335, rend_intergenic: 21071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32246, rend_intergenic: 28889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52717, rend_intergenic: 50825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66478, rend_intergenic: 63015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70104, rend_intergenic: 67333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80523, rend_intergenic: 73960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83377, rend_intergenic: 80826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102966, rend_intergenic: 83457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107007, rend_intergenic: 102984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125836, rend_intergenic: 109772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127813, rend_intergenic: 126104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133249, rend_intergenic: 127932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152175, rend_intergenic: 145802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167886, rend_intergenic: 156858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182176, rend_intergenic: 178294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183270
-exon list size: 307


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.6    
3.9    
4.2    
4.5    
4.9    
5.2    
5.5    
5.8    
6.1    
6.5    
6.8    
7.1    
7.4    
7.8    
8.1    
8.4    
8.7    
9.1    
9.4    
9.7    
10.0    
10.4    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.9    
16.2    
16.5    
16.8    
17.2    
17.5    
17.8    
18.1    
18.4    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.4    
21.7    
22.0    
22.3    
22.7    
23.0    
23.3    
23.6    
23.9    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.9    
27.2    
27.5    
27.8    
28.2    
28.5    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.7    
31.1    
31.4    
31.7    
32.0    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
35.0    
35.3    
35.6    
35.9    
36.2    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.2    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.4    
43.7    
44.0    
44.3    
44.7    
45.0    
45.3    
45.6    
46.0    
46.3    
46.6    
46.9    
47.2    
47.6    
47.9    
48.2    
48.5    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.5    
51.8    
52.1    
52.4    
52.8    
53.1    
53.4    
53.7    
54.0    
54.4    
54.7    
55.0    
55.3    
55.7    
56.0    
56.3    
56.6    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.8    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.8    
64.1    
64.4    
64.7    
65.0    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
68.0    
68.3    
68.6    
68.9    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.2    
72.5    
72.8    
73.1    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.1    
76.4    
76.7    
77.0    
77.3    
77.7    
78.0    
78.3    
78.6    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.6    
81.9    
82.2    
82.5    
82.8    
83.2    
83.5    
83.8    
84.1    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.6    
90.0    
90.3    
90.6    
90.9    
91.3    
91.6    
91.9    
92.2    
92.6    
92.9    
93.2    
93.5    
93.9    
94.2    
94.5    
94.8    
95.1    
95.5    
95.8    
96.1    
96.4    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 7568, rend_intergenic: 3716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14340, rend_intergenic: 8942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20013, rend_intergenic: 15741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27335, rend_intergenic: 21071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32246, rend_intergenic: 28889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52717, rend_intergenic: 50825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66478, rend_intergenic: 63015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70104, rend_intergenic: 67333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80523, rend_intergenic: 73960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83377, rend_intergenic: 80826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102966, rend_intergenic: 83457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107007, rend_intergenic: 102984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125836, rend_intergenic: 109772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127813, rend_intergenic: 126104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133249, rend_intergenic: 127932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152175, rend_intergenic: 145802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167886, rend_intergenic: 156858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182176, rend_intergenic: 178294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support