-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_9551646-9776739

-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_25239-T1
Valid prediction for snap_scaffold_10-snap.1893-T1
Valid prediction for snap_scaffold_10-snap.1872-T1
Valid prediction for GlimmerHMM_glimmerT_25233-T1
Valid prediction for GlimmerHMM_glimmerT_25225-T1
Valid prediction for Augustus_model.g16809.t1
Valid prediction for GlimmerHMM_glimmerT_25250-T1
Couldn't classify 2707, 2781
Sorry, prediction pasa_asmbl_3402.p1 fails validation.
(TGC)	 AG	2707-2781	GT	AGG
(GAA)	 AG	3168-3216	GT	AGG
(ACC)	 AG	3352-3468	GT	AGG
(GGA)	 AG	3729-3935	GT	AGG
(GAG)	 AG	5454-5590	CC	AAC
-recovered pasa_asmbl_3402.p1, terminal, 5454, 5590
-recovered pasa_asmbl_3402.p1, internal, 2707, 2781
-recovered pasa_asmbl_3402.p1, internal, 3168, 3216
-recovered pasa_asmbl_3402.p1, internal, 3352, 3468
-recovered pasa_asmbl_3402.p1, internal, 3729, 3935
Valid prediction for GlimmerHMM_glimmerT_25247-T1
Valid prediction for GlimmerHMM_glimmerT_25234-T1
Valid prediction for snap_scaffold_10-snap.1855-T1
Valid prediction for Augustus_model.g16801.t1
Valid prediction for snap_scaffold_10-snap.1859-T1
Valid prediction for Augustus_model.g16802.t1
Valid prediction for GlimmerHMM_glimmerT_25226-T1
Valid prediction for snap_scaffold_10-snap.1880-T1
Valid prediction for GlimmerHMM_glimmerT_25231-T1
Valid prediction for GlimmerHMM_glimmerT_25232-T1
Valid prediction for snap_scaffold_10-snap.1857-T1
Valid prediction for GlimmerHMM_glimmerT_25241-T1
Valid prediction for snap_scaffold_10-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_25246-T1
Valid prediction for snap_scaffold_10-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_25229-T1
Valid prediction for Augustus_model.g16810.t1
Valid prediction for snap_scaffold_10-snap.1885-T1
Valid prediction for Augustus_model.g16799.t1
Valid prediction for snap_scaffold_10-snap.1889-T1
Valid prediction for snap_scaffold_10-snap.1870-T1
Valid prediction for snap_scaffold_10-snap.1891-T1
Valid prediction for snap_scaffold_10-snap.1890-T1
Valid prediction for GlimmerHMM_glimmerT_25227-T1
Valid prediction for GlimmerHMM_glimmerT_25238-T1
Valid prediction for GlimmerHMM_glimmerT_25223-T1
Valid prediction for GlimmerHMM_glimmerT_25243-T1
Valid prediction for Augustus_model.g16807.t1
Valid prediction for snap_scaffold_10-snap.1867-T1
Valid prediction for snap_scaffold_10-snap.1883-T1
Valid prediction for Augustus_model.g16806.t1
Valid prediction for snap_scaffold_10-snap.1882-T1
Valid prediction for GlimmerHMM_glimmerT_25249-T1
Valid prediction for GlimmerHMM_glimmerT_25242-T1
Valid prediction for GlimmerHMM_glimmerT_25230-T1
Valid prediction for snap_scaffold_10-snap.1862-T1
Valid prediction for snap_scaffold_10-snap.1887-T1
Valid prediction for snap_scaffold_10-snap.1879-T1
Valid prediction for Augustus_model.g16800.t1
Valid prediction for GlimmerHMM_glimmerT_25228-T1
Valid prediction for snap_scaffold_10-snap.1865-T1
Valid prediction for Augustus_model.g16808.t1
Valid prediction for snap_scaffold_10-snap.1871-T1
Valid prediction for GlimmerHMM_glimmerT_25244-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_10-snap.1858-T1
Valid prediction for CodingQuarry_transcript_5539-T1
Valid prediction for snap_scaffold_10-snap.1864-T1
Couldn't classify 91265, 91327
Couldn't classify 91706, 91740
Sorry, prediction CodingQuarry_transcript_5541-T1 fails validation.
(ATG)	 CA	87115-87466	GT	AGG
(GTA)	 AG	89401-89552	GT	GGG
(AAA)	 AG	89744-89824	GT	AGG
(CTT)	 AG	90040-90159	GT	AGG
(GTG)	 AG	90251-90382	GT	AGG
(GTG)	 AG	90578-90731	GT	AGG
(ACC)	 AG	91265-91327	TG	GGT
(ACA)	 AC	91706-91740	AA	AGA
-recovered CodingQuarry_transcript_5541-T1, initial, 87115, 87466
-recovered CodingQuarry_transcript_5541-T1, internal, 89401, 89552
-recovered CodingQuarry_transcript_5541-T1, internal, 89744, 89824
-recovered CodingQuarry_transcript_5541-T1, internal, 90040, 90159
-recovered CodingQuarry_transcript_5541-T1, internal, 90251, 90382
-recovered CodingQuarry_transcript_5541-T1, internal, 90578, 90731
Valid prediction for HiQ_model.g16805.t1
Valid prediction for GlimmerHMM_glimmerT_25245-T1
Valid prediction for snap_scaffold_10-snap.1875-T1
Valid prediction for GlimmerHMM_glimmerT_25235-T1
Valid prediction for snap_scaffold_10-snap.1878-T1
Valid prediction for GlimmerHMM_glimmerT_25237-T1
Valid prediction for snap_scaffold_10-snap.1861-T1
Valid prediction for snap_scaffold_10-snap.1874-T1
Valid prediction for snap_scaffold_10-snap.1866-T1
Valid prediction for snap_scaffold_10-snap.1876-T1
Valid prediction for snap_scaffold_10-snap.1869-T1
Valid prediction for snap_scaffold_10-snap.1863-T1
Valid prediction for pasa_asmbl_4698.p1
Valid prediction for snap_scaffold_10-snap.1888-T1
Valid prediction for snap_scaffold_10-snap.1881-T1
Valid prediction for snap_scaffold_10-snap.1892-T1
Valid prediction for Augustus_model.g16803.t1
Valid prediction for snap_scaffold_10-snap.1856-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_25248-T1
Couldn't classify 217022, 217116
Sorry, prediction pasa_asmbl_5193.p1 fails validation.
(ATG)	 AA	213563-213724	GT	GGG
(ATG)	 AG	214053-214197	GT	CGG
(TGA)	 AG	215012-215142	GT	AGG
(GCC)	 AG	215325-215445	GT	GGG
(AGA)	 AG	216525-216680	GT	CGG
(AGT)	 AG	217022-217116	CA	CTC
-recovered pasa_asmbl_5193.p1, initial, 213563, 213724
-recovered pasa_asmbl_5193.p1, initial, 214053, 214197
-recovered pasa_asmbl_5193.p1, internal, 214053, 214197
-recovered pasa_asmbl_5193.p1, internal, 215012, 215142
-recovered pasa_asmbl_5193.p1, internal, 215325, 215445
-recovered pasa_asmbl_5193.p1, internal, 216525, 216680
Valid prediction for snap_scaffold_10-snap.1884-T1
Valid prediction for snap_scaffold_10-snap.1886-T1
Valid prediction for GlimmerHMM_glimmerT_25236-T1
Couldn't classify 92826, 92996
Sorry, prediction pasa_asmbl_4700.p1 fails validation.
(ATG)	 CA	87115-87466	GT	AGG
(GTA)	 AG	89401-89552	GT	GGG
(AAA)	 AG	89744-89824	GT	AGG
(CTT)	 AG	90040-90159	GT	AGG
(GTG)	 AG	90251-90382	GT	AGG
(GTG)	 AG	90578-90731	GT	AGG
(ACC)	 AG	91265-91326	GT	AGG
(GAC)	 AG	91703-91802	GT	CTG
(ACC)	 AG	92044-92177	GT	AGG
(ACT)	 AG	92511-92570	GT	AGG
(ATC)	 AG	92826-92996	TG	TGT
-recovered pasa_asmbl_4700.p1, initial, 87115, 87466
-recovered pasa_asmbl_4700.p1, internal, 89401, 89552
-recovered pasa_asmbl_4700.p1, internal, 89744, 89824
-recovered pasa_asmbl_4700.p1, internal, 90040, 90159
-recovered pasa_asmbl_4700.p1, internal, 90251, 90382
-recovered pasa_asmbl_4700.p1, internal, 90578, 90731
-recovered pasa_asmbl_4700.p1, internal, 91265, 91326
-recovered pasa_asmbl_4700.p1, internal, 91703, 91802
-recovered pasa_asmbl_4700.p1, internal, 92044, 92177
-recovered pasa_asmbl_4700.p1, internal, 92511, 92570
Valid prediction for GlimmerHMM_glimmerT_25240-T1
Valid prediction for snap_scaffold_10-snap.1873-T1
Valid prediction for Augustus_model.g16804.t1
Valid prediction for GlimmerHMM_glimmerT_25224-T1
Valid prediction for Augustus_model.g16798.t1
Valid prediction for snap_scaffold_10-snap.1868-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26480, rend_intergenic: 16209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29055, rend_intergenic: 26612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32918, rend_intergenic: 30010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42798, rend_intergenic: 33348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58270, rend_intergenic: 53791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67739, rend_intergenic: 58782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129784, rend_intergenic: 121764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137980, rend_intergenic: 132895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154058, rend_intergenic: 153898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160734, rend_intergenic: 155528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165997, rend_intergenic: 161501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183021, rend_intergenic: 177885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212969, rend_intergenic: 207366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225094
-exon list size: 301


building trellis

0.3    
0.7    
1.0    
1.3    
1.7    
2.0    
2.3    
2.6    
3.0    
3.3    
3.6    
4.0    
4.3    
4.6    
5.0    
5.3    
5.6    
5.9    
6.3    
6.6    
6.9    
7.3    
7.6    
7.9    
8.3    
8.6    
8.9    
9.2    
9.6    
9.9    
10.2    
10.6    
10.9    
11.2    
11.6    
11.9    
12.2    
12.5    
12.9    
13.2    
13.5    
13.9    
14.2    
14.5    
14.9    
15.2    
15.5    
15.8    
16.2    
16.5    
16.8    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.5    
19.8    
20.1    
20.5    
20.8    
21.1    
21.5    
21.8    
22.1    
22.4    
22.8    
23.1    
23.4    
23.8    
24.1    
24.4    
24.8    
25.1    
25.4    
25.7    
26.1    
26.4    
26.7    
27.1    
27.4    
27.7    
28.1    
28.4    
28.7    
29.0    
29.4    
29.7    
30.0    
30.4    
30.7    
31.0    
31.4    
31.7    
32.0    
32.3    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.7    
35.0    
35.3    
35.6    
36.0    
36.3    
36.6    
37.0    
37.3    
37.6    
38.0    
38.3    
38.6    
38.9    
39.3    
39.6    
39.9    
40.3    
40.6    
40.9    
41.3    
41.6    
41.9    
42.2    
42.6    
42.9    
43.2    
43.6    
43.9    
44.2    
44.6    
44.9    
45.2    
45.5    
45.9    
46.2    
46.5    
46.9    
47.2    
47.5    
47.9    
48.2    
48.5    
48.8    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.2    
51.5    
51.8    
52.1    
52.5    
52.8    
53.1    
53.5    
53.8    
54.1    
54.5    
54.8    
55.1    
55.4    
55.8    
56.1    
56.4    
56.8    
57.1    
57.4    
57.8    
58.1    
58.4    
58.7    
59.1    
59.4    
59.7    
60.1    
60.4    
60.7    
61.1    
61.4    
61.7    
62.0    
62.4    
62.7    
63.0    
63.4    
63.7    
64.0    
64.4    
64.7    
65.0    
65.3    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.7    
68.0    
68.3    
68.6    
69.0    
69.3    
69.6    
70.0    
70.3    
70.6    
71.0    
71.3    
71.6    
71.9    
72.3    
72.6    
72.9    
73.3    
73.6    
73.9    
74.3    
74.6    
74.9    
75.2    
75.6    
75.9    
76.2    
76.6    
76.9    
77.2    
77.6    
77.9    
78.2    
78.5    
78.9    
79.2    
79.5    
79.9    
80.2    
80.5    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.2    
83.5    
83.8    
84.2    
84.5    
84.8    
85.1    
85.5    
85.8    
86.1    
86.5    
86.8    
87.1    
87.5    
87.8    
88.1    
88.4    
88.8    
89.1    
89.4    
89.8    
90.1    
90.4    
90.8    
91.1    
91.4    
91.7    
92.1    
92.4    
92.7    
93.1    
93.4    
93.7    
94.1    
94.4    
94.7    
95.0    
95.4    
95.7    
96.0    
96.4    
96.7    
97.0    
97.4    
97.7    
98.0    
98.3    
98.7    
99.0    
99.3    
99.7    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 26480, rend_intergenic: 16209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29055, rend_intergenic: 26612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32918, rend_intergenic: 30010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42798, rend_intergenic: 33348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58270, rend_intergenic: 53791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67739, rend_intergenic: 58782  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129784, rend_intergenic: 121764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137980, rend_intergenic: 132895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154058, rend_intergenic: 153898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160734, rend_intergenic: 155528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165997, rend_intergenic: 161501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183021, rend_intergenic: 177885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212969, rend_intergenic: 207366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support