-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_10244701-10452630

-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_6-snap.2252-T1
Valid prediction for snap_scaffold_6-snap.2242-T1
Valid prediction for snap_scaffold_6-snap.2234-T1
Valid prediction for snap_scaffold_6-snap.2225-T1
Valid prediction for snap_scaffold_6-snap.2232-T1
Valid prediction for snap_scaffold_6-snap.2236-T1
Valid prediction for snap_scaffold_6-snap.2247-T1
Valid prediction for CodingQuarry_transcript_55200-T1
Valid prediction for snap_scaffold_6-snap.2220-T1
Valid prediction for GlimmerHMM_glimmerT_15385-T1
Valid prediction for snap_scaffold_6-snap.2244-T1
Valid prediction for CodingQuarry_transcript_55201-T1
Valid prediction for Augustus_model.g10249.t1
Valid prediction for snap_scaffold_6-snap.2255-T1
Valid prediction for Augustus_model.g10237.t1
Valid prediction for GlimmerHMM_glimmerT_15382-T1
Valid prediction for HiQ_model.g10245.t1
Valid prediction for snap_scaffold_6-snap.2241-T1
Valid prediction for HiQ_model.g10243.t1
Valid prediction for pasa_asmbl_47282.p1
Valid prediction for GlimmerHMM_glimmerT_15377-T1
Valid prediction for GlimmerHMM_glimmerT_15392-T1
Valid prediction for snap_scaffold_6-snap.2228-T1
Valid prediction for Augustus_model.g10235.t1
Valid prediction for GlimmerHMM_glimmerT_15388-T1
Valid prediction for GlimmerHMM_glimmerT_15390-T1
Valid prediction for snap_scaffold_6-snap.2219-T1
Valid prediction for GlimmerHMM_glimmerT_15379-T1
Valid prediction for snap_scaffold_6-snap.2230-T1
Valid prediction for snap_scaffold_6-snap.2238-T1
Valid prediction for snap_scaffold_6-snap.2224-T1
Valid prediction for snap_scaffold_6-snap.2253-T1
Valid prediction for pasa_asmbl_47281.p1

-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_6-snap.2248-T1
Couldn't classify 196593, 196707
Couldn't classify 200693, 200870
Sorry, prediction pasa_asmbl_48681.p1 fails validation.
(GCC)	 GC	196593-196707	GT	CTG
(CCG)	 AG	197118-197282	GT	CGG
(GTG)	 AG	197481-197654	GT	AGG
(AGT)	 AG	197784-197933	GT	AGG
(GTA)	 AG	199321-199539	GT	AGG
(CAG)	 AG	199877-199950	GT	AGG
(ATT)	 AG	200123-200262	GT	ATG
(GTG)	 AG	200693-200870	AA	GGA
-recovered pasa_asmbl_48681.p1, internal, 197118, 197282
-recovered pasa_asmbl_48681.p1, internal, 197481, 197654
-recovered pasa_asmbl_48681.p1, internal, 197784, 197933
-recovered pasa_asmbl_48681.p1, internal, 199321, 199539
-recovered pasa_asmbl_48681.p1, internal, 199877, 199950
-recovered pasa_asmbl_48681.p1, internal, 200123, 200262
Valid prediction for GlimmerHMM_glimmerT_15376-T1
Valid prediction for GlimmerHMM_glimmerT_15397-T1
Valid prediction for snap_scaffold_6-snap.2221-T1
Valid prediction for snap_scaffold_6-snap.2223-T1
Valid prediction for GlimmerHMM_glimmerT_15396-T1
Valid prediction for snap_scaffold_6-snap.2240-T1
Couldn't classify 192947, 193088
Couldn't classify 194784, 194860
Sorry, prediction pasa_asmbl_48683.p3 fails validation.
(CAC)	 CT	192947-193088	GT	AGG
(GCT)	 AG	194180-194374	GT	AGG
(CCC)	 AG	194784-194860	GA	AGG
-recovered pasa_asmbl_48683.p3, internal, 194180, 194374
Valid prediction for snap_scaffold_6-snap.2250-T1
Couldn't classify 61652, 61742
Couldn't classify 63509, 63549
Sorry, prediction pasa_asmbl_48696.p1 fails validation.
(CTG)	 AG	61652-61742	GT	AGG
(GTC)	 AG	61845-61948	GT	AGG
(TTG)	 AG	62049-62129	GT	AGG
(GAT)	 AG	62384-62521	GT	AGG
(GAA)	 AG	62618-62699	GT	AGG
(GAG)	 AG	62774-62890	GT	TGG
(ATG)	 AG	63102-63371	GT	TGG
(GCC)	 AG	63509-63549	CC	AAC
add_exon() Sorry, pasa_asmbl_48696.p1 63102-63371-initial-1 is invalid.
-recovered pasa_asmbl_48696.p1, initial, 63102, 63371
add_exon() Sorry, pasa_asmbl_48696.p1 62618-62699-terminal-3 is invalid.
-recovered pasa_asmbl_48696.p1, terminal, 62618, 62699
-recovered pasa_asmbl_48696.p1, internal, 61652, 61742
-recovered pasa_asmbl_48696.p1, internal, 61845, 61948
-recovered pasa_asmbl_48696.p1, internal, 62049, 62129
-recovered pasa_asmbl_48696.p1, internal, 62384, 62521
-recovered pasa_asmbl_48696.p1, internal, 62618, 62699
-recovered pasa_asmbl_48696.p1, internal, 62774, 62890
-recovered pasa_asmbl_48696.p1, internal, 63102, 63371
Valid prediction for Augustus_model.g10247.t1
Valid prediction for CodingQuarry_transcript_55202-T1
Valid prediction for snap_scaffold_6-snap.2235-T1
Valid prediction for GlimmerHMM_glimmerT_15381-T1
Valid prediction for HiQ_model.g10241.t1
Valid prediction for HiQ_model.g10246.t1
Valid prediction for Augustus_model.g10233.t1
Valid prediction for GlimmerHMM_glimmerT_15394-T1
Valid prediction for GlimmerHMM_glimmerT_15380-T1
Valid prediction for GlimmerHMM_glimmerT_15395-T1
Valid prediction for GlimmerHMM_glimmerT_15383-T1
Valid prediction for snap_scaffold_6-snap.2218-T1
Valid prediction for snap_scaffold_6-snap.2222-T1
Valid prediction for pasa_asmbl_48690.p1
Couldn't classify 55667, 55684
Sorry, prediction pasa_asmbl_48698.p1 fails validation.
(GTT)	 AC	55667-55684	GT	AGG
(GTC)	 AG	55782-55874	GT	AGG
(GTG)	 AG	56034-56261	CC	GAC
-recovered pasa_asmbl_48698.p1, terminal, 56034, 56261
-recovered pasa_asmbl_48698.p1, internal, 55782, 55874
Valid prediction for Augustus_model.g10236.t1
Valid prediction for Augustus_model.g10238.t1
Valid prediction for GlimmerHMM_glimmerT_15384-T1
Valid prediction for CodingQuarry_transcript_55203-T1
Valid prediction for GlimmerHMM_glimmerT_15386-T1
Couldn't classify 117131, 117490
Sorry, prediction pasa_asmbl_48685.p2 fails validation.
(CTG)	 GC	117131-117490	AC	GAA
Couldn't classify 51601, 51702
Sorry, prediction pasa_asmbl_48701.p1 fails validation.
(GTG)	 GG	51601-51702	GT	AGG
(GTT)	 AG	51835-52009	GT	CGG
(GAA)	 AG	52351-52481	GT	AGG
(GTG)	 AG	52725-52904	GC	GAG
-recovered pasa_asmbl_48701.p1, terminal, 52725, 52904
-recovered pasa_asmbl_48701.p1, internal, 51835, 52009
-recovered pasa_asmbl_48701.p1, internal, 52351, 52481
-recovered pasa_asmbl_48701.p1, internal, 52725, 52904
Valid prediction for Augustus_model.g10239.t1
Valid prediction for GlimmerHMM_glimmerT_15387-T1
Valid prediction for snap_scaffold_6-snap.2245-T1
Valid prediction for snap_scaffold_6-snap.2231-T1
Valid prediction for snap_scaffold_6-snap.2254-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.2227-T1
Valid prediction for GlimmerHMM_glimmerT_15389-T1
Valid prediction for Augustus_model.g10244.t1
Valid prediction for GlimmerHMM_glimmerT_15391-T1
Valid prediction for Augustus_model.g10240.t1
Valid prediction for snap_scaffold_6-snap.2239-T1
Valid prediction for snap_scaffold_6-snap.2243-T1
Valid prediction for CodingQuarry_transcript_55198-T1
Valid prediction for snap_scaffold_6-snap.2249-T1
Valid prediction for snap_scaffold_6-snap.2229-T1
Valid prediction for GlimmerHMM_glimmerT_15393-T1
Valid prediction for snap_scaffold_6-snap.2237-T1
Valid prediction for snap_scaffold_6-snap.2233-T1
Valid prediction for Augustus_model.g10234.t1
Valid prediction for snap_scaffold_6-snap.2246-T1
Valid prediction for Augustus_model.g10248.t1
Valid prediction for snap_scaffold_6-snap.2226-T1
Valid prediction for GlimmerHMM_glimmerT_15378-T1
Valid prediction for HiQ_model.g10242.t1
Valid prediction for CodingQuarry_transcript_55199-T1
Valid prediction for snap_scaffold_6-snap.2251-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 121021, rend_intergenic: 121018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10781, rend_intergenic: 4513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36327, rend_intergenic: 23042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69002, rend_intergenic: 63554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74414, rend_intergenic: 69301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106876, rend_intergenic: 102674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109461, rend_intergenic: 107712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116153, rend_intergenic: 112280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161784, rend_intergenic: 160648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186774, rend_intergenic: 182543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207930
-exon list size: 347


building trellis

0.3    
0.6    
0.9    
1.1    
1.4    
1.7    
2.0    
2.3    
2.6    
2.9    
3.2    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.7    
10.0    
10.3    
10.6    
10.9    
11.2    
11.5    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.0    
14.3    
14.6    
14.9    
15.2    
15.5    
15.8    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.1    
18.3    
18.6    
18.9    
19.2    
19.5    
19.8    
20.1    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.1    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.6    
24.9    
25.2    
25.5    
25.8    
26.1    
26.4    
26.6    
26.9    
27.2    
27.5    
27.8    
28.1    
28.4    
28.7    
28.9    
29.2    
29.5    
29.8    
30.1    
30.4    
30.7    
30.9    
31.2    
31.5    
31.8    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.4    
34.7    
35.0    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.2    
37.5    
37.8    
38.1    
38.4    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.5    
41.8    
42.1    
42.4    
42.7    
43.0    
43.3    
43.6    
43.8    
44.1    
44.4    
44.7    
45.0    
45.3    
45.6    
45.8    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.1    
48.4    
48.7    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.3    
51.6    
51.9    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
54.2    
54.4    
54.7    
55.0    
55.3    
55.6    
55.9    
56.2    
56.4    
56.7    
57.0    
57.3    
57.6    
57.9    
58.2    
58.5    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.6    
61.9    
62.2    
62.5    
62.8    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.0    
65.3    
65.6    
65.9    
66.2    
66.5    
66.8    
67.0    
67.3    
67.6    
67.9    
68.2    
68.5    
68.8    
69.1    
69.3    
69.6    
69.9    
70.2    
70.5    
70.8    
71.1    
71.3    
71.6    
71.9    
72.2    
72.5    
72.8    
73.1    
73.4    
73.6    
73.9    
74.2    
74.5    
74.8    
75.1    
75.4    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
77.9    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
79.9    
80.2    
80.5    
80.8    
81.1    
81.4    
81.7    
81.9    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.2    
84.5    
84.8    
85.1    
85.4    
85.7    
86.0    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.5    
88.8    
89.1    
89.4    
89.7    
90.0    
90.3    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.8    
97.1    
97.4    
97.7    
98.0    
98.3    
98.6    
98.9    
99.1    
99.4    
99.7    
-found 24 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 121021, rend_intergenic: 121018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10781, rend_intergenic: 4513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36327, rend_intergenic: 23042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69002, rend_intergenic: 63554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74414, rend_intergenic: 69301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106876, rend_intergenic: 102674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109461, rend_intergenic: 107712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116153, rend_intergenic: 112280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161784, rend_intergenic: 160648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186774, rend_intergenic: 182543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support