-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_4979192-5136554

-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_10-snap.1115-T1
Valid prediction for GlimmerHMM_glimmerT_24707-T1
Valid prediction for snap_scaffold_10-snap.1122-T1
Valid prediction for Augustus_model.g16438.t1
Valid prediction for Augustus_model.g16444.t1
Valid prediction for snap_scaffold_10-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_24704-T1
Valid prediction for GlimmerHMM_glimmerT_24722-T1
Valid prediction for snap_scaffold_10-snap.1112-T1
Valid prediction for GlimmerHMM_glimmerT_24716-T1
Valid prediction for snap_scaffold_10-snap.1095-T1
Valid prediction for Augustus_model.g16443.t1
Valid prediction for snap_scaffold_10-snap.1100-T1
Valid prediction for Augustus_model.g16452.t1
Valid prediction for snap_scaffold_10-snap.1124-T1
Valid prediction for snap_scaffold_10-snap.1117-T1
Valid prediction for snap_scaffold_10-snap.1126-T1
Valid prediction for GlimmerHMM_glimmerT_24703-T1
Valid prediction for GlimmerHMM_glimmerT_24697-T1
Valid prediction for snap_scaffold_10-snap.1105-T1
Couldn't classify 53315, 53466
Sorry, prediction pasa_asmbl_3139.p1 fails validation.
(ATG)	 CT	48235-48388	GT	AGG
(GCG)	 AG	49284-49513	GT	AGG
(GTG)	 AG	49909-50126	GT	GGG
(GTA)	 AG	50326-50413	GT	AGG
(GTT)	 AG	50513-50601	GT	AGG
(AGC)	 AG	51228-51415	GT	TGG
(GTC)	 AG	51562-51695	GT	AGG
(GGT)	 AG	51806-51997	GT	AGG
(AAT)	 AG	52577-52730	GT	AGG
(GTT)	 AG	53315-53466	GC	ACG
-recovered pasa_asmbl_3139.p1, initial, 48235, 48388
-recovered pasa_asmbl_3139.p1, internal, 49284, 49513
-recovered pasa_asmbl_3139.p1, internal, 49909, 50126
-recovered pasa_asmbl_3139.p1, internal, 50326, 50413
-recovered pasa_asmbl_3139.p1, internal, 50513, 50601
-recovered pasa_asmbl_3139.p1, internal, 51228, 51415
-recovered pasa_asmbl_3139.p1, internal, 51562, 51695
-recovered pasa_asmbl_3139.p1, internal, 51806, 51997
-recovered pasa_asmbl_3139.p1, internal, 52577, 52730
-recovered pasa_asmbl_3139.p1, internal, 53315, 53466
Couldn't classify 57869, 57961
Sorry, prediction pasa_asmbl_3141.p1 fails validation.
(AGT)	 GC	57869-57961	GT	TGG
(GGT)	 AG	58351-58530	GT	TGG
(GCT)	 AG	58758-58917	GT	TGG
(GGT)	 AG	60593-60674	GT	AGG
(GTT)	 AG	62321-62439	GT	TGG
(AAA)	 AG	62539-62654	GT	AGG
(GTG)	 AG	63175-63318	CC	AAC
-recovered pasa_asmbl_3141.p1, terminal, 63175, 63318
-recovered pasa_asmbl_3141.p1, internal, 58351, 58530
-recovered pasa_asmbl_3141.p1, internal, 58758, 58917
-recovered pasa_asmbl_3141.p1, internal, 60593, 60674
-recovered pasa_asmbl_3141.p1, internal, 62321, 62439
-recovered pasa_asmbl_3141.p1, internal, 62539, 62654
Valid prediction for snap_scaffold_10-snap.1132-T1
Valid prediction for Augustus_model.g16441.t1
Valid prediction for snap_scaffold_10-snap.1107-T1
Valid prediction for snap_scaffold_10-snap.1109-T1
Valid prediction for snap_scaffold_10-snap.1121-T1
Valid prediction for snap_scaffold_10-snap.1103-T1
Valid prediction for GlimmerHMM_glimmerT_24708-T1
Valid prediction for snap_scaffold_10-snap.1097-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.1133-T1
Valid prediction for snap_scaffold_10-snap.1129-T1
Valid prediction for GlimmerHMM_glimmerT_24715-T1
Valid prediction for GlimmerHMM_glimmerT_24700-T1
Valid prediction for snap_scaffold_10-snap.1130-T1
Valid prediction for snap_scaffold_10-snap.1110-T1
Valid prediction for snap_scaffold_10-snap.1104-T1
Valid prediction for GlimmerHMM_glimmerT_24698-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 HiQ_model.g16439.t1
Valid prediction for Augustus_model.g16445.t1
Valid prediction for snap_scaffold_10-snap.1094-T1
Valid prediction for snap_scaffold_10-snap.1098-T1
Valid prediction for snap_scaffold_10-snap.1131-T1
Valid prediction for Augustus_model.g16449.t1
Valid prediction for Augustus_model.g16451.t1
Valid prediction for Augustus_model.g16446.t1
Valid prediction for Augustus_model.g16450.t1
Valid prediction for GlimmerHMM_glimmerT_24706-T1
Couldn't classify 40811, 40867
Sorry, prediction pasa_asmbl_4336.p1 fails validation.
(CCC)	 CC	40811-40867	GT	AGG
(GAG)	 AG	41015-41161	GT	AGG
(GTG)	 AG	41689-41790	GT	AGG
(AAG)	 AG	41949-42766	GT	AGG
(TGA)	 AG	43175-43880	GT	GGG
(ATT)	 AG	43994-44149	GT	CTG
(GAG)	 AG	44353-44418	GT	AGG
(GGT)	 AG	44563-44649	AA	GAA
-recovered pasa_asmbl_4336.p1, terminal, 44563, 44649
-recovered pasa_asmbl_4336.p1, internal, 41015, 41161
-recovered pasa_asmbl_4336.p1, internal, 41689, 41790
-recovered pasa_asmbl_4336.p1, internal, 41949, 42766
-recovered pasa_asmbl_4336.p1, internal, 43175, 43880
-recovered pasa_asmbl_4336.p1, internal, 43994, 44149
-recovered pasa_asmbl_4336.p1, internal, 44353, 44418
Valid prediction for Augustus_model.g16448.t1
Valid prediction for GlimmerHMM_glimmerT_24719-T1
Valid prediction for snap_scaffold_10-snap.1125-T1
Valid prediction for GlimmerHMM_glimmerT_24701-T1
Valid prediction for GlimmerHMM_glimmerT_24710-T1
Valid prediction for GlimmerHMM_glimmerT_24711-T1
Valid prediction for GlimmerHMM_glimmerT_24695-T1
Valid prediction for snap_scaffold_10-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_24718-T1
Valid prediction for GlimmerHMM_glimmerT_24721-T1
Valid prediction for Augustus_model.g16436.t1
Valid prediction for GlimmerHMM_glimmerT_24705-T1
Valid prediction for snap_scaffold_10-snap.1127-T1
Valid prediction for Augustus_model.g16440.t1
Valid prediction for snap_scaffold_10-snap.1119-T1
Valid prediction for GlimmerHMM_glimmerT_24713-T1
Valid prediction for GlimmerHMM_glimmerT_24723-T1
Valid prediction for snap_scaffold_10-snap.1116-T1
Couldn't classify 123573, 123981
Sorry, prediction pasa_asmbl_4335.p1 fails validation.
(CCG)	 CC	123573-123981	GT	TGG
(GTG)	 AG	124449-124569	GT	ATG
(GTT)	 AG	124679-124716	GT	TGG
(GGG)	 AG	124820-124836	GT	AGG
(GGC)	 AG	124961-125140	GT	AGG
(TTT)	 AG	125247-125406	GT	CTG
(ACG)	 AG	125529-125625	GT	AGG
(TGA)	 AG	125713-125729	GT	AGG
(TGG)	 AG	125921-125993	GT	AGG
(CCC)	 AG	126126-126230	GT	CAG
(CCT)	 AG	126645-126688	GT	AGG
(CAG)	 AG	126950-127028	GT	AGG
(CCA)	 AG	127152-127248	GT	AAG
(TTT)	 AG	127386-127548	GT	GTG
(TCG)	 AG	128205-128238	GT	GAG
(GGA)	 AG	128427-128455	GT	TGG
(GCG)	 AG	128562-128584	GA	GAG
-recovered pasa_asmbl_4335.p1, terminal, 128562, 128584
-recovered pasa_asmbl_4335.p1, internal, 124449, 124569
-recovered pasa_asmbl_4335.p1, internal, 124679, 124716
-recovered pasa_asmbl_4335.p1, internal, 124820, 124836
-recovered pasa_asmbl_4335.p1, internal, 124961, 125140
-recovered pasa_asmbl_4335.p1, internal, 125247, 125406
-recovered pasa_asmbl_4335.p1, internal, 125529, 125625
-recovered pasa_asmbl_4335.p1, internal, 125713, 125729
-recovered pasa_asmbl_4335.p1, internal, 125921, 125993
-recovered pasa_asmbl_4335.p1, internal, 126126, 126230
-recovered pasa_asmbl_4335.p1, internal, 126645, 126688
-recovered pasa_asmbl_4335.p1, internal, 126950, 127028
-recovered pasa_asmbl_4335.p1, internal, 127152, 127248
-recovered pasa_asmbl_4335.p1, internal, 127386, 127548
-recovered pasa_asmbl_4335.p1, internal, 128205, 128238
-recovered pasa_asmbl_4335.p1, internal, 128427, 128455
Valid prediction for snap_scaffold_10-snap.1096-T1
Valid prediction for snap_scaffold_10-snap.1108-T1
Valid prediction for GlimmerHMM_glimmerT_24717-T1
Valid prediction for GlimmerHMM_glimmerT_24709-T1
Valid prediction for snap_scaffold_10-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_24702-T1
Valid prediction for CodingQuarry_transcript_5391-T1
Valid prediction for snap_scaffold_10-snap.1102-T1
Valid prediction for Augustus_model.g16442.t1
Valid prediction for snap_scaffold_10-snap.1106-T1
Couldn't classify 35623, 35729
Couldn't classify 40313, 40393
Sorry, prediction pasa_asmbl_4338.p1 fails validation.
(GAG)	 AC	35623-35729	GT	GCG
(CCT)	 AG	36115-36203	GT	AGG
(GAC)	 AG	36443-36507	GT	AGG
(AGT)	 AG	36680-36737	GT	AGG
(CTG)	 AG	36834-36904	GT	CTG
(GAG)	 AG	38846-38952	GT	AGG
(GAC)	 AG	39045-39229	GT	AGG
(ATA)	 AG	39796-39821	GT	AGG
(CAT)	 AG	40313-40393	GT	AGG
-recovered pasa_asmbl_4338.p1, internal, 36115, 36203
-recovered pasa_asmbl_4338.p1, internal, 36443, 36507
-recovered pasa_asmbl_4338.p1, internal, 36680, 36737
-recovered pasa_asmbl_4338.p1, internal, 36834, 36904
-recovered pasa_asmbl_4338.p1, internal, 38846, 38952
-recovered pasa_asmbl_4338.p1, internal, 39045, 39229
-recovered pasa_asmbl_4338.p1, internal, 39796, 39821
-recovered pasa_asmbl_4338.p1, internal, 40313, 40393
Valid prediction for snap_scaffold_10-snap.1099-T1
Valid prediction for snap_scaffold_10-snap.1101-T1
Valid prediction for GlimmerHMM_glimmerT_24696-T1
Valid prediction for GlimmerHMM_glimmerT_24712-T1
Valid prediction for snap_scaffold_10-snap.1114-T1
Valid prediction for Augustus_model.g16453.t1
Valid prediction for snap_scaffold_10-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_24714-T1
Valid prediction for snap_scaffold_10-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_24699-T1
Valid prediction for snap_scaffold_10-snap.1123-T1
Valid prediction for Augustus_model.g16437.t1
Valid prediction for Augustus_model.g16447.t1
Valid prediction for GlimmerHMM_glimmerT_24720-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6939, rend_intergenic: 4586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8438, rend_intergenic: 7257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16784, rend_intergenic: 11608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19796, rend_intergenic: 16791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25429, rend_intergenic: 20386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34659, rend_intergenic: 30663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60687, rend_intergenic: 53608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72205, rend_intergenic: 65676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75528, rend_intergenic: 72742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83699, rend_intergenic: 75720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88902, rend_intergenic: 85700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90125, rend_intergenic: 89331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99109, rend_intergenic: 90939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110792, rend_intergenic: 107194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125074, rend_intergenic: 112864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129302, rend_intergenic: 125880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156891, rend_intergenic: 146768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 157363
-exon list size: 418


building trellis

0.2    
0.5    
0.7    
1.0    
1.2    
1.4    
1.7    
1.9    
2.1    
2.4    
2.6    
2.9    
3.1    
3.3    
3.6    
3.8    
4.0    
4.3    
4.5    
4.8    
5.0    
5.2    
5.5    
5.7    
6.0    
6.2    
6.4    
6.7    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.3    
8.6    
8.8    
9.0    
9.3    
9.5    
9.8    
10.0    
10.2    
10.5    
10.7    
11.0    
11.2    
11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.3    
13.6    
13.8    
14.0    
14.3    
14.5    
14.8    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.4    
16.7    
16.9    
17.1    
17.4    
17.6    
17.9    
18.1    
18.3    
18.6    
18.8    
19.0    
19.3    
19.5    
19.8    
20.0    
20.2    
20.5    
20.7    
21.0    
21.2    
21.4    
21.7    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.3    
23.6    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.3    
28.6    
28.8    
29.0    
29.3    
29.5    
29.8    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.4    
31.7    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.3    
39.5    
39.8    
40.0    
40.2    
40.5    
40.7    
41.0    
41.2    
41.4    
41.7    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
46.4    
46.7    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.3    
48.6    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.4    
51.7    
51.9    
52.1    
52.4    
52.6    
52.9    
53.1    
53.3    
53.6    
53.8    
54.0    
54.3    
54.5    
54.8    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.4    
56.7    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.3    
58.6    
58.8    
59.0    
59.3    
59.5    
59.8    
60.0    
60.2    
60.5    
60.7    
61.0    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.3    
63.6    
63.8    
64.0    
64.3    
64.5    
64.8    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
67.4    
67.6    
67.9    
68.1    
68.3    
68.6    
68.8    
69.0    
69.3    
69.5    
69.8    
70.0    
70.2    
70.5    
70.7    
71.0    
71.2    
71.4    
71.7    
71.9    
72.1    
72.4    
72.6    
72.9    
73.1    
73.3    
73.6    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.4    
77.6    
77.9    
78.1    
78.3    
78.6    
78.8    
79.0    
79.3    
79.5    
79.8    
80.0    
80.2    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
82.1    
82.4    
82.6    
82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.3    
89.5    
89.8    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.0    
94.3    
94.5    
94.8    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.4    
96.7    
96.9    
97.1    
97.4    
97.6    
97.9    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 6939, rend_intergenic: 4586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8438, rend_intergenic: 7257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16784, rend_intergenic: 11608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19796, rend_intergenic: 16791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25429, rend_intergenic: 20386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34659, rend_intergenic: 30663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60687, rend_intergenic: 53608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72205, rend_intergenic: 65676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75528, rend_intergenic: 72742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83699, rend_intergenic: 75720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88902, rend_intergenic: 85700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90125, rend_intergenic: 89331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99109, rend_intergenic: 90939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110792, rend_intergenic: 107194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125074, rend_intergenic: 112864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129302, rend_intergenic: 125880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156891, rend_intergenic: 146768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support