-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_6136998-6320147

-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 GeneMark_model.30123_t
Valid prediction for GeneMark_model.30100_t
Valid prediction for GlimmerHMM_glimmerT_17932-T1
Valid prediction for snap_scaffold_7-snap.1303-T1
Valid prediction for Augustus_model.g12035.t1
Valid prediction for GeneMark_model.30088_t
Valid prediction for snap_scaffold_7-snap.1289-T1
Valid prediction for GeneMark_model.30102_t
Valid prediction for GeneMark_model.30101_t
Couldn't classify 92853, 92984
Sorry, prediction pasa_asmbl_50742.p1 fails validation.
(GTG)	 CA	92853-92984	GT	CGG
(ACA)	 AG	94495-94689	GT	GGG
(GAT)	 AG	95117-95235	GT	CGG
(GTA)	 AG	95550-95772	GT	AGG
-recovered pasa_asmbl_50742.p1, terminal, 95550, 95772
-recovered pasa_asmbl_50742.p1, internal, 94495, 94689
-recovered pasa_asmbl_50742.p1, internal, 95117, 95235
-recovered pasa_asmbl_50742.p1, internal, 95550, 95772
Valid prediction for HiQ_model.g12042.t1
Valid prediction for snap_scaffold_7-snap.1302-T1
Valid prediction for GeneMark_model.30111_t
Valid prediction for GlimmerHMM_glimmerT_17936-T1
Couldn't classify 60154, 60242
Couldn't classify 63469, 63535
Sorry, prediction pasa_asmbl_50734.p1 fails validation.
(ATT)	 AT	60154-60242	GT	AAG
(TAT)	 AG	60387-60492	GT	AGG
(ATT)	 AG	60696-60778	GT	AGG
(GGT)	 AG	60947-61016	GT	AGG
(GCT)	 AG	61196-61351	GT	AGG
(ATC)	 AG	63119-63228	GT	GAG
(GCT)	 AG	63469-63535	AG	GCA
-recovered pasa_asmbl_50734.p1, internal, 60387, 60492
-recovered pasa_asmbl_50734.p1, internal, 60696, 60778
-recovered pasa_asmbl_50734.p1, internal, 60947, 61016
-recovered pasa_asmbl_50734.p1, internal, 61196, 61351
-recovered pasa_asmbl_50734.p1, internal, 63119, 63228
Valid prediction for GeneMark_model.30121_t
Valid prediction for GeneMark_model.30117_t
Valid prediction for GeneMark_model.30087_t
Valid prediction for Augustus_model.g12038.t1
Valid prediction for CodingQuarry_transcript_57376-T1
Valid prediction for snap_scaffold_7-snap.1292-T1
Valid prediction for Augustus_model.g12039.t1
Valid prediction for GeneMark_model.30095_t
Valid prediction for GeneMark_model.30093_t
Valid prediction for Augustus_model.g12043.t1
Valid prediction for Augustus_model.g12040.t1
Valid prediction for GeneMark_model.30084_t
Valid prediction for Augustus_model.g12044.t1
Valid prediction for GeneMark_model.30109_t
Valid prediction for Augustus_model.g12037.t1
Valid prediction for snap_scaffold_7-snap.1298-T1
Valid prediction for snap_scaffold_7-snap.1312-T1
Valid prediction for Augustus_model.g12033.t1
Valid prediction for GeneMark_model.30118_t
Valid prediction for snap_scaffold_7-snap.1320-T1
Valid prediction for snap_scaffold_7-snap.1295-T1
Valid prediction for GeneMark_model.30113_t
Valid prediction for GeneMark_model.30107_t
Valid prediction for snap_scaffold_7-snap.1310-T1
Valid prediction for snap_scaffold_7-snap.1304-T1
Couldn't classify 86837, 87007
Sorry, prediction pasa_asmbl_50740.p1 fails validation.
(ATG)	 AC	85071-85151	GT	TGG
(ACC)	 AG	85838-86062	GT	CTG
(GGT)	 AG	86837-87007	GT	GGG
-recovered pasa_asmbl_50740.p1, initial, 85071, 85151
-recovered pasa_asmbl_50740.p1, internal, 85838, 86062
-recovered pasa_asmbl_50740.p1, internal, 86837, 87007
Valid prediction for GeneMark_model.30098_t
Valid prediction for snap_scaffold_7-snap.1301-T1
Valid prediction for GlimmerHMM_glimmerT_17928-T1
Valid prediction for GeneMark_model.30097_t
Valid prediction for GlimmerHMM_glimmerT_17924-T1
Valid prediction for Augustus_model.g12032.t1
Valid prediction for GlimmerHMM_glimmerT_17925-T1
Valid prediction for GeneMark_model.30119_t
Valid prediction for snap_scaffold_7-snap.1305-T1
Valid prediction for Augustus_model.g12041.t1
Valid prediction for GeneMark_model.30082_t
Valid prediction for snap_scaffold_7-snap.1299-T1
Valid prediction for snap_scaffold_7-snap.1317-T1
Valid prediction for GeneMark_model.30091_t
Valid prediction for GeneMark_model.30114_t
Valid prediction for snap_scaffold_7-snap.1296-T1
Couldn't classify 52483, 52737
Sorry, prediction pasa_asmbl_50730.p2 fails validation.
(ATG)	 TT	50973-51068	GT	TGG
(GTG)	 AG	52483-52737	GA	TAG
-recovered pasa_asmbl_50730.p2, initial, 50973, 51068
Valid prediction for GeneMark_model.30104_t
Valid prediction for GlimmerHMM_glimmerT_17943-T1
Valid prediction for GeneMark_model.30106_t
Valid prediction for GlimmerHMM_glimmerT_17941-T1
Valid prediction for Augustus_model.g12049.t1
Valid prediction for Augustus_model.g12036.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_7-snap.1294-T1
Valid prediction for snap_scaffold_7-snap.1308-T1
Valid prediction for GlimmerHMM_glimmerT_17934-T1
Valid prediction for GeneMark_model.30092_t
Valid prediction for Augustus_model.g12034.t1
Valid prediction for GlimmerHMM_glimmerT_17939-T1
Valid prediction for snap_scaffold_7-snap.1293-T1
Valid prediction for snap_scaffold_7-snap.1306-T1
Valid prediction for GeneMark_model.30081_t
Valid prediction for GeneMark_model.30116_t
Valid prediction for GlimmerHMM_glimmerT_17923-T1
Valid prediction for snap_scaffold_7-snap.1314-T1
Valid prediction for GeneMark_model.30090_t
Valid prediction for snap_scaffold_7-snap.1322-T1
Valid prediction for GeneMark_model.30108_t
Valid prediction for snap_scaffold_7-snap.1319-T1
Valid prediction for snap_scaffold_7-snap.1297-T1
Valid prediction for snap_scaffold_7-snap.1316-T1
Valid prediction for Augustus_model.g12047.t1
Valid prediction for GeneMark_model.30085_t
Valid prediction for GeneMark_model.30112_t
Valid prediction for GlimmerHMM_glimmerT_17927-T1
Valid prediction for snap_scaffold_7-snap.1290-T1
Valid prediction for Augustus_model.g12048.t1
Valid prediction for GeneMark_model.30099_t
Valid prediction for GeneMark_model.30110_t
Valid prediction for GlimmerHMM_glimmerT_17930-T1
Valid prediction for GlimmerHMM_glimmerT_17935-T1
Valid prediction for Augustus_model.g12050.t1
Valid prediction for snap_scaffold_7-snap.1318-T1
Valid prediction for snap_scaffold_7-snap.1309-T1
Valid prediction for snap_scaffold_7-snap.1291-T1
Valid prediction for snap_scaffold_7-snap.1311-T1
Valid prediction for snap_scaffold_7-snap.1321-T1
Valid prediction for GeneMark_model.30124_t
Valid prediction for GeneMark_model.30094_t
Valid prediction for Augustus_model.g12046.t1
Valid prediction for GlimmerHMM_glimmerT_17938-T1
Valid prediction for GlimmerHMM_glimmerT_17926-T1
Valid prediction for GeneMark_model.30083_t
Valid prediction for GeneMark_model.30086_t
Valid prediction for GeneMark_model.30115_t
Valid prediction for GeneMark_model.30103_t
Valid prediction for snap_scaffold_7-snap.1300-T1
Valid prediction for GeneMark_model.30105_t
Valid prediction for GeneMark_model.30096_t
Valid prediction for GeneMark_model.30089_t
Valid prediction for GlimmerHMM_glimmerT_17931-T1
Valid prediction for GlimmerHMM_glimmerT_17942-T1
Valid prediction for GlimmerHMM_glimmerT_17940-T1
Valid prediction for Augustus_model.g12045.t1
Valid prediction for GlimmerHMM_glimmerT_17937-T1
Valid prediction for GlimmerHMM_glimmerT_17933-T1
Valid prediction for GeneMark_model.30120_t
Valid prediction for GeneMark_model.30122_t
Valid prediction for snap_scaffold_7-snap.1313-T1
Valid prediction for Augustus_model.g12031.t1
Valid prediction for snap_scaffold_7-snap.1315-T1
Valid prediction for GlimmerHMM_glimmerT_17929-T1
Valid prediction for snap_scaffold_7-snap.1307-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11771, rend_intergenic: 7187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16157, rend_intergenic: 12985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41300, rend_intergenic: 38525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57071, rend_intergenic: 45854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122759, rend_intergenic: 118946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 183150
-exon list size: 566


building trellis

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6.9    
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7.6    
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9.2    
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11.8    
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12.1    
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12.7    
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13.0    
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14.1    
14.3    
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14.6    
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15.0    
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16.2    
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16.5    
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17.4    
17.6    
17.8    
18.0    
18.1    
18.3    
18.5    
18.7    
18.8    
19.0    
19.2    
19.4    
19.5    
19.7    
19.9    
20.1    
20.2    
20.4    
20.6    
20.8    
21.0    
21.1    
21.3    
21.5    
21.7    
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22.0    
22.2    
22.4    
22.5    
22.7    
22.9    
23.1    
23.2    
23.4    
23.6    
23.8    
23.9    
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24.3    
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24.6    
24.8    
25.0    
25.2    
25.4    
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25.9    
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26.2    
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26.6    
26.8    
26.9    
27.1    
27.3    
27.5    
27.6    
27.8    
28.0    
28.2    
28.3    
28.5    
28.7    
28.9    
29.0    
29.2    
29.4    
29.6    
29.8    
29.9    
30.1    
30.3    
30.5    
30.6    
30.8    
31.0    
31.2    
31.3    
31.5    
31.7    
31.9    
32.0    
32.2    
32.4    
32.6    
32.7    
32.9    
33.1    
33.3    
33.5    
33.6    
33.8    
34.0    
34.2    
34.3    
34.5    
34.7    
34.9    
35.0    
35.2    
35.4    
35.6    
35.7    
35.9    
36.1    
36.3    
36.4    
36.6    
36.8    
37.0    
37.1    
37.3    
37.5    
37.7    
37.9    
38.0    
38.2    
38.4    
38.6    
38.7    
38.9    
39.1    
39.3    
39.4    
39.6    
39.8    
40.0    
40.1    
40.3    
40.5    
40.7    
40.8    
41.0    
41.2    
41.4    
41.5    
41.7    
41.9    
42.1    
42.3    
42.4    
42.6    
42.8    
43.0    
43.1    
43.3    
43.5    
43.7    
43.8    
44.0    
44.2    
44.4    
44.5    
44.7    
44.9    
45.1    
45.2    
45.4    
45.6    
45.8    
46.0    
46.1    
46.3    
46.5    
46.7    
46.8    
47.0    
47.2    
47.4    
47.5    
47.7    
47.9    
48.1    
48.2    
48.4    
48.6    
48.8    
48.9    
49.1    
49.3    
49.5    
49.6    
49.8    
50.0    
50.2    
50.4    
50.5    
50.7    
50.9    
51.1    
51.2    
51.4    
51.6    
51.8    
51.9    
52.1    
52.3    
52.5    
52.6    
52.8    
53.0    
53.2    
53.3    
53.5    
53.7    
53.9    
54.0    
54.2    
54.4    
54.6    
54.8    
54.9    
55.1    
55.3    
55.5    
55.6    
55.8    
56.0    
56.2    
56.3    
56.5    
56.7    
56.9    
57.0    
57.2    
57.4    
57.6    
57.7    
57.9    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.2    
59.3    
59.5    
59.7    
59.9    
60.0    
60.2    
60.4    
60.6    
60.7    
60.9    
61.1    
61.3    
61.4    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.7    
62.9    
63.0    
63.2    
63.4    
63.6    
63.7    
63.9    
64.1    
64.3    
64.4    
64.6    
64.8    
65.0    
65.1    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.4    
66.5    
66.7    
66.9    
67.1    
67.3    
67.4    
67.6    
67.8    
68.0    
68.1    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.4    
69.5    
69.7    
69.9    
70.1    
70.2    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.7    
71.8    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.1    
73.2    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.5    
74.6    
74.8    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.1    
76.2    
76.4    
76.6    
76.8    
76.9    
77.1    
77.3    
77.5    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.8    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.3    
81.5    
81.7    
81.9    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.9    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
87.0    
87.1    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.8    
91.0    
91.2    
91.4    
91.5    
91.7    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.7    
93.8    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 11771, rend_intergenic: 7187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16157, rend_intergenic: 12985  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41300, rend_intergenic: 38525  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57071, rend_intergenic: 45854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122759, rend_intergenic: 118946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support