-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_4324212-4505382

-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.1053-T1
Valid prediction for snap_scaffold_6-snap.1039-T1
Valid prediction for snap_scaffold_6-snap.1052-T1
Valid prediction for snap_scaffold_6-snap.1029-T1
Valid prediction for snap_scaffold_6-snap.1055-T1
Valid prediction for Augustus_model.g9597.t1
Valid prediction for GlimmerHMM_glimmerT_14492-T1
Valid prediction for snap_scaffold_6-snap.1033-T1
Valid prediction for snap_scaffold_6-snap.1051-T1
Valid prediction for GlimmerHMM_glimmerT_14497-T1
Valid prediction for snap_scaffold_6-snap.1057-T1
Couldn't classify 108704, 108817
Couldn't classify 112987, 113142
Sorry, prediction pasa_asmbl_46886.p1 fails validation.
(TCA)	 CC	108704-108817	GT	AGG
(TGG)	 AG	110334-110468	GT	AGG
(GGG)	 AG	112987-113142	GG	GGG
-recovered pasa_asmbl_46886.p1, internal, 110334, 110468
Valid prediction for snap_scaffold_6-snap.1040-T1
Valid prediction for snap_scaffold_6-snap.1038-T1
Valid prediction for snap_scaffold_6-snap.1024-T1
Valid prediction for Augustus_model.g9598.t1
Valid prediction for GlimmerHMM_glimmerT_14484-T1
Valid prediction for CodingQuarry_transcript_55015-T1
Valid prediction for GlimmerHMM_glimmerT_14501-T1
Valid prediction for snap_scaffold_6-snap.1047-T1
Valid prediction for snap_scaffold_6-snap.1049-T1
Valid prediction for snap_scaffold_6-snap.1043-T1
Valid prediction for GlimmerHMM_glimmerT_14499-T1
Valid prediction for snap_scaffold_6-snap.1046-T1
Valid prediction for snap_scaffold_6-snap.1058-T1
Valid prediction for snap_scaffold_6-snap.1027-T1
Valid prediction for snap_scaffold_6-snap.1036-T1
Valid prediction for Augustus_model.g9596.t1
Valid prediction for Augustus_model.g9591.t1
Valid prediction for Augustus_model.g9586.t1
Valid prediction for snap_scaffold_6-snap.1044-T1
Valid prediction for GlimmerHMM_glimmerT_14493-T1
Valid prediction for snap_scaffold_6-snap.1022-T1
Valid prediction for GlimmerHMM_glimmerT_14498-T1
Valid prediction for snap_scaffold_6-snap.1030-T1
Valid prediction for snap_scaffold_6-snap.1020-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_6-snap.1045-T1
Valid prediction for snap_scaffold_6-snap.1061-T1
Valid prediction for GlimmerHMM_glimmerT_14494-T1
Valid prediction for snap_scaffold_6-snap.1042-T1
Valid prediction for GlimmerHMM_glimmerT_14488-T1
Valid prediction for GlimmerHMM_glimmerT_14507-T1
Valid prediction for CodingQuarry_transcript_55013-T1
Valid prediction for snap_scaffold_6-snap.1060-T1
Valid prediction for GlimmerHMM_glimmerT_14506-T1
Valid prediction for GlimmerHMM_glimmerT_14502-T1
Valid prediction for Augustus_model.g9588.t1
Valid prediction for snap_scaffold_6-snap.1025-T1
Valid prediction for Augustus_model.g9600.t1
Valid prediction for snap_scaffold_6-snap.1019-T1
Valid prediction for GlimmerHMM_glimmerT_14483-T1
Valid prediction for pasa_asmbl_48310.p1
Couldn't classify 21163, 21252
Sorry, prediction pasa_asmbl_48321.p1 fails validation.
(ATG)	 CC	19260-19340	GT	AGG
(GGC)	 AG	20619-20690	GT	AGG
(ACT)	 AG	20792-20861	GT	AGG
(GAA)	 AG	20965-21008	GT	AGG
(TTT)	 AG	21163-21252	CC	CCC
-recovered pasa_asmbl_48321.p1, initial, 19260, 19340
-recovered pasa_asmbl_48321.p1, internal, 20619, 20690
-recovered pasa_asmbl_48321.p1, internal, 20792, 20861
-recovered pasa_asmbl_48321.p1, internal, 20965, 21008
Valid prediction for snap_scaffold_6-snap.1063-T1
Valid prediction for snap_scaffold_6-snap.1041-T1
Valid prediction for GlimmerHMM_glimmerT_14495-T1
Valid prediction for snap_scaffold_6-snap.1021-T1
Couldn't classify 7406, 7425
Couldn't classify 8846, 8980
Sorry, prediction pasa_asmbl_48326.p1 fails validation.
(GTG)	 CT	7406-7425	GT	GGG
(GCT)	 AG	7580-7754	GT	ACG
(GAA)	 AG	7857-8018	GT	TGG
(GAC)	 AG	8125-8220	GT	CGG
(AAC)	 AG	8348-8437	GT	AGG
(AAG)	 AG	8596-8730	GT	CGG
(GTG)	 AG	8846-8980	CA	ACC
-recovered pasa_asmbl_48326.p1, internal, 7580, 7754
-recovered pasa_asmbl_48326.p1, internal, 7857, 8018
-recovered pasa_asmbl_48326.p1, internal, 8125, 8220
-recovered pasa_asmbl_48326.p1, internal, 8348, 8437
-recovered pasa_asmbl_48326.p1, internal, 8596, 8730
Couldn't classify 135804, 136117
Sorry, prediction pasa_asmbl_48312.p1 fails validation.
(ATG)	 AC	131007-132059	GT	AGG
(TGT)	 AG	132696-132843	GT	CGG
(CCC)	 AG	133368-133483	GT	AGG
(AAT)	 AG	134320-134464	GT	AGG
(GAG)	 AG	135804-136117	CT	GCC
-recovered pasa_asmbl_48312.p1, initial, 131007, 132059
-recovered pasa_asmbl_48312.p1, internal, 132696, 132843
-recovered pasa_asmbl_48312.p1, internal, 133368, 133483
-recovered pasa_asmbl_48312.p1, internal, 134320, 134464
Valid prediction for snap_scaffold_6-snap.1037-T1
Valid prediction for snap_scaffold_6-snap.1062-T1
Valid prediction for snap_scaffold_6-snap.1031-T1
Valid prediction for HiQ_model.g9602.t1
Valid prediction for GlimmerHMM_glimmerT_14486-T1
Valid prediction for GlimmerHMM_glimmerT_14504-T1
Valid prediction for Augustus_model.g9594.t1
Valid prediction for Augustus_model.g9595.t1
Valid prediction for Augustus_model.g9603.t1
Valid prediction for GlimmerHMM_glimmerT_14485-T1
Valid prediction for Augustus_model.g9599.t1
Valid prediction for pasa_asmbl_48319.p1
Valid prediction for GlimmerHMM_glimmerT_14503-T1
Valid prediction for snap_scaffold_6-snap.1035-T1
Valid prediction for HiQ_model.g9587.t1
Valid prediction for snap_scaffold_6-snap.1056-T1
Valid prediction for Augustus_model.g9593.t1
Valid prediction for Augustus_model.g9601.t1
Valid prediction for GlimmerHMM_glimmerT_14491-T1
Couldn't classify 14523, 14689
Sorry, prediction pasa_asmbl_48322.p1 fails validation.
(CGT)	 AG	14523-14689	GT	TGG
(GGA)	 AG	14894-14982	GT	AGG
(AGG)	 AG	15096-15364	GT	AGG
(GTT)	 AG	15443-15492	GT	AAG
(TGA)	 AG	15659-15719	GT	AGG
(ACA)	 AG	15816-15955	GT	AGG
(GAT)	 AG	16242-16348	GT	AGG
(GAA)	 AG	16517-16582	GT	AGG
(ATG)	 AG	16672-16880	CA	GAC
-recovered pasa_asmbl_48322.p1, terminal, 16672, 16880
-recovered pasa_asmbl_48322.p1, internal, 14523, 14689
-recovered pasa_asmbl_48322.p1, internal, 14894, 14982
-recovered pasa_asmbl_48322.p1, internal, 15096, 15364
-recovered pasa_asmbl_48322.p1, internal, 15443, 15492
-recovered pasa_asmbl_48322.p1, internal, 15659, 15719
-recovered pasa_asmbl_48322.p1, internal, 15816, 15955
-recovered pasa_asmbl_48322.p1, internal, 16242, 16348
-recovered pasa_asmbl_48322.p1, internal, 16517, 16582
Couldn't classify 12470, 12560
Sorry, prediction pasa_asmbl_48324.p1 fails validation.
(ACA)	 GC	12470-12560	GT	AGG
(AGT)	 AG	13058-13224	GT	CGG
(GGT)	 AG	13385-13450	GG	AAG
-recovered pasa_asmbl_48324.p1, terminal, 13385, 13450
-recovered pasa_asmbl_48324.p1, internal, 13058, 13224
Valid prediction for snap_scaffold_6-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_14500-T1
Valid prediction for GlimmerHMM_glimmerT_14490-T1
Valid prediction for Augustus_model.g9585.t1
Valid prediction for pasa_asmbl_48317.p2
Valid prediction for GlimmerHMM_glimmerT_14487-T1
Valid prediction for HiQ_model.g9589.t1
Valid prediction for snap_scaffold_6-snap.1032-T1
Valid prediction for snap_scaffold_6-snap.1023-T1
Valid prediction for snap_scaffold_6-snap.1048-T1
Valid prediction for GlimmerHMM_glimmerT_14496-T1
Valid prediction for CodingQuarry_transcript_55014-T1
Valid prediction for snap_scaffold_6-snap.1054-T1
Valid prediction for snap_scaffold_6-snap.1050-T1
Valid prediction for snap_scaffold_6-snap.1034-T1
Valid prediction for CodingQuarry_transcript_55016-T1
Valid prediction for snap_scaffold_6-snap.1028-T1
Valid prediction for GlimmerHMM_glimmerT_14508-T1
Valid prediction for HiQ_model.g9590.t1
Valid prediction for GlimmerHMM_glimmerT_14509-T1
Valid prediction for GlimmerHMM_glimmerT_14489-T1
Valid prediction for Augustus_model.g9592.t1
Valid prediction for GlimmerHMM_glimmerT_14505-T1
Valid prediction for pasa_asmbl_48313.p1
Valid prediction for snap_scaffold_6-snap.1026-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7776, rend_intergenic: 6535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14387, rend_intergenic: 10760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16895, rend_intergenic: 14793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20986, rend_intergenic: 17903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35454, rend_intergenic: 28856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45724, rend_intergenic: 44755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77551, rend_intergenic: 72577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88966, rend_intergenic: 78855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107791, rend_intergenic: 107161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112119, rend_intergenic: 108323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117459, rend_intergenic: 114370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117583, rend_intergenic: 117469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127054, rend_intergenic: 117632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137184, rend_intergenic: 136978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142062, rend_intergenic: 137505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150225, rend_intergenic: 142223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 181171
-exon list size: 410


building trellis

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0.7    
1.0    
1.2    
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2.4    
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2.9    
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3.9    
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9.5    
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10.0    
10.2    
10.4    
10.7    
10.9    
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11.4    
11.7    
11.9    
12.1    
12.4    
12.6    
12.9    
13.1    
13.3    
13.6    
13.8    
14.1    
14.3    
14.6    
14.8    
15.0    
15.3    
15.5    
15.8    
16.0    
16.3    
16.5    
16.7    
17.0    
17.2    
17.5    
17.7    
18.0    
18.2    
18.4    
18.7    
18.9    
19.2    
19.4    
19.7    
19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
21.4    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.3    
23.5    
23.8    
24.0    
24.3    
24.5    
24.8    
25.0    
25.2    
25.5    
25.7    
26.0    
26.2    
26.5    
26.7    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.7    
42.0    
42.2    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.8    
47.1    
47.3    
47.6    
47.8    
48.1    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
51.9    
52.2    
52.4    
52.7    
52.9    
53.2    
53.4    
53.6    
53.9    
54.1    
54.4    
54.6    
54.9    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.8    
57.0    
57.3    
57.5    
57.8    
58.0    
58.3    
58.5    
58.7    
59.0    
59.2    
59.5    
59.7    
60.0    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.1    
62.4    
62.6    
62.9    
63.1    
63.3    
63.6    
63.8    
64.1    
64.3    
64.6    
64.8    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.5    
66.7    
67.0    
67.2    
67.5    
67.7    
68.0    
68.2    
68.4    
68.7    
68.9    
69.2    
69.4    
69.7    
69.9    
70.1    
70.4    
70.6    
70.9    
71.1    
71.4    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.3    
73.5    
73.8    
74.0    
74.3    
74.5    
74.8    
75.0    
75.2    
75.5    
75.7    
76.0    
76.2    
76.5    
76.7    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.4    
78.6    
78.9    
79.1    
79.4    
79.6    
79.9    
80.1    
80.3    
80.6    
80.8    
81.1    
81.3    
81.6    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.4    
85.7    
85.9    
86.2    
86.4    
86.7    
86.9    
87.1    
87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.8    
91.0    
91.3    
91.5    
91.7    
92.0    
92.2    
92.5    
92.7    
93.0    
93.2    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 7776, rend_intergenic: 6535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14387, rend_intergenic: 10760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16895, rend_intergenic: 14793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20986, rend_intergenic: 17903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35454, rend_intergenic: 28856  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45724, rend_intergenic: 44755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77551, rend_intergenic: 72577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88966, rend_intergenic: 78855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107791, rend_intergenic: 107161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112119, rend_intergenic: 108323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117459, rend_intergenic: 114370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117583, rend_intergenic: 117469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127054, rend_intergenic: 117632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137184, rend_intergenic: 136978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142062, rend_intergenic: 137505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150225, rend_intergenic: 142223  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support