-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_6263727-6440237

-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 HiQ_model.g22715.t1
Couldn't classify 162012, 162092
Sorry, prediction pasa_asmbl_12720.p1 fails validation.
(ATG)	 AC	159861-159933	GT	AGG
(CGG)	 AG	160244-160373	GT	GAG
(GGA)	 AG	160627-160823	GT	CAG
(TAA)	 AG	161005-161159	GT	ATG
(GTT)	 AG	161249-161417	GT	TGG
(CGT)	 AG	161560-161662	GT	AAG
(AAT)	 AG	161771-161849	GT	AGG
(AGC)	 AG	162012-162092	AC	TCA
-recovered pasa_asmbl_12720.p1, initial, 159861, 159933
-recovered pasa_asmbl_12720.p1, internal, 160244, 160373
-recovered pasa_asmbl_12720.p1, internal, 160627, 160823
-recovered pasa_asmbl_12720.p1, internal, 161005, 161159
-recovered pasa_asmbl_12720.p1, internal, 161249, 161417
-recovered pasa_asmbl_12720.p1, internal, 161560, 161662
-recovered pasa_asmbl_12720.p1, internal, 161771, 161849
Valid prediction for GlimmerHMM_glimmerT_34002-T1
Valid prediction for Augustus_model.g22704.t1
Valid prediction for GlimmerHMM_glimmerT_34004-T1
Valid prediction for pasa_asmbl_12077.p1
Valid prediction for snap_scaffold_14-snap.1290-T1
Valid prediction for pasa_asmbl_12071.p1
Valid prediction for GlimmerHMM_glimmerT_33992-T1
Couldn't classify 27196, 27283
Sorry, prediction pasa_asmbl_12063.p1 fails validation.
(CTT)	 CT	27196-27283	GT	AGG
(ATG)	 AG	27546-27653	GT	AGG
(ACA)	 AG	27878-27911	GT	AGG
(TTC)	 AG	28054-28175	GT	AGG
(TGC)	 AG	28456-28520	GT	TGG
(CCA)	 AG	28797-28922	AC	GAA
add_exon() Sorry, pasa_asmbl_12063.p1 27546-27653-initial-1 is invalid.
-recovered pasa_asmbl_12063.p1, initial, 27546, 27653
-recovered pasa_asmbl_12063.p1, terminal, 28797, 28922
-recovered pasa_asmbl_12063.p1, internal, 27546, 27653
-recovered pasa_asmbl_12063.p1, internal, 27878, 27911
-recovered pasa_asmbl_12063.p1, internal, 28054, 28175
-recovered pasa_asmbl_12063.p1, internal, 28456, 28520
Valid prediction for snap_scaffold_14-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_33983-T1
Valid prediction for CodingQuarry_transcript_15657-T1
Valid prediction for GlimmerHMM_glimmerT_33989-T1
Valid prediction for HiQ_model.g22709.t1
Valid prediction for snap_scaffold_14-snap.1288-T1
Valid prediction for GlimmerHMM_glimmerT_33988-T1
Valid prediction for GlimmerHMM_glimmerT_33980-T1
Valid prediction for snap_scaffold_14-snap.1277-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_33993-T1
Valid prediction for snap_scaffold_14-snap.1278-T1
Valid prediction for GlimmerHMM_glimmerT_34008-T1
Valid prediction for GlimmerHMM_glimmerT_33998-T1
Valid prediction for snap_scaffold_14-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_34007-T1
Valid prediction for snap_scaffold_14-snap.1283-T1
Valid prediction for GlimmerHMM_glimmerT_33990-T1
Couldn't classify 23403, 23809
Sorry, prediction pasa_asmbl_12061.p1 fails validation.
(ATG)	 AA	22608-22659	GT	AGG
(ATG)	 AG	23403-23809	GG	GAG
-recovered pasa_asmbl_12061.p1, initial, 22608, 22659
Valid prediction for Augustus_model.g22703.t1
Valid prediction for snap_scaffold_14-snap.1275-T1
Valid prediction for snap_scaffold_14-snap.1301-T1
Valid prediction for CodingQuarry_transcript_15660-T1
Valid prediction for snap_scaffold_14-snap.1306-T1
Valid prediction for CodingQuarry_transcript_15659-T1
Valid prediction for Augustus_model.g22702.t1
Valid prediction for Augustus_model.g22700.t1
Valid prediction for GlimmerHMM_glimmerT_34005-T1
Valid prediction for GlimmerHMM_glimmerT_33984-T1
Valid prediction for snap_scaffold_14-snap.1317-T1
Valid prediction for GlimmerHMM_glimmerT_34000-T1
Valid prediction for Augustus_model.g22701.t1
Valid prediction for GlimmerHMM_glimmerT_33997-T1
Valid prediction for snap_scaffold_14-snap.1299-T1
Valid prediction for snap_scaffold_14-snap.1281-T1
Couldn't classify 35392, 35502
Couldn't classify 35679, 35876
Sorry, prediction pasa_asmbl_12069.p3 fails validation.
(GTC)	 AG	35392-35502	GT	AGG
(CTG)	 AG	35679-35876	CT	TGC
-recovered pasa_asmbl_12069.p3, internal, 35392, 35502
Valid prediction for Augustus_model.g22708.t1
Valid prediction for Augustus_model.g22710.t1
Valid prediction for GlimmerHMM_glimmerT_33986-T1
Valid prediction for Augustus_model.g22717.t1
Valid prediction for snap_scaffold_14-snap.1311-T1
Valid prediction for snap_scaffold_14-snap.1310-T1
Valid prediction for CodingQuarry_transcript_15663-T1
Valid prediction for snap_scaffold_14-snap.1285-T1
Valid prediction for snap_scaffold_14-snap.1294-T1
Valid prediction for snap_scaffold_14-snap.1312-T1
Valid prediction for GlimmerHMM_glimmerT_33995-T1
Valid prediction for Augustus_model.g22712.t1
Couldn't classify 155576, 155742
Sorry, prediction pasa_asmbl_12079.p1 fails validation.
(ATG)	 CC	154788-154899	GT	ACG
(AGT)	 AG	154999-155157	GT	AGG
(AGT)	 AG	155332-155469	GT	ATG
(CAA)	 AG	155576-155742	AG	TAA
-recovered pasa_asmbl_12079.p1, initial, 154788, 154899
-recovered pasa_asmbl_12079.p1, internal, 154999, 155157
-recovered pasa_asmbl_12079.p1, internal, 155332, 155469
Valid prediction for Augustus_model.g22706.t1
Valid prediction for snap_scaffold_14-snap.1284-T1
Valid prediction for HiQ_model.g22699.t1
Valid prediction for snap_scaffold_14-snap.1296-T1
Valid prediction for Augustus_model.g22718.t1
Valid prediction for GlimmerHMM_glimmerT_33994-T1
Valid prediction for snap_scaffold_14-snap.1314-T1
Valid prediction for Augustus_model.g22696.t1
Valid prediction for GlimmerHMM_glimmerT_33985-T1
Valid prediction for snap_scaffold_14-snap.1302-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 Augustus_model.g22698.t1
Valid prediction for CodingQuarry_transcript_15662-T1
Valid prediction for GlimmerHMM_glimmerT_34003-T1
Valid prediction for GlimmerHMM_glimmerT_34006-T1
Valid prediction for GlimmerHMM_glimmerT_33987-T1
Valid prediction for GlimmerHMM_glimmerT_33996-T1
Couldn't classify 56981, 57352
Sorry, prediction pasa_asmbl_13121.p1 fails validation.
(ACC)	 AC	56981-57352	GA	GTG
Valid prediction for Augustus_model.g22711.t1
Valid prediction for snap_scaffold_14-snap.1286-T1
Valid prediction for snap_scaffold_14-snap.1280-T1
Valid prediction for snap_scaffold_14-snap.1305-T1
Valid prediction for pasa_asmbl_13125.p2
Valid prediction for CodingQuarry_transcript_15661-T1
Valid prediction for GlimmerHMM_glimmerT_33981-T1
Valid prediction for snap_scaffold_14-snap.1279-T1
Valid prediction for snap_scaffold_14-snap.1307-T1
Valid prediction for GlimmerHMM_glimmerT_33999-T1
Valid prediction for Augustus_model.g22697.t1
Valid prediction for snap_scaffold_14-snap.1309-T1
Valid prediction for CodingQuarry_transcript_15664-T1
Valid prediction for snap_scaffold_14-snap.1282-T1
Valid prediction for GlimmerHMM_glimmerT_34009-T1
Valid prediction for HiQ_model.g22713.t1
Valid prediction for snap_scaffold_14-snap.1295-T1
Valid prediction for snap_scaffold_14-snap.1293-T1
Valid prediction for GlimmerHMM_glimmerT_33982-T1
Valid prediction for Augustus_model.g22705.t1
Valid prediction for snap_scaffold_14-snap.1291-T1
Valid prediction for snap_scaffold_14-snap.1304-T1
Valid prediction for snap_scaffold_14-snap.1308-T1
Valid prediction for HiQ_model.g22714.t1
Valid prediction for snap_scaffold_14-snap.1292-T1
Valid prediction for HiQ_model.g22719.t1
Valid prediction for snap_scaffold_14-snap.1297-T1
Valid prediction for snap_scaffold_14-snap.1289-T1
Valid prediction for Augustus_model.g22707.t1
Valid prediction for Augustus_model.g22720.t1
Valid prediction for CodingQuarry_transcript_15665-T1
Valid prediction for snap_scaffold_14-snap.1313-T1
Valid prediction for pasa_asmbl_13128.p1
Valid prediction for snap_scaffold_14-snap.1315-T1
Valid prediction for GlimmerHMM_glimmerT_33991-T1
Valid prediction for snap_scaffold_14-snap.1276-T1
Valid prediction for GlimmerHMM_glimmerT_34001-T1
Couldn't classify 1867, 1975
Sorry, prediction pasa_asmbl_13132.p1 fails validation.
(GAT)	 AG	1867-1975	GT	AGG
(GTG)	 AG	2303-2394	GT	AGG
(GCT)	 AG	2618-2713	GT	AGG
(CTC)	 AG	5201-5326	GT	AGG
(ATT)	 AG	7483-7512	AG	GAA
-recovered pasa_asmbl_13132.p1, terminal, 7483, 7512
-recovered pasa_asmbl_13132.p1, internal, 1867, 1975
-recovered pasa_asmbl_13132.p1, internal, 2303, 2394
-recovered pasa_asmbl_13132.p1, internal, 2618, 2713
-recovered pasa_asmbl_13132.p1, internal, 5201, 5326
Valid prediction for Augustus_model.g22716.t1
Valid prediction for snap_scaffold_14-snap.1300-T1
Valid prediction for snap_scaffold_14-snap.1298-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12971, rend_intergenic: 5514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16291, rend_intergenic: 14669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23595, rend_intergenic: 21489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25554, rend_intergenic: 24505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27724, rend_intergenic: 26444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79098, rend_intergenic: 75765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82625, rend_intergenic: 82464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84438, rend_intergenic: 82847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100744, rend_intergenic: 86298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107251, rend_intergenic: 106008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109940, rend_intergenic: 107704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146235, rend_intergenic: 141463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176511
-exon list size: 404


building trellis

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21.4    
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22.4    
22.7    
22.9    
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24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.8    
27.1    
27.3    
27.6    
27.8    
28.1    
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28.6    
28.8    
29.1    
29.3    
29.6    
29.8    
30.0    
30.3    
30.5    
30.8    
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31.3    
31.5    
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    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
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    
52.0    
52.2    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
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56.9    
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57.4    
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57.9    
58.1    
58.4    
58.6    
58.9    
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59.4    
59.6    
59.9    
60.1    
60.3    
60.6    
60.8    
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61.6    
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64.3    
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65.3    
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66.3    
66.5    
66.7    
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67.2    
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68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
70.7    
70.9    
71.2    
71.4    
71.7    
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72.2    
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73.2    
73.4    
73.6    
73.9    
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74.4    
74.6    
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75.4    
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76.6    
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78.3    
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79.6    
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80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
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    
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85.5    
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86.0    
86.2    
86.5    
86.7    
86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
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89.4    
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90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
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92.4    
92.6    
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93.1    
93.3    
93.6    
93.8    
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94.3    
94.6    
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95.1    
95.3    
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96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 12971, rend_intergenic: 5514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16291, rend_intergenic: 14669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23595, rend_intergenic: 21489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25554, rend_intergenic: 24505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27724, rend_intergenic: 26444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79098, rend_intergenic: 75765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82625, rend_intergenic: 82464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84438, rend_intergenic: 82847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100744, rend_intergenic: 86298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107251, rend_intergenic: 106008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109940, rend_intergenic: 107704  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146235, rend_intergenic: 141463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support