-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_14735574-14909839

-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.3099-T1
Valid prediction for snap_scaffold_6-snap.3127-T1
Valid prediction for GlimmerHMM_glimmerT_16013-T1
Valid prediction for snap_scaffold_6-snap.3101-T1
Valid prediction for HiQ_model.g10751.t1
Valid prediction for GlimmerHMM_glimmerT_16008-T1
Valid prediction for snap_scaffold_6-snap.3116-T1
Valid prediction for snap_scaffold_6-snap.3118-T1
Valid prediction for snap_scaffold_6-snap.3122-T1
Valid prediction for GlimmerHMM_glimmerT_16009-T1
Valid prediction for Augustus_model.g10755.t1
Valid prediction for snap_scaffold_6-snap.3093-T1
Valid prediction for snap_scaffold_6-snap.3112-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_15997-T1
Valid prediction for snap_scaffold_6-snap.3088-T1
Valid prediction for snap_scaffold_6-snap.3119-T1
Valid prediction for GlimmerHMM_glimmerT_16015-T1
Valid prediction for snap_scaffold_6-snap.3103-T1
Valid prediction for snap_scaffold_6-snap.3107-T1
Valid prediction for Augustus_model.g10760.t1
Valid prediction for Augustus_model.g10753.t1
Valid prediction for snap_scaffold_6-snap.3105-T1
Valid prediction for snap_scaffold_6-snap.3124-T1
Valid prediction for CodingQuarry_transcript_55352-T1
Valid prediction for snap_scaffold_6-snap.3091-T1
Valid prediction for pasa_asmbl_47642.p1
Valid prediction for GlimmerHMM_glimmerT_15995-T1
Valid prediction for Augustus_model.g10759.t1
Valid prediction for CodingQuarry_transcript_55348-T1
Valid prediction for snap_scaffold_6-snap.3128-T1
Valid prediction for snap_scaffold_6-snap.3130-T1
Valid prediction for CodingQuarry_transcript_55353-T1
Valid prediction for GlimmerHMM_glimmerT_16001-T1
Valid prediction for snap_scaffold_6-snap.3123-T1
Valid prediction for snap_scaffold_6-snap.3121-T1
Valid prediction for GlimmerHMM_glimmerT_16012-T1
Valid prediction for snap_scaffold_6-snap.3109-T1
Valid prediction for GlimmerHMM_glimmerT_16007-T1
Valid prediction for pasa_asmbl_47646.p1
Valid prediction for GlimmerHMM_glimmerT_15998-T1
Valid prediction for snap_scaffold_6-snap.3096-T1
Couldn't classify 55917, 56036
Couldn't classify 56405, 56528
Sorry, prediction pasa_asmbl_47926.p1 fails validation.
(GCA)	 TC	55917-56036	GT	AGG
(GCC)	 AG	56105-56190	GT	CGG
(AAA)	 AG	56405-56528	GC	GGG
-recovered pasa_asmbl_47926.p1, internal, 56105, 56190
-recovered pasa_asmbl_47926.p1, internal, 56405, 56528
Valid prediction for Augustus_model.g10763.t1
Valid prediction for GlimmerHMM_glimmerT_15991-T1
Couldn't classify 57752, 57823
Sorry, prediction pasa_asmbl_47643.p1 fails validation.
(GGG)	 CA	57752-57823	GT	ACG
(GGG)	 AG	57910-58092	GT	TGG
(GCG)	 AG	58223-58366	GT	CGG
(GAC)	 AG	58465-58551	TG	AAT
-recovered pasa_asmbl_47643.p1, terminal, 58465, 58551
-recovered pasa_asmbl_47643.p1, internal, 57910, 58092
-recovered pasa_asmbl_47643.p1, internal, 58223, 58366
Valid prediction for HiQ_model.g10766.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.g10756.t1
Valid prediction for snap_scaffold_6-snap.3114-T1
Couldn't classify 107338, 107549
Sorry, prediction pasa_asmbl_49031.p1 fails validation.
(ATG)	 TG	106623-106809	GT	GGG
(GTC)	 AG	106911-107033	GT	AGG
(GGC)	 AG	107338-107549	CC	CAC
-recovered pasa_asmbl_49031.p1, initial, 106623, 106809
-recovered pasa_asmbl_49031.p1, internal, 106911, 107033
Valid prediction for snap_scaffold_6-snap.3094-T1
Valid prediction for GlimmerHMM_glimmerT_15994-T1
Valid prediction for snap_scaffold_6-snap.3117-T1
Valid prediction for snap_scaffold_6-snap.3113-T1
Valid prediction for GlimmerHMM_glimmerT_16006-T1
Valid prediction for snap_scaffold_6-snap.3125-T1
Valid prediction for GlimmerHMM_glimmerT_16016-T1
Valid prediction for Augustus_model.g10746.t1
Valid prediction for snap_scaffold_6-snap.3090-T1
Valid prediction for GlimmerHMM_glimmerT_16004-T1
Valid prediction for snap_scaffold_6-snap.3089-T1
Couldn't classify 120778, 120856
Sorry, prediction pasa_asmbl_49028.p1 fails validation.
(TAC)	 AC	120778-120856	GT	GGG
(GCA)	 AG	121115-121269	GT	ATG
(GCG)	 AG	121472-121620	GT	CGG
(AGT)	 AG	122348-122519	GT	AGG
(GCC)	 AG	122637-122743	GT	AAG
(GTT)	 AG	122903-123014	GT	AGG
(CCA)	 AG	123128-123312	GT	AGG
(GAT)	 AG	123570-123712	GT	GAG
(CCA)	 AG	123813-123909	GT	AGG
(GTG)	 AG	124228-124339	GT	TGG
(GTC)	 AG	124678-125079	TC	AGT
add_exon() Sorry, pasa_asmbl_49028.p1 122637-122743-terminal-2 is invalid.
-recovered pasa_asmbl_49028.p1, terminal, 122637, 122743
-recovered pasa_asmbl_49028.p1, terminal, 123570, 123712
-recovered pasa_asmbl_49028.p1, terminal, 124678, 125079
-recovered pasa_asmbl_49028.p1, internal, 121115, 121269
-recovered pasa_asmbl_49028.p1, internal, 121472, 121620
-recovered pasa_asmbl_49028.p1, internal, 122348, 122519
-recovered pasa_asmbl_49028.p1, internal, 122637, 122743
-recovered pasa_asmbl_49028.p1, internal, 122903, 123014
-recovered pasa_asmbl_49028.p1, internal, 123128, 123312
-recovered pasa_asmbl_49028.p1, internal, 123570, 123712
-recovered pasa_asmbl_49028.p1, internal, 123813, 123909
-recovered pasa_asmbl_49028.p1, internal, 124228, 124339
Valid prediction for pasa_asmbl_49029.p1
Valid prediction for GlimmerHMM_glimmerT_15996-T1
Valid prediction for Augustus_model.g10761.t1
Valid prediction for HiQ_model.g10754.t1
Valid prediction for snap_scaffold_6-snap.3131-T1
Valid prediction for snap_scaffold_6-snap.3095-T1
Valid prediction for HiQ_model.g10757.t1
Valid prediction for snap_scaffold_6-snap.3108-T1
Valid prediction for Augustus_model.g10752.t1
Valid prediction for Augustus_model.g10767.t1
Valid prediction for GlimmerHMM_glimmerT_16000-T1
Valid prediction for Augustus_model.g10747.t1
Valid prediction for Augustus_model.g10764.t1
Valid prediction for snap_scaffold_6-snap.3111-T1
Couldn't classify 108354, 108941
Sorry, prediction pasa_asmbl_49030.p1 fails validation.
(GTC)	 TC	108354-108941	CA	GAC
Valid prediction for snap_scaffold_6-snap.3115-T1
Valid prediction for CodingQuarry_transcript_55350-T1
Valid prediction for GlimmerHMM_glimmerT_16005-T1
Valid prediction for Augustus_model.g10762.t1
Valid prediction for snap_scaffold_6-snap.3098-T1
Valid prediction for snap_scaffold_6-snap.3110-T1
Valid prediction for snap_scaffold_6-snap.3102-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3120-T1
Valid prediction for Augustus_model.g10758.t1
Valid prediction for GlimmerHMM_glimmerT_15992-T1
Valid prediction for snap_scaffold_6-snap.3097-T1
Valid prediction for GlimmerHMM_glimmerT_16014-T1
Valid prediction for Augustus_model.g10748.t1
Valid prediction for GlimmerHMM_glimmerT_16003-T1
Valid prediction for GlimmerHMM_glimmerT_15993-T1
Valid prediction for snap_scaffold_6-snap.3106-T1
Valid prediction for snap_scaffold_6-snap.3100-T1
Couldn't classify 130653, 130669
Couldn't classify 130891, 131233
Sorry, prediction pasa_asmbl_49027.p1 fails validation.
(GAT)	 GC	130653-130669	GT	CGG
(GGT)	 AG	130891-131233	CC	CGC
Valid prediction for snap_scaffold_6-snap.3104-T1
Valid prediction for snap_scaffold_6-snap.3126-T1
Valid prediction for Augustus_model.g10749.t1
Valid prediction for CodingQuarry_transcript_55351-T1
Valid prediction for snap_scaffold_6-snap.3129-T1
Valid prediction for GlimmerHMM_glimmerT_16002-T1
Couldn't classify 101061, 101172
Sorry, prediction pasa_asmbl_49399.p1 fails validation.
(GGG)	 CT	101061-101172	GT	AGG
(ATG)	 AG	101479-101526	GT	GGG
(ATC)	 AG	101730-101823	GT	AGG
(CCT)	 AG	102337-102439	AC	AGA
-recovered pasa_asmbl_49399.p1, initial, 101479, 101526
-recovered pasa_asmbl_49399.p1, terminal, 102337, 102439
-recovered pasa_asmbl_49399.p1, internal, 101479, 101526
-recovered pasa_asmbl_49399.p1, internal, 101730, 101823
Valid prediction for Augustus_model.g10750.t1
Valid prediction for GlimmerHMM_glimmerT_15990-T1
Valid prediction for Augustus_model.g10765.t1
Valid prediction for GlimmerHMM_glimmerT_16011-T1
Valid prediction for snap_scaffold_6-snap.3092-T1
Valid prediction for GlimmerHMM_glimmerT_15999-T1
Valid prediction for GlimmerHMM_glimmerT_16010-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10862, rend_intergenic: 5012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25083, rend_intergenic: 18932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26407, rend_intergenic: 26162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49353, rend_intergenic: 49188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70279, rend_intergenic: 68569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75360, rend_intergenic: 71868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82604, rend_intergenic: 76889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86114, rend_intergenic: 84484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97031, rend_intergenic: 94650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111617, rend_intergenic: 106292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120552, rend_intergenic: 116920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129642, rend_intergenic: 120807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135921, rend_intergenic: 130708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141211, rend_intergenic: 137041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153758, rend_intergenic: 141830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174266
-exon list size: 411


building trellis

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11.9    
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15.3    
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16.9    
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17.4    
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18.6    
18.9    
19.1    
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19.6    
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20.1    
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20.6    
20.8    
21.1    
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21.8    
22.0    
22.3    
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23.5    
23.7    
24.0    
24.2    
24.5    
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24.9    
25.2    
25.4    
25.7    
25.9    
26.2    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.8    
28.1    
28.3    
28.6    
28.8    
29.1    
29.3    
29.5    
29.8    
30.0    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.4    
32.7    
32.9    
33.2    
33.4    
33.7    
33.9    
34.1    
34.4    
34.6    
34.9    
35.1    
35.4    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
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    
45.0    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
47.0    
47.2    
47.5    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.8    
51.1    
51.3    
51.6    
51.8    
52.1    
52.3    
52.5    
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53.3    
53.5    
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54.2    
54.5    
54.7    
55.0    
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55.9    
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56.9    
57.1    
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57.6    
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58.1    
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58.6    
58.8    
59.1    
59.3    
59.6    
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60.0    
60.3    
60.5    
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68.3    
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68.8    
69.0    
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70.0    
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73.4    
73.6    
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74.1    
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74.6    
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75.1    
75.3    
75.5    
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76.0    
76.3    
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78.2    
78.5    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.8    
82.1    
82.3    
82.6    
82.8    
83.1    
83.3    
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84.0    
84.3    
84.5    
84.7    
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85.2    
85.5    
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86.0    
86.2    
86.4    
86.7    
86.9    
87.2    
87.4    
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87.9    
88.1    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.1    
90.3    
90.6    
90.8    
91.0    
91.3    
91.5    
91.8    
92.0    
92.3    
92.5    
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93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
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94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
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 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 10862, rend_intergenic: 5012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25083, rend_intergenic: 18932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26407, rend_intergenic: 26162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49353, rend_intergenic: 49188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70279, rend_intergenic: 68569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75360, rend_intergenic: 71868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82604, rend_intergenic: 76889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86114, rend_intergenic: 84484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97031, rend_intergenic: 94650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111617, rend_intergenic: 106292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120552, rend_intergenic: 116920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129642, rend_intergenic: 120807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135921, rend_intergenic: 130708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141211, rend_intergenic: 137041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153758, rend_intergenic: 141830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support