-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_10389885-10575952

-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.12227_t
Couldn't classify 56905, 57182
Sorry, prediction pasa_asmbl_40226.p1 fails validation.
(GCA)	 AT	56905-57182	GT	CAG
(ATT)	 AG	57413-57462	GT	GAG
(TGG)	 AG	57665-57748	GT	GGG
(GGG)	 AG	58125-58198	GT	AGG
(TTA)	 AG	58400-58483	GT	AGG
(GCA)	 AG	59311-59384	GT	AGG
(GAC)	 AG	60089-60173	GT	GGG
(GTA)	 AG	62279-62362	GT	AGG
(AGT)	 AG	62791-62864	GT	CAG
(GGT)	 AG	63015-63205	GT	TGG
(ATG)	 AG	65021-65154	CT	AGC
add_exon() Sorry, pasa_asmbl_40226.p1 57413-57462-terminal-2 is invalid.
-recovered pasa_asmbl_40226.p1, terminal, 57413, 57462
-recovered pasa_asmbl_40226.p1, terminal, 59311, 59384
-recovered pasa_asmbl_40226.p1, terminal, 65021, 65154
-recovered pasa_asmbl_40226.p1, internal, 57413, 57462
-recovered pasa_asmbl_40226.p1, internal, 57665, 57748
-recovered pasa_asmbl_40226.p1, internal, 58125, 58198
-recovered pasa_asmbl_40226.p1, internal, 58400, 58483
-recovered pasa_asmbl_40226.p1, internal, 59311, 59384
-recovered pasa_asmbl_40226.p1, internal, 60089, 60173
-recovered pasa_asmbl_40226.p1, internal, 62279, 62362
-recovered pasa_asmbl_40226.p1, internal, 62791, 62864
-recovered pasa_asmbl_40226.p1, internal, 63015, 63205
Valid prediction for GeneMark_model.12218_t
Valid prediction for GeneMark_model.12234_t
Valid prediction for HiQ_model.g4836.t1
Valid prediction for snap_scaffold_3-snap.2079-T1
Valid prediction for GlimmerHMM_glimmerT_7389-T1
Valid prediction for GeneMark_model.12237_t
Valid prediction for GlimmerHMM_glimmerT_7393-T1
Valid prediction for GeneMark_model.12210_t
Valid prediction for GeneMark_model.12239_t
Valid prediction for GeneMark_model.12233_t
Valid prediction for GeneMark_model.12216_t
Valid prediction for snap_scaffold_3-snap.2084-T1
Valid prediction for GeneMark_model.12208_t
Valid prediction for snap_scaffold_3-snap.2088-T1
Valid prediction for GlimmerHMM_glimmerT_7380-T1
Valid prediction for GeneMark_model.12225_t
Valid prediction for snap_scaffold_3-snap.2091-T1
Valid prediction for snap_scaffold_3-snap.2089-T1
Valid prediction for GeneMark_model.12196_t
Valid prediction for Augustus_model.g4839.t1
Valid prediction for snap_scaffold_3-snap.2076-T1
Valid prediction for snap_scaffold_3-snap.2110-T1
Valid prediction for GeneMark_model.12215_t
Valid prediction for GeneMark_model.12214_t
Valid prediction for GlimmerHMM_glimmerT_7391-T1
Valid prediction for snap_scaffold_3-snap.2093-T1
Valid prediction for GeneMark_model.12243_t
Valid prediction for GlimmerHMM_glimmerT_7377-T1
Valid prediction for GlimmerHMM_glimmerT_7379-T1
Valid prediction for GeneMark_model.12206_t
Couldn't classify 172220, 172264
Sorry, prediction pasa_asmbl_40228.p1 fails validation.
(AAA)	 TG	172220-172264	GT	AGG
(GGA)	 AG	173807-173883	GT	AGG
(AGA)	 AG	175700-175775	GT	TGG
(GTG)	 AG	176898-177033	GT	TGG
(ACC)	 AG	177424-177543	GT	AGG
(GGG)	 AG	177712-177917	GT	AGG
(GAA)	 AG	180139-180294	GA	AAG
-recovered pasa_asmbl_40228.p1, terminal, 177424, 177543
-recovered pasa_asmbl_40228.p1, terminal, 180139, 180294
-recovered pasa_asmbl_40228.p1, internal, 173807, 173883
-recovered pasa_asmbl_40228.p1, internal, 175700, 175775
-recovered pasa_asmbl_40228.p1, internal, 176898, 177033
-recovered pasa_asmbl_40228.p1, internal, 177424, 177543
-recovered pasa_asmbl_40228.p1, internal, 177712, 177917
Valid prediction for snap_scaffold_3-snap.2106-T1
Valid prediction for snap_scaffold_3-snap.2107-T1
Valid prediction for snap_scaffold_3-snap.2103-T1
Valid prediction for Augustus_model.g4834.t1
Valid prediction for GeneMark_model.12230_t
Valid prediction for GeneMark_model.12204_t
Valid prediction for GeneMark_model.12193_t
Valid prediction for snap_scaffold_3-snap.2104-T1
Valid prediction for GeneMark_model.12217_t
Valid prediction for snap_scaffold_3-snap.2100-T1
Valid prediction for GeneMark_model.12200_t
Valid prediction for snap_scaffold_3-snap.2098-T1
Valid prediction for snap_scaffold_3-snap.2099-T1
Couldn't classify 36590, 36640
Couldn't classify 39267, 39374
Sorry, prediction pasa_asmbl_40225.p1 fails validation.
(TTC)	 AT	36590-36640	GT	AGG
(GAA)	 AG	37966-38083	GT	TGG
(GTG)	 AG	38674-38867	GT	AGG
(CAA)	 AG	39267-39374	GT	AGG
-recovered pasa_asmbl_40225.p1, internal, 37966, 38083
-recovered pasa_asmbl_40225.p1, internal, 38674, 38867
-recovered pasa_asmbl_40225.p1, internal, 39267, 39374
Valid prediction for Augustus_model.g4847.t1
Valid prediction for GeneMark_model.12199_t
Valid prediction for GeneMark_model.12242_t
Valid prediction for GeneMark_model.12245_t
Valid prediction for Augustus_model.g4833.t1
Valid prediction for GeneMark_model.12221_t
Valid prediction for GeneMark_model.12202_t
Valid prediction for snap_scaffold_3-snap.2077-T1
Valid prediction for snap_scaffold_3-snap.2086-T1
Couldn't classify 169998, 170033
Couldn't classify 171252, 171325
Sorry, prediction pasa_asmbl_40227.p1 fails validation.
(GCC)	 TG	169998-170033	GT	TGG
(AAT)	 AG	170175-170252	GT	CTG
(GCC)	 AG	170446-170561	GT	AGG
(GTT)	 AG	170736-170836	GT	CTG
(GTT)	 AG	171252-171325	GT	AGG
-recovered pasa_asmbl_40227.p1, internal, 170175, 170252
-recovered pasa_asmbl_40227.p1, internal, 170446, 170561
-recovered pasa_asmbl_40227.p1, internal, 170736, 170836
-recovered pasa_asmbl_40227.p1, internal, 171252, 171325
Valid prediction for snap_scaffold_3-snap.2082-T1
Valid prediction for GeneMark_model.12212_t
Valid prediction for GlimmerHMM_glimmerT_7390-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 GeneMark_model.12224_t
Valid prediction for Augustus_model.g4841.t1
Valid prediction for GeneMark_model.12201_t
Valid prediction for GeneMark_model.12191_t
Valid prediction for GlimmerHMM_glimmerT_7376-T1
Valid prediction for snap_scaffold_3-snap.2101-T1
Valid prediction for GeneMark_model.12207_t
Couldn't classify 80600, 81759
Couldn't classify 82004, 82124
Sorry, prediction pasa_asmbl_39037.p1 fails validation.
(CAG)	 AG	80600-81759	GT	AGG
(CTG)	 AG	82004-82124	AG	GCA
-recovered pasa_asmbl_39037.p1, internal, 80600, 81759
Valid prediction for GeneMark_model.12213_t
Valid prediction for GeneMark_model.12205_t
Valid prediction for GeneMark_model.12219_t
Couldn't classify 83862, 83917
Couldn't classify 86487, 86630
Sorry, prediction pasa_asmbl_39036.p1 fails validation.
(CTG)	 GC	83862-83917	GT	AGG
(TGA)	 AG	85271-85317	GT	CGG
(TGA)	 AG	86021-86223	GT	AGG
(CTG)	 AG	86487-86630	CG	CCC
-recovered pasa_asmbl_39036.p1, internal, 85271, 85317
-recovered pasa_asmbl_39036.p1, internal, 86021, 86223
Valid prediction for CodingQuarry_transcript_46146-T1
Valid prediction for GlimmerHMM_glimmerT_7383-T1
Valid prediction for GeneMark_model.12197_t
Valid prediction for snap_scaffold_3-snap.2092-T1
Valid prediction for GeneMark_model.12195_t
Valid prediction for snap_scaffold_3-snap.2081-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.12231_t
Valid prediction for GeneMark_model.12223_t
Valid prediction for snap_scaffold_3-snap.2097-T1
Valid prediction for Augustus_model.g4838.t1
Valid prediction for GeneMark_model.12209_t
Valid prediction for GeneMark_model.12238_t
Couldn't classify 131915, 131987
Sorry, prediction pasa_asmbl_39702.p1 fails validation.
(ATG)	 GC	129227-129331	GT	TTG
(GGT)	 AG	129646-129697	GT	AGG
(GTC)	 AG	130576-130649	GT	CGG
(GCT)	 AG	131379-131458	GT	AGG
(TCC)	 AG	131915-131987	GA	GTG
-recovered pasa_asmbl_39702.p1, initial, 129227, 129331
-recovered pasa_asmbl_39702.p1, internal, 129646, 129697
-recovered pasa_asmbl_39702.p1, internal, 130576, 130649
-recovered pasa_asmbl_39702.p1, internal, 131379, 131458
Valid prediction for snap_scaffold_3-snap.2087-T1
Valid prediction for GeneMark_model.12235_t
Valid prediction for GlimmerHMM_glimmerT_7388-T1
Valid prediction for GlimmerHMM_glimmerT_7384-T1
Valid prediction for GlimmerHMM_glimmerT_7382-T1
Valid prediction for Augustus_model.g4845.t1
Couldn't classify 58605, 58731
Couldn't classify 63682, 63729
Sorry, prediction pasa_asmbl_39044.p1 fails validation.
(GGG)	 AG	58605-58731	GT	AGG
(TGG)	 AG	59035-59166	GT	ATG
(CTG)	 AG	60265-60399	GT	TGG
(GTC)	 AG	60530-60647	GT	CTG
(AGA)	 AG	60868-60978	GT	AGG
(GAG)	 AG	61130-61226	GT	AGG
(TGT)	 AG	61549-61656	GT	ACG
(ATC)	 AG	62941-63054	GT	AGG
(TGT)	 AG	63234-63368	GT	GGG
(GCG)	 AG	63682-63729	AA	ACA
-recovered pasa_asmbl_39044.p1, internal, 58605, 58731
-recovered pasa_asmbl_39044.p1, internal, 59035, 59166
-recovered pasa_asmbl_39044.p1, internal, 60265, 60399
-recovered pasa_asmbl_39044.p1, internal, 60530, 60647
-recovered pasa_asmbl_39044.p1, internal, 60868, 60978
-recovered pasa_asmbl_39044.p1, internal, 61130, 61226
-recovered pasa_asmbl_39044.p1, internal, 61549, 61656
-recovered pasa_asmbl_39044.p1, internal, 62941, 63054
-recovered pasa_asmbl_39044.p1, internal, 63234, 63368
Valid prediction for Augustus_model.g4843.t1
Valid prediction for GlimmerHMM_glimmerT_7392-T1
Valid prediction for snap_scaffold_3-snap.2109-T1
Valid prediction for snap_scaffold_3-snap.2090-T1
Valid prediction for snap_scaffold_3-snap.2095-T1
Valid prediction for snap_scaffold_3-snap.2102-T1
Valid prediction for GlimmerHMM_glimmerT_7381-T1
Valid prediction for GeneMark_model.12232_t
Valid prediction for GeneMark_model.12198_t
Valid prediction for GeneMark_model.12211_t
Valid prediction for GeneMark_model.12246_t
Valid prediction for Augustus_model.g4840.t1
Valid prediction for GeneMark_model.12244_t
Valid prediction for snap_scaffold_3-snap.2096-T1
Valid prediction for GlimmerHMM_glimmerT_7386-T1
Valid prediction for snap_scaffold_3-snap.2080-T1
Valid prediction for snap_scaffold_3-snap.2083-T1
Couldn't classify 77780, 78514
Sorry, prediction pasa_asmbl_39040.p1 fails validation.
(CTG)	 AG	77780-78514	TC	CCT
Valid prediction for GeneMark_model.12192_t
Valid prediction for snap_scaffold_3-snap.2108-T1
Valid prediction for snap_scaffold_3-snap.2085-T1
Couldn't classify 79994, 80518
Sorry, prediction pasa_asmbl_39038.p1 fails validation.
(AAG)	 CC	79994-80518	GA	AGG
Valid prediction for Augustus_model.g4846.t1
Valid prediction for GlimmerHMM_glimmerT_7387-T1
Valid prediction for GeneMark_model.12241_t
Couldn't classify 79175, 79891
Sorry, prediction pasa_asmbl_39039.p1 fails validation.
(TCA)	 CC	79175-79891	CT	GCC
Valid prediction for GeneMark_model.12220_t
Valid prediction for snap_scaffold_3-snap.2078-T1
Valid prediction for Augustus_model.g4844.t1
Valid prediction for snap_scaffold_3-snap.2094-T1
Valid prediction for GeneMark_model.12222_t
Couldn't classify 75436, 75498
Couldn't classify 77451, 77497
Sorry, prediction pasa_asmbl_39041.p1 fails validation.
(AAA)	 AC	75436-75498	GT	AGG
(ATC)	 AG	75591-75644	GT	AGG
(TCT)	 AG	75811-75942	GT	AGG
(TGC)	 AG	76698-76956	GT	CTG
(CCG)	 AG	77451-77497	AC	AGA
-recovered pasa_asmbl_39041.p1, internal, 75591, 75644
-recovered pasa_asmbl_39041.p1, internal, 75811, 75942
-recovered pasa_asmbl_39041.p1, internal, 76698, 76956
Valid prediction for snap_scaffold_3-snap.2112-T1
Valid prediction for GeneMark_model.12194_t
Valid prediction for CodingQuarry_transcript_46145-T1
Valid prediction for GeneMark_model.12229_t
Valid prediction for GeneMark_model.12226_t
Valid prediction for GlimmerHMM_glimmerT_7378-T1
Valid prediction for GeneMark_model.12228_t
Valid prediction for GlimmerHMM_glimmerT_7385-T1
Valid prediction for snap_scaffold_3-snap.2105-T1
Valid prediction for GeneMark_model.12203_t
Valid prediction for Augustus_model.g4837.t1
Valid prediction for Augustus_model.g4835.t1
Valid prediction for GeneMark_model.12240_t
Valid prediction for Augustus_model.g4842.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23071, rend_intergenic: 6408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35602, rend_intergenic: 25716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44677, rend_intergenic: 37957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48392, rend_intergenic: 47189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53309, rend_intergenic: 51002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63813, rend_intergenic: 59128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73026, rend_intergenic: 70886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75640, rend_intergenic: 74032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138375, rend_intergenic: 118757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145648, rend_intergenic: 138635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153891, rend_intergenic: 146035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175308, rend_intergenic: 161295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178719, rend_intergenic: 177290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186068
-exon list size: 736


building trellis

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55.0    
55.1    
55.3    
55.4    
55.6    
55.7    
55.8    
56.0    
56.1    
56.2    
56.4    
56.5    
56.6    
56.8    
56.9    
57.0    
57.2    
57.3    
57.5    
57.6    
57.7    
57.9    
58.0    
58.1    
58.3    
58.4    
58.5    
58.7    
58.8    
58.9    
59.1    
59.2    
59.3    
59.5    
59.6    
59.8    
59.9    
60.0    
60.2    
60.3    
60.4    
60.6    
60.7    
60.8    
61.0    
61.1    
61.2    
61.4    
61.5    
61.7    
61.8    
61.9    
62.1    
62.2    
62.3    
62.5    
62.6    
62.7    
62.9    
63.0    
63.1    
63.3    
63.4    
63.6    
63.7    
63.8    
64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.8    
64.9    
65.0    
65.2    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.1    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.5    
67.6    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.6    
68.7    
68.8    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.2    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.6    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.5    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.5    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 23071, rend_intergenic: 6408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35602, rend_intergenic: 25716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44677, rend_intergenic: 37957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48392, rend_intergenic: 47189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53309, rend_intergenic: 51002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63813, rend_intergenic: 59128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73026, rend_intergenic: 70886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75640, rend_intergenic: 74032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138375, rend_intergenic: 118757  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145648, rend_intergenic: 138635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153891, rend_intergenic: 146035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175308, rend_intergenic: 161295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178719, rend_intergenic: 177290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support