-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_8518432-8666838

-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.67685_t
Valid prediction for GlimmerHMM_glimmerT_39545-T1
Valid prediction for snap_scaffold_16-snap.1573-T1
Couldn't classify 123434, 123523
Couldn't classify 127474, 127591
Sorry, prediction pasa_asmbl_17232.p1 fails validation.
(TCA)	 CC	123434-123523	GT	AGG
(GAT)	 AG	123947-123997	GT	AGG
(ACG)	 AG	124994-125153	GT	AGG
(CGA)	 AG	125228-125444	GT	GGG
(GCC)	 AG	125597-125686	GT	GGG
(CCT)	 AG	125803-125985	GT	AGG
(GCC)	 AG	126743-126892	GT	AGG
(AAT)	 AG	127474-127591	CC	CCC
-recovered pasa_asmbl_17232.p1, internal, 123947, 123997
-recovered pasa_asmbl_17232.p1, internal, 124994, 125153
-recovered pasa_asmbl_17232.p1, internal, 125228, 125444
-recovered pasa_asmbl_17232.p1, internal, 125597, 125686
-recovered pasa_asmbl_17232.p1, internal, 125803, 125985
-recovered pasa_asmbl_17232.p1, internal, 126743, 126892
Valid prediction for snap_scaffold_16-snap.1595-T1
Valid prediction for CodingQuarry_transcript_19996-T1
Valid prediction for GeneMark_model.67654_t
Valid prediction for CodingQuarry_transcript_20001-T1
Valid prediction for HiQ_model.g26573.t1
Valid prediction for GeneMark_model.67665_t
Valid prediction for Augustus_model.g26582.t1
Valid prediction for GlimmerHMM_glimmerT_39550-T1
Valid prediction for Augustus_model.g26572.t1
Valid prediction for pasa_asmbl_17209.p1
Valid prediction for Augustus_model.g26580.t1
Valid prediction for GeneMark_model.67652_t
Valid prediction for GeneMark_model.67642_t
Valid prediction for GlimmerHMM_glimmerT_39541-T1
Valid prediction for snap_scaffold_16-snap.1581-T1
Valid prediction for GlimmerHMM_glimmerT_39537-T1
Valid prediction for snap_scaffold_16-snap.1572-T1
Valid prediction for Augustus_model.g26577.t1
Valid prediction for GeneMark_model.67680_t
Valid prediction for snap_scaffold_16-snap.1585-T1
Valid prediction for GlimmerHMM_glimmerT_39532-T1
Valid prediction for snap_scaffold_16-snap.1583-T1
Valid prediction for GlimmerHMM_glimmerT_39540-T1
Couldn't classify 98691, 98725
Couldn't classify 102125, 102231
Sorry, prediction pasa_asmbl_17222.p1 fails validation.
(GAG)	 TG	98691-98725	GT	AGG
(GTT)	 AG	98915-99004	GT	AAG
(CCT)	 AG	99426-99482	GT	ACG
(GTC)	 AG	100040-100103	GT	TGG
(CCT)	 AG	101119-101193	GT	CAG
(GAG)	 AG	101300-101444	GT	AGG
(GCA)	 AG	102125-102231	AA	AGA
add_exon() Sorry, pasa_asmbl_17222.p1 101300-101444-terminal-3 is invalid.
-recovered pasa_asmbl_17222.p1, terminal, 101300, 101444
-recovered pasa_asmbl_17222.p1, internal, 98915, 99004
-recovered pasa_asmbl_17222.p1, internal, 99426, 99482
-recovered pasa_asmbl_17222.p1, internal, 100040, 100103
-recovered pasa_asmbl_17222.p1, internal, 101119, 101193
-recovered pasa_asmbl_17222.p1, internal, 101300, 101444
Valid prediction for snap_scaffold_16-snap.1590-T1
Valid prediction for HiQ_model.g26578.t1
Couldn't classify 37182, 37312
Sorry, prediction pasa_asmbl_17201.p1 fails validation.
(GGA)	 GT	37182-37312	GT	CTG
(AAT)	 AG	37636-37729	GT	AGG
(GAG)	 AG	38012-38278	AA	AAA
-recovered pasa_asmbl_17201.p1, terminal, 38012, 38278
-recovered pasa_asmbl_17201.p1, internal, 37636, 37729
Valid prediction for GeneMark_model.67653_t
Valid prediction for GlimmerHMM_glimmerT_39546-T1
Valid prediction for GlimmerHMM_glimmerT_39534-T1
Valid prediction for HiQ_model.g26574.t1
Valid prediction for Augustus_model.g26576.t1
Couldn't classify 103273, 103414
Couldn't classify 104435, 104518
Sorry, prediction pasa_asmbl_17223.p1 fails validation.
(GCC)	 TG	103273-103414	GT	GGG
(AGA)	 AG	103584-103711	GT	GGG
(GGT)	 AG	104193-104318	GT	AGG
(GAG)	 AG	104435-104518	AG	AGA
-recovered pasa_asmbl_17223.p1, internal, 103584, 103711
-recovered pasa_asmbl_17223.p1, internal, 104193, 104318
Valid prediction for GeneMark_model.67645_t
Valid prediction for GlimmerHMM_glimmerT_39547-T1
Valid prediction for Augustus_model.g26575.t1
Valid prediction for Augustus_model.g26587.t1
Valid prediction for GeneMark_model.67682_t
Valid prediction for CodingQuarry_transcript_19999-T1
Valid prediction for GeneMark_model.67658_t
Couldn't classify 120113, 120358
Couldn't classify 127474, 127591
Sorry, prediction pasa_asmbl_17227.p1 fails validation.
(CTC)	 CC	120113-120358	GC	AGG
(GCA)	 AG	121306-121377	GT	CGG
(CCC)	 AG	121619-121675	GT	TCG
(GCC)	 AG	122228-122278	GT	CAG
(ACG)	 AG	122522-122647	GT	CTG
(GAT)	 AG	123947-123997	GT	AGG
(ACG)	 AG	124994-125153	GT	AGG
(CGA)	 AG	125228-125444	GT	GGG
(GCC)	 AG	125597-125686	GT	GGG
(CCT)	 AG	125803-125985	GT	AGG
(AAT)	 AG	127474-127591	CC	CCC
-recovered pasa_asmbl_17227.p1, internal, 121306, 121377
-recovered pasa_asmbl_17227.p1, internal, 121619, 121675
-recovered pasa_asmbl_17227.p1, internal, 122228, 122278
-recovered pasa_asmbl_17227.p1, internal, 122522, 122647
-recovered pasa_asmbl_17227.p1, internal, 123947, 123997
-recovered pasa_asmbl_17227.p1, internal, 124994, 125153
-recovered pasa_asmbl_17227.p1, internal, 125228, 125444
-recovered pasa_asmbl_17227.p1, internal, 125597, 125686
-recovered pasa_asmbl_17227.p1, internal, 125803, 125985
Valid prediction for GeneMark_model.67668_t
Valid prediction for CodingQuarry_transcript_20002-T1
Valid prediction for Augustus_model.g26571.t1
Valid prediction for GlimmerHMM_glimmerT_39554-T1
Valid prediction for GlimmerHMM_glimmerT_39543-T1
Valid prediction for snap_scaffold_16-snap.1588-T1
Valid prediction for CodingQuarry_transcript_20003-T1
Valid prediction for GlimmerHMM_glimmerT_39536-T1
Valid prediction for GeneMark_model.67678_t
Valid prediction for GlimmerHMM_glimmerT_39544-T1
Valid prediction for CodingQuarry_transcript_20000-T1
Valid prediction for GeneMark_model.67647_t
Valid prediction for Augustus_model.g26583.t1
Valid prediction for snap_scaffold_16-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_39538-T1
Valid prediction for GeneMark_model.67643_t
Valid prediction for snap_scaffold_16-snap.1587-T1
Valid prediction for GeneMark_model.67676_t
Valid prediction for Augustus_model.g26581.t1
Valid prediction for GlimmerHMM_glimmerT_39539-T1
Valid prediction for GeneMark_model.67649_t
Couldn't classify 30746, 30967
Sorry, prediction pasa_asmbl_17199.p1 fails validation.
(TCC)	 GC	30746-30967	GT	AGG
(CCT)	 AG	31238-31342	GT	GAG
(CCT)	 AG	31472-31573	GT	AGG
(GAT)	 AG	31731-31820	AC	GAA
-recovered pasa_asmbl_17199.p1, terminal, 31731, 31820
-recovered pasa_asmbl_17199.p1, internal, 31238, 31342
-recovered pasa_asmbl_17199.p1, internal, 31472, 31573
Valid prediction for GlimmerHMM_glimmerT_39551-T1
Valid prediction for GeneMark_model.67659_t
Valid prediction for snap_scaffold_16-snap.1580-T1
Valid prediction for GeneMark_model.67657_t
Valid prediction for pasa_asmbl_17200.p2
Valid prediction for CodingQuarry_transcript_19998-T1
Valid prediction for snap_scaffold_16-snap.1599-T1
Couldn't classify 112115, 112165
Couldn't classify 115504, 115530
Sorry, prediction pasa_asmbl_17224.p1 fails validation.
(GGG)	 GT	112115-112165	GT	CTG
(ATC)	 AG	113940-114200	GT	AGG
(GAA)	 AG	114621-114731	GT	AGG
(GTG)	 AG	115015-115191	GT	AGG
(GAA)	 AG	115504-115530	GA	GAG
-recovered pasa_asmbl_17224.p1, internal, 113940, 114200
-recovered pasa_asmbl_17224.p1, internal, 114621, 114731
-recovered pasa_asmbl_17224.p1, internal, 115015, 115191
Couldn't classify 59283, 59408
Sorry, prediction pasa_asmbl_17205.p1 fails validation.
(CAG)	 TG	59283-59408	GT	AGG
(GAG)	 AG	59585-59686	GT	GGG
(GTC)	 AG	59832-59921	GT	AGG
(GCA)	 AG	60128-60168	GT	AGG
(TTA)	 AG	60441-60535	GT	AGG
(TGT)	 AG	60799-60822	GT	TGG
(TGT)	 AG	61025-61105	GT	CAG
(CGG)	 AG	61381-61436	GT	AGG
(ATG)	 AG	61669-61764	GT	GAG
(GAG)	 AG	62022-62154	GT	GTG
(ACC)	 AG	62263-62365	GT	AAG
(GTA)	 AG	62451-62501	GT	AAG
(GAA)	 AG	62618-62753	GT	AGG
(GTC)	 AG	62865-62918	GT	ATG
(CTC)	 AG	63147-63210	GT	AAG
(CTG)	 AG	63370-63425	GT	AGG
(GAG)	 AG	63555-63641	AC	GAA
-recovered pasa_asmbl_17205.p1, initial, 61669, 61764
-recovered pasa_asmbl_17205.p1, terminal, 63555, 63641
-recovered pasa_asmbl_17205.p1, internal, 59585, 59686
-recovered pasa_asmbl_17205.p1, internal, 59832, 59921
-recovered pasa_asmbl_17205.p1, internal, 60128, 60168
-recovered pasa_asmbl_17205.p1, internal, 60441, 60535
-recovered pasa_asmbl_17205.p1, internal, 60799, 60822
-recovered pasa_asmbl_17205.p1, internal, 61025, 61105
-recovered pasa_asmbl_17205.p1, internal, 61381, 61436
-recovered pasa_asmbl_17205.p1, internal, 61669, 61764
-recovered pasa_asmbl_17205.p1, internal, 62022, 62154
-recovered pasa_asmbl_17205.p1, internal, 62263, 62365
-recovered pasa_asmbl_17205.p1, internal, 62451, 62501
-recovered pasa_asmbl_17205.p1, internal, 62618, 62753
-recovered pasa_asmbl_17205.p1, internal, 62865, 62918
-recovered pasa_asmbl_17205.p1, internal, 63147, 63210
-recovered pasa_asmbl_17205.p1, internal, 63370, 63425
Valid prediction for GlimmerHMM_glimmerT_39542-T1
Valid prediction for Augustus_model.g26584.t1
Valid prediction for Augustus_model.g26585.t1
Valid prediction for GeneMark_model.67655_t
Valid prediction for CodingQuarry_transcript_19997-T1
Valid prediction for snap_scaffold_16-snap.1575-T1
Valid prediction for snap_scaffold_16-snap.1584-T1
Valid prediction for GeneMark_model.67660_t
Valid prediction for GeneMark_model.67650_t
Valid prediction for GeneMark_model.67672_t
Valid prediction for GeneMark_model.67663_t
Couldn't classify 117233, 117295
Sorry, prediction pasa_asmbl_17225.p1 fails validation.
(ATG)	 GG	115892-115993	GT	AGG
(GCT)	 AG	116125-116244	GT	AGG
(GAG)	 AG	116370-116426	GT	TGG
(AGC)	 AG	117233-117295	CT	GCC
-recovered pasa_asmbl_17225.p1, initial, 115892, 115993
-recovered pasa_asmbl_17225.p1, internal, 116125, 116244
-recovered pasa_asmbl_17225.p1, internal, 116370, 116426
Valid prediction for HiQ_model.g26579.t1
Valid prediction for GlimmerHMM_glimmerT_39549-T1
Valid prediction for snap_scaffold_16-snap.1582-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_16-snap.1594-T1
Valid prediction for GeneMark_model.67669_t
Valid prediction for GeneMark_model.67661_t
Valid prediction for GlimmerHMM_glimmerT_39548-T1
Valid prediction for HiQ_model.g26588.t1
Valid prediction for snap_scaffold_16-snap.1597-T1
Valid prediction for GlimmerHMM_glimmerT_39535-T1
Valid prediction for snap_scaffold_16-snap.1579-T1
Valid prediction for snap_scaffold_16-snap.1598-T1
Valid prediction for GlimmerHMM_glimmerT_39552-T1
Valid prediction for snap_scaffold_16-snap.1577-T1
Valid prediction for GlimmerHMM_glimmerT_39533-T1
Valid prediction for GeneMark_model.67686_t
Valid prediction for GeneMark_model.67671_t
Valid prediction for GeneMark_model.67648_t
Valid prediction for snap_scaffold_16-snap.1600-T1
Valid prediction for GeneMark_model.67683_t
Valid prediction for CodingQuarry_transcript_20004-T1
Valid prediction for GlimmerHMM_glimmerT_39553-T1
Valid prediction for GeneMark_model.67684_t
Valid prediction for GeneMark_model.67667_t
Valid prediction for snap_scaffold_16-snap.1601-T1
Valid prediction for GeneMark_model.67646_t
Valid prediction for snap_scaffold_16-snap.1596-T1
Valid prediction for GeneMark_model.67656_t
Valid prediction for snap_scaffold_16-snap.1592-T1
Valid prediction for snap_scaffold_16-snap.1576-T1
Valid prediction for snap_scaffold_16-snap.1593-T1
Valid prediction for GeneMark_model.67677_t
Valid prediction for Augustus_model.g26586.t1
Valid prediction for GlimmerHMM_glimmerT_39555-T1
Valid prediction for GeneMark_model.67666_t
Valid prediction for GeneMark_model.67644_t
Valid prediction for snap_scaffold_16-snap.1574-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.67664_t
Valid prediction for GeneMark_model.67673_t
Valid prediction for snap_scaffold_16-snap.1578-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.67679_t
Valid prediction for GeneMark_model.67670_t
Valid prediction for GeneMark_model.67651_t
Valid prediction for snap_scaffold_16-snap.1589-T1
Valid prediction for pasa_asmbl_16427.p1
Valid prediction for GeneMark_model.67681_t
Valid prediction for snap_scaffold_16-snap.1591-T1
Valid prediction for GeneMark_model.67687_t
Valid prediction for GeneMark_model.67675_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14093, rend_intergenic: 12311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16090, rend_intergenic: 14513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27448, rend_intergenic: 18822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80620, rend_intergenic: 78712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84380, rend_intergenic: 81792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117865, rend_intergenic: 87474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132085, rend_intergenic: 124958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136748, rend_intergenic: 134996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139990, rend_intergenic: 136986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 148407
-exon list size: 669


building trellis

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59.6    
59.8    
59.9    
60.1    
60.2    
60.4    
60.5    
60.7    
60.8    
61.0    
61.1    
61.3    
61.4    
61.5    
61.7    
61.8    
62.0    
62.1    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.7    
65.9    
66.0    
66.2    
66.3    
66.5    
66.6    
66.8    
66.9    
67.1    
67.2    
67.4    
67.5    
67.7    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.7    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.2    
80.3    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 14093, rend_intergenic: 12311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16090, rend_intergenic: 14513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27448, rend_intergenic: 18822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80620, rend_intergenic: 78712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84380, rend_intergenic: 81792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117865, rend_intergenic: 87474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132085, rend_intergenic: 124958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136748, rend_intergenic: 134996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139990, rend_intergenic: 136986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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