-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_6434019-6647303

-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 Augustus_model.g38138.t1
Valid prediction for snap_scaffold_26-snap.1523-T1
Valid prediction for snap_scaffold_26-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_57227-T1
Valid prediction for GeneMark_model.99806_t
Valid prediction for snap_scaffold_26-snap.1494-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_26-snap.1517-T1
Valid prediction for snap_scaffold_26-snap.1515-T1
Valid prediction for snap_scaffold_26-snap.1530-T1
Valid prediction for GlimmerHMM_glimmerT_57240-T1
Valid prediction for GeneMark_model.99824_t
Valid prediction for Augustus_model.g38156.t1
Valid prediction for GlimmerHMM_glimmerT_57224-T1
Valid prediction for GeneMark_model.99822_t
Valid prediction for GlimmerHMM_glimmerT_57249-T1
Valid prediction for snap_scaffold_26-snap.1524-T1
Valid prediction for GlimmerHMM_glimmerT_57231-T1
Valid prediction for GlimmerHMM_glimmerT_57251-T1
Valid prediction for Augustus_model.g38141.t1
Valid prediction for snap_scaffold_26-snap.1526-T1
Valid prediction for snap_scaffold_26-snap.1499-T1
Valid prediction for GeneMark_model.99819_t
Valid prediction for Augustus_model.g38136.t1
Valid prediction for GlimmerHMM_glimmerT_57255-T1
Valid prediction for snap_scaffold_26-snap.1520-T1
Valid prediction for snap_scaffold_26-snap.1501-T1
Valid prediction for GlimmerHMM_glimmerT_57247-T1
Valid prediction for snap_scaffold_26-snap.1513-T1
Valid prediction for snap_scaffold_26-snap.1503-T1
Valid prediction for snap_scaffold_26-snap.1489-T1
Valid prediction for Augustus_model.g38148.t1
Valid prediction for GlimmerHMM_glimmerT_57226-T1
Valid prediction for GeneMark_model.99849_t
Valid prediction for GlimmerHMM_glimmerT_57229-T1
Valid prediction for GeneMark_model.99847_t
Valid prediction for snap_scaffold_26-snap.1502-T1
Valid prediction for Augustus_model.g38151.t1
Valid prediction for GeneMark_model.99814_t
Valid prediction for GeneMark_model.99836_t
Valid prediction for snap_scaffold_26-snap.1534-T1
Valid prediction for snap_scaffold_26-snap.1512-T1
Valid prediction for GlimmerHMM_glimmerT_57241-T1
Valid prediction for Augustus_model.g38152.t1
Valid prediction for GlimmerHMM_glimmerT_57234-T1
Valid prediction for snap_scaffold_26-snap.1536-T1
Valid prediction for GeneMark_model.99823_t
Valid prediction for GeneMark_model.99810_t
Couldn't classify 59824, 59880
Couldn't classify 63321, 63479
Sorry, prediction pasa_asmbl_35840.p1 fails validation.
(GTT)	 AG	59824-59880	GT	AGG
(AAG)	 AG	59972-60150	GT	AAG
(ATG)	 AG	60250-60350	GT	AGG
(CCA)	 AG	60552-60728	GT	AGG
(AGT)	 AG	60827-60975	GT	CTG
(AAA)	 AG	61197-61385	GT	AGG
(GCT)	 AG	61605-61795	GT	GAG
(GCT)	 AG	62517-62637	GT	TGG
(GAC)	 AG	62808-63002	GT	AGG
(CTT)	 AG	63092-63223	GT	AGG
(GTG)	 AG	63321-63479	TT	TGT
add_exon() Sorry, pasa_asmbl_35840.p1 60250-60350-initial-1 is invalid.
-recovered pasa_asmbl_35840.p1, initial, 60250, 60350
-recovered pasa_asmbl_35840.p1, internal, 59824, 59880
-recovered pasa_asmbl_35840.p1, internal, 59972, 60150
-recovered pasa_asmbl_35840.p1, internal, 60250, 60350
-recovered pasa_asmbl_35840.p1, internal, 60552, 60728
-recovered pasa_asmbl_35840.p1, internal, 60827, 60975
-recovered pasa_asmbl_35840.p1, internal, 61197, 61385
-recovered pasa_asmbl_35840.p1, internal, 61605, 61795
-recovered pasa_asmbl_35840.p1, internal, 62517, 62637
-recovered pasa_asmbl_35840.p1, internal, 62808, 63002
-recovered pasa_asmbl_35840.p1, internal, 63092, 63223
Valid prediction for snap_scaffold_26-snap.1491-T1
Valid prediction for snap_scaffold_26-snap.1497-T1
Valid prediction for GlimmerHMM_glimmerT_57252-T1
Valid prediction for GeneMark_model.99828_t
Valid prediction for GlimmerHMM_glimmerT_57254-T1
Valid prediction for GeneMark_model.99807_t
Valid prediction for GlimmerHMM_glimmerT_57238-T1
Valid prediction for GlimmerHMM_glimmerT_57228-T1
Valid prediction for GeneMark_model.99818_t
Valid prediction for GeneMark_model.99830_t
Valid prediction for snap_scaffold_26-snap.1507-T1
Valid prediction for GlimmerHMM_glimmerT_57232-T1
Valid prediction for snap_scaffold_26-snap.1495-T1
Valid prediction for snap_scaffold_26-snap.1508-T1
Valid prediction for GeneMark_model.99832_t
Valid prediction for Augustus_model.g38150.t1
Valid prediction for GeneMark_model.99841_t
Valid prediction for GeneMark_model.99808_t
Valid prediction for Augustus_model.g38147.t1
Valid prediction for snap_scaffold_26-snap.1509-T1
Valid prediction for snap_scaffold_26-snap.1490-T1
Valid prediction for GeneMark_model.99845_t
Valid prediction for pasa_asmbl_35616.p1
Valid prediction for snap_scaffold_26-snap.1496-T1
Valid prediction for GeneMark_model.99834_t
Valid prediction for Augustus_model.g38158.t1
Couldn't classify 51553, 51561
Couldn't classify 52743, 52877
Sorry, prediction pasa_asmbl_35609.p1 fails validation.
(GGA)	 GA	51553-51561	GT	CTG
(GGG)	 AG	51674-51736	GT	GGG
(GAT)	 AG	51835-52000	GT	CGG
(GGA)	 AG	52109-52215	GT	AGG
(GTG)	 AG	52296-52376	GT	AGG
(TTT)	 AG	52466-52648	GT	TGG
(CCC)	 AG	52743-52877	GG	TGG
-recovered pasa_asmbl_35609.p1, internal, 51674, 51736
-recovered pasa_asmbl_35609.p1, internal, 51835, 52000
-recovered pasa_asmbl_35609.p1, internal, 52109, 52215
-recovered pasa_asmbl_35609.p1, internal, 52296, 52376
-recovered pasa_asmbl_35609.p1, internal, 52466, 52648
Valid prediction for GlimmerHMM_glimmerT_57245-T1
Valid prediction for GeneMark_model.99812_t
Valid prediction for GlimmerHMM_glimmerT_57253-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.99817_t
Valid prediction for snap_scaffold_26-snap.1531-T1
Valid prediction for GlimmerHMM_glimmerT_57225-T1
Valid prediction for Augustus_model.g38140.t1
Valid prediction for GeneMark_model.99839_t
Valid prediction for snap_scaffold_26-snap.1529-T1
Couldn't classify 138696, 138764
Sorry, prediction pasa_asmbl_35615.p2 fails validation.
(ATG)	 AC	134834-134857	GT	AGG
(ATC)	 AG	136288-136392	GT	TGG
(ATC)	 AG	136527-136689	GT	AGG
(CGG)	 AG	137361-137548	GT	AGG
(CAC)	 AG	137755-137910	GC	AGG
(CAA)	 AG	138696-138764	GG	ACG
-recovered pasa_asmbl_35615.p2, initial, 134834, 134857
-recovered pasa_asmbl_35615.p2, internal, 136288, 136392
-recovered pasa_asmbl_35615.p2, internal, 136527, 136689
-recovered pasa_asmbl_35615.p2, internal, 137361, 137548
-recovered pasa_asmbl_35615.p2, internal, 137755, 137910
Valid prediction for GlimmerHMM_glimmerT_57250-T1
Valid prediction for GlimmerHMM_glimmerT_57233-T1
Couldn't classify 127831, 127959
Couldn't classify 129848, 129888
Sorry, prediction pasa_asmbl_35614.p1 fails validation.
(AGG)	 CG	127831-127959	GT	AGG
(GTT)	 AG	129036-129164	GT	TGG
(TCC)	 AG	129567-129672	GT	TGG
(GTG)	 AG	129848-129888	GC	GCG
-recovered pasa_asmbl_35614.p1, internal, 129036, 129164
-recovered pasa_asmbl_35614.p1, internal, 129567, 129672
-recovered pasa_asmbl_35614.p1, internal, 129848, 129888
Valid prediction for Augustus_model.g38146.t1
Valid prediction for Augustus_model.g38144.t1
Valid prediction for Augustus_model.g38137.t1
Valid prediction for GeneMark_model.99820_t
Valid prediction for Augustus_model.g38153.t1
Valid prediction for snap_scaffold_26-snap.1533-T1
Valid prediction for Augustus_model.g38143.t1
Valid prediction for GeneMark_model.99826_t
Valid prediction for GeneMark_model.99838_t
Valid prediction for Augustus_model.g38145.t1
Valid prediction for GeneMark_model.99843_t
Valid prediction for GeneMark_model.99815_t
Valid prediction for GlimmerHMM_glimmerT_57243-T1
Valid prediction for snap_scaffold_26-snap.1521-T1
Valid prediction for snap_scaffold_26-snap.1505-T1
Valid prediction for GlimmerHMM_glimmerT_57246-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.99835_t
Valid prediction for GeneMark_model.99837_t
Valid prediction for snap_scaffold_26-snap.1522-T1
Valid prediction for GeneMark_model.99844_t
Valid prediction for GeneMark_model.99809_t
Valid prediction for snap_scaffold_26-snap.1500-T1
Valid prediction for HiQ_model.g38142.t1
Valid prediction for GlimmerHMM_glimmerT_57244-T1
Valid prediction for GlimmerHMM_glimmerT_57239-T1
Valid prediction for snap_scaffold_26-snap.1492-T1
Valid prediction for GlimmerHMM_glimmerT_57236-T1
Valid prediction for GlimmerHMM_glimmerT_57230-T1
Valid prediction for GeneMark_model.99848_t
Valid prediction for GlimmerHMM_glimmerT_57242-T1
Valid prediction for snap_scaffold_26-snap.1510-T1
Valid prediction for CodingQuarry_transcript_40300-T1
Valid prediction for snap_scaffold_26-snap.1518-T1
Valid prediction for GlimmerHMM_glimmerT_57235-T1
Valid prediction for GeneMark_model.99816_t
Valid prediction for snap_scaffold_26-snap.1528-T1
Valid prediction for snap_scaffold_26-snap.1504-T1
Valid prediction for GeneMark_model.99825_t
Valid prediction for Augustus_model.g38139.t1
Valid prediction for snap_scaffold_26-snap.1514-T1
Couldn't classify 9292, 9386
Sorry, prediction pasa_asmbl_34963.p1 fails validation.
(GGA)	 AT	9292-9386	GT	GGG
(TTT)	 AG	9608-9668	GT	TTG
(AGA)	 AG	9788-9837	GT	AGG
(GTC)	 AG	9952-10136	GT	CGG
(GTT)	 AG	10307-10354	GT	AGG
(GGT)	 AG	10461-10554	GT	AGG
(AAA)	 AG	10684-10732	AG	AAA
-recovered pasa_asmbl_34963.p1, terminal, 10684, 10732
-recovered pasa_asmbl_34963.p1, internal, 9608, 9668
-recovered pasa_asmbl_34963.p1, internal, 9788, 9837
-recovered pasa_asmbl_34963.p1, internal, 9952, 10136
-recovered pasa_asmbl_34963.p1, internal, 10307, 10354
-recovered pasa_asmbl_34963.p1, internal, 10461, 10554
Valid prediction for Augustus_model.g38149.t1
Valid prediction for snap_scaffold_26-snap.1493-T1
Valid prediction for snap_scaffold_26-snap.1519-T1
Valid prediction for GeneMark_model.99831_t
Valid prediction for snap_scaffold_26-snap.1532-T1
Valid prediction for GeneMark_model.99813_t
Valid prediction for snap_scaffold_26-snap.1525-T1
Valid prediction for snap_scaffold_26-snap.1506-T1
Valid prediction for snap_scaffold_26-snap.1511-T1
Valid prediction for snap_scaffold_26-snap.1535-T1
Valid prediction for Augustus_model.g38155.t1
Valid prediction for snap_scaffold_26-snap.1516-T1
Valid prediction for Augustus_model.g38154.t1
Valid prediction for GlimmerHMM_glimmerT_57237-T1
Valid prediction for GeneMark_model.99811_t
Valid prediction for GeneMark_model.99827_t
Valid prediction for GeneMark_model.99829_t
Valid prediction for GeneMark_model.99846_t
Valid prediction for GeneMark_model.99840_t
Valid prediction for GeneMark_model.99833_t
Valid prediction for CodingQuarry_transcript_40298-T1
Valid prediction for pasa_asmbl_34961.p1
Valid prediction for snap_scaffold_26-snap.1527-T1
Valid prediction for Augustus_model.g38157.t1
Valid prediction for GlimmerHMM_glimmerT_57248-T1
Valid prediction for GeneMark_model.99821_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 142299, rend_intergenic: 142296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21037, rend_intergenic: 13056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52898, rend_intergenic: 45059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75586, rend_intergenic: 71696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94192, rend_intergenic: 91780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106247, rend_intergenic: 103416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115792, rend_intergenic: 110690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128586, rend_intergenic: 121580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140428, rend_intergenic: 132706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153370, rend_intergenic: 151102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176901, rend_intergenic: 165126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186316, rend_intergenic: 180081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213285
-exon list size: 885


building trellis

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56.6    
56.7    
56.8    
56.9    
57.0    
57.2    
57.3    
57.4    
57.5    
57.6    
57.7    
57.8    
57.9    
58.1    
58.2    
58.3    
58.4    
58.5    
58.6    
58.7    
58.9    
59.0    
59.1    
59.2    
59.3    
59.4    
59.5    
59.6    
59.8    
59.9    
60.0    
60.1    
60.2    
60.3    
60.4    
60.5    
60.7    
60.8    
60.9    
61.0    
61.1    
61.2    
61.3    
61.4    
61.6    
61.7    
61.8    
61.9    
62.0    
62.1    
62.2    
62.3    
62.5    
62.6    
62.7    
62.8    
62.9    
63.0    
63.1    
63.2    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.3    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
66.0    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.8    
70.9    
71.0    
71.1    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.1    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.2    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.5    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 38 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 142299, rend_intergenic: 142296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21037, rend_intergenic: 13056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52898, rend_intergenic: 45059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75586, rend_intergenic: 71696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94192, rend_intergenic: 91780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106247, rend_intergenic: 103416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115792, rend_intergenic: 110690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128586, rend_intergenic: 121580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140428, rend_intergenic: 132706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153370, rend_intergenic: 151102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176901, rend_intergenic: 165126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186316, rend_intergenic: 180081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support