-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_6549966-6745722

-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 GlimmerHMM_glimmerT_45297-T1
Valid prediction for snap_scaffold_19-snap.1362-T1
Valid prediction for pasa_asmbl_22235.p1
Valid prediction for GeneMark_model.79229_t
Couldn't classify 182234, 182369
Couldn't classify 184122, 184173
Sorry, prediction pasa_asmbl_22240.p1 fails validation.
(CAG)	 TA	182234-182369	GT	AGG
(ATT)	 AG	182770-182848	GT	AGG
(AGA)	 AG	182954-183013	GT	GAG
(AAC)	 AG	183121-183261	GT	ATG
(ACC)	 AG	183434-183542	GT	TGG
(ATA)	 AG	183643-183738	GT	ATG
(GGT)	 AG	183950-183975	GT	AGG
(GAT)	 AG	184122-184173	AG	TCA
-recovered pasa_asmbl_22240.p1, internal, 182770, 182848
-recovered pasa_asmbl_22240.p1, internal, 182954, 183013
-recovered pasa_asmbl_22240.p1, internal, 183121, 183261
-recovered pasa_asmbl_22240.p1, internal, 183434, 183542
-recovered pasa_asmbl_22240.p1, internal, 183643, 183738
-recovered pasa_asmbl_22240.p1, internal, 183950, 183975
Valid prediction for HiQ_model.g30214.t1
Valid prediction for snap_scaffold_19-snap.1358-T1
Valid prediction for snap_scaffold_19-snap.1386-T1
Valid prediction for snap_scaffold_19-snap.1388-T1
Valid prediction for CodingQuarry_transcript_25641-T1
Valid prediction for GlimmerHMM_glimmerT_45309-T1
Valid prediction for GlimmerHMM_glimmerT_45294-T1
Valid prediction for GeneMark_model.79191_t
Valid prediction for GeneMark_model.79204_t
Valid prediction for CodingQuarry_transcript_25642-T1
Couldn't classify 100010, 100075
Couldn't classify 103941, 104005
Sorry, prediction pasa_asmbl_22225.p1 fails validation.
(CAG)	 CC	100010-100075	GT	CGG
(GCC)	 AG	100205-100354	GT	AGG
(GAG)	 AG	100508-100632	GT	AGG
(ACT)	 AG	101013-101127	GT	AGG
(GTG)	 AG	101695-101814	GT	GTG
(GAG)	 AG	102965-103156	GT	AGG
(GCC)	 AG	103290-103481	GT	GGG
(GAC)	 AG	103601-103760	GT	TGG
(CAC)	 AG	103941-104005	GT	AAG
-recovered pasa_asmbl_22225.p1, internal, 100205, 100354
-recovered pasa_asmbl_22225.p1, internal, 100508, 100632
-recovered pasa_asmbl_22225.p1, internal, 101013, 101127
-recovered pasa_asmbl_22225.p1, internal, 101695, 101814
-recovered pasa_asmbl_22225.p1, internal, 102965, 103156
-recovered pasa_asmbl_22225.p1, internal, 103290, 103481
-recovered pasa_asmbl_22225.p1, internal, 103601, 103760
-recovered pasa_asmbl_22225.p1, internal, 103941, 104005
Valid prediction for GlimmerHMM_glimmerT_45303-T1
Valid prediction for GeneMark_model.79185_t
Valid prediction for pasa_asmbl_22228.p1
Valid prediction for snap_scaffold_19-snap.1371-T1
Valid prediction for CodingQuarry_transcript_25639-T1
Valid prediction for GeneMark_model.79227_t
Valid prediction for GeneMark_model.79223_t
Valid prediction for GlimmerHMM_glimmerT_45311-T1
Valid prediction for Augustus_model.g30218.t1
Valid prediction for GeneMark_model.79201_t
Valid prediction for snap_scaffold_19-snap.1384-T1
Couldn't classify 73907, 73957
Sorry, prediction pasa_asmbl_22223.p1 fails validation.
(TCA)	 CC	73907-73957	GT	AGG
(GTG)	 AG	74118-74249	GT	GGG
(TCG)	 AG	74406-74546	GT	AGG
(GGT)	 AG	75133-75249	GT	AGG
(GGC)	 AG	75541-75702	CA	GAC
-recovered pasa_asmbl_22223.p1, terminal, 75541, 75702
-recovered pasa_asmbl_22223.p1, internal, 74118, 74249
-recovered pasa_asmbl_22223.p1, internal, 74406, 74546
-recovered pasa_asmbl_22223.p1, internal, 75133, 75249
Valid prediction for GeneMark_model.79195_t
Valid prediction for GeneMark_model.79200_t
Valid prediction for snap_scaffold_19-snap.1374-T1
Valid prediction for GeneMark_model.79225_t
Valid prediction for GlimmerHMM_glimmerT_45312-T1
Couldn't classify 192655, 192742
Couldn't classify 193805, 194115
Sorry, prediction pasa_asmbl_22243.p1 fails validation.
(CTC)	 AC	192655-192742	GT	AGG
(GTG)	 AG	192881-192978	GT	AGG
(GGC)	 AG	193184-193268	GT	AGG
(TAA)	 AG	193805-194115	CC	AGC
-recovered pasa_asmbl_22243.p1, internal, 192881, 192978
-recovered pasa_asmbl_22243.p1, internal, 193184, 193268
Valid prediction for GeneMark_model.79193_t
Valid prediction for GeneMark_model.79209_t
Valid prediction for snap_scaffold_19-snap.1382-T1
Valid prediction for GlimmerHMM_glimmerT_45289-T1
Valid prediction for snap_scaffold_19-snap.1390-T1
Valid prediction for Augustus_model.g30213.t1
Valid prediction for snap_scaffold_19-snap.1361-T1
Valid prediction for GeneMark_model.79186_t
Valid prediction for snap_scaffold_19-snap.1387-T1
Valid prediction for snap_scaffold_19-snap.1377-T1
Valid prediction for snap_scaffold_19-snap.1356-T1
Valid prediction for GeneMark_model.79184_t
Valid prediction for Augustus_model.g30217.t1
Valid prediction for GeneMark_model.79199_t
Couldn't classify 187661, 187696
Couldn't classify 192307, 192392
Sorry, prediction pasa_asmbl_22242.p1 fails validation.
(TAC)	 AG	187661-187696	GT	TGG
(CAA)	 AG	188351-188590	GT	AGG
(ATG)	 AG	188726-188849	GT	AGG
(GAT)	 AG	190477-190637	GT	AGG
(GTA)	 AG	190810-191000	GT	AGG
(TTC)	 AG	191573-191679	GT	AGG
(GTA)	 AG	192307-192392	CC	CCC
-recovered pasa_asmbl_22242.p1, initial, 188726, 188849
-recovered pasa_asmbl_22242.p1, internal, 187661, 187696
-recovered pasa_asmbl_22242.p1, internal, 188351, 188590
-recovered pasa_asmbl_22242.p1, internal, 188726, 188849
-recovered pasa_asmbl_22242.p1, internal, 190477, 190637
-recovered pasa_asmbl_22242.p1, internal, 190810, 191000
-recovered pasa_asmbl_22242.p1, internal, 191573, 191679
Valid prediction for snap_scaffold_19-snap.1367-T1
Valid prediction for GeneMark_model.79213_t
Valid prediction for snap_scaffold_19-snap.1368-T1
Valid prediction for GlimmerHMM_glimmerT_45313-T1
Valid prediction for snap_scaffold_19-snap.1372-T1
Valid prediction for GeneMark_model.79212_t
Valid prediction for GlimmerHMM_glimmerT_45298-T1
Valid prediction for snap_scaffold_19-snap.1364-T1
Valid prediction for GlimmerHMM_glimmerT_45304-T1
Valid prediction for HiQ_model.g30210.t1
Valid prediction for snap_scaffold_19-snap.1376-T1
Valid prediction for GeneMark_model.79218_t
Valid prediction for GeneMark_model.79197_t
Valid prediction for GeneMark_model.79217_t
Valid prediction for snap_scaffold_19-snap.1359-T1
Valid prediction for snap_scaffold_19-snap.1381-T1
Valid prediction for snap_scaffold_19-snap.1355-T1
Valid prediction for GeneMark_model.79215_t
Valid prediction for GlimmerHMM_glimmerT_45291-T1
Couldn't classify 105417, 105440
Couldn't classify 106512, 106589
Sorry, prediction pasa_asmbl_22226.p1 fails validation.
(TGC)	 AG	105417-105440	GT	AGG
(GAA)	 AG	105534-105626	GT	AGG
(GAG)	 AG	105746-105871	GT	AGG
(GCC)	 AG	106121-106342	GT	ACG
(ATG)	 AG	106512-106589	GT	AGG
-recovered pasa_asmbl_22226.p1, initial, 106512, 106589
-recovered pasa_asmbl_22226.p1, internal, 105417, 105440
-recovered pasa_asmbl_22226.p1, internal, 105534, 105626
-recovered pasa_asmbl_22226.p1, internal, 105746, 105871
-recovered pasa_asmbl_22226.p1, internal, 106121, 106342
-recovered pasa_asmbl_22226.p1, internal, 106512, 106589
Valid prediction for GlimmerHMM_glimmerT_45299-T1
Valid prediction for GeneMark_model.79221_t
Valid prediction for GeneMark_model.79188_t
Valid prediction for snap_scaffold_19-snap.1369-T1
Valid prediction for GeneMark_model.79207_t
Valid prediction for Augustus_model.g30204.t1
Valid prediction for Augustus_model.g30207.t1
Valid prediction for Augustus_model.g30209.t1
Valid prediction for GeneMark_model.79203_t
Valid prediction for Augustus_model.g30208.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.79220_t
Valid prediction for snap_scaffold_19-snap.1385-T1
Valid prediction for GeneMark_model.79189_t
Valid prediction for GlimmerHMM_glimmerT_45292-T1
Valid prediction for snap_scaffold_19-snap.1357-T1
Valid prediction for snap_scaffold_19-snap.1360-T1
Valid prediction for GeneMark_model.79206_t
Valid prediction for snap_scaffold_19-snap.1383-T1
Valid prediction for GeneMark_model.79190_t
Valid prediction for snap_scaffold_19-snap.1389-T1
Valid prediction for pasa_asmbl_21429.p1
Valid prediction for GeneMark_model.79219_t
Valid prediction for GeneMark_model.79198_t
Valid prediction for Augustus_model.g30205.t1
Valid prediction for GeneMark_model.79187_t
Valid prediction for snap_scaffold_19-snap.1379-T1
Valid prediction for GeneMark_model.79216_t
Valid prediction for Augustus_model.g30216.t1
Valid prediction for GeneMark_model.79194_t
Valid prediction for GeneMark_model.79202_t
Valid prediction for GeneMark_model.79196_t
Valid prediction for GeneMark_model.79210_t
Valid prediction for snap_scaffold_19-snap.1370-T1
Valid prediction for GlimmerHMM_glimmerT_45302-T1
Valid prediction for Augustus_model.g30215.t1
Valid prediction for GeneMark_model.79224_t
Valid prediction for snap_scaffold_19-snap.1363-T1
Valid prediction for snap_scaffold_19-snap.1365-T1
Valid prediction for GlimmerHMM_glimmerT_45296-T1
Valid prediction for snap_scaffold_19-snap.1373-T1
Valid prediction for Augustus_model.g30206.t1
Valid prediction for GlimmerHMM_glimmerT_45290-T1
Valid prediction for snap_scaffold_19-snap.1375-T1
Valid prediction for GeneMark_model.79214_t
Valid prediction for snap_scaffold_19-snap.1380-T1
Valid prediction for CodingQuarry_transcript_25640-T1
Valid prediction for GlimmerHMM_glimmerT_45293-T1
Valid prediction for GeneMark_model.79211_t
Valid prediction for GlimmerHMM_glimmerT_45307-T1
Valid prediction for GlimmerHMM_glimmerT_45300-T1
Valid prediction for GeneMark_model.79205_t
Valid prediction for GeneMark_model.79226_t
Valid prediction for GeneMark_model.79208_t
Valid prediction for GeneMark_model.79192_t
Valid prediction for GlimmerHMM_glimmerT_45310-T1
Valid prediction for GlimmerHMM_glimmerT_45306-T1
Valid prediction for HiQ_model.g30212.t1
Valid prediction for GlimmerHMM_glimmerT_45301-T1
Couldn't classify 64424, 64597
Couldn't classify 65224, 65264
Sorry, prediction pasa_asmbl_21432.p1 fails validation.
(CCC)	 CC	64424-64597	GT	AGG
(GTG)	 AG	64789-64939	GT	AGG
(ACG)	 AG	65224-65264	CT	AGC
-recovered pasa_asmbl_21432.p1, internal, 64789, 64939
Valid prediction for GlimmerHMM_glimmerT_45305-T1
Valid prediction for GlimmerHMM_glimmerT_45295-T1
Valid prediction for GlimmerHMM_glimmerT_45308-T1
Valid prediction for snap_scaffold_19-snap.1366-T1
Valid prediction for snap_scaffold_19-snap.1378-T1
Valid prediction for GeneMark_model.79222_t
Valid prediction for GeneMark_model.79228_t
Valid prediction for Augustus_model.g30211.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14409, rend_intergenic: 10710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21532, rend_intergenic: 14540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45337, rend_intergenic: 35980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50167, rend_intergenic: 49349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52914, rend_intergenic: 50307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59091, rend_intergenic: 53060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74906, rend_intergenic: 70089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80961, rend_intergenic: 77991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105031, rend_intergenic: 82394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109205, rend_intergenic: 105501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119383, rend_intergenic: 115787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152090, rend_intergenic: 148075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167746, rend_intergenic: 155673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175895, rend_intergenic: 174474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181510, rend_intergenic: 177816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195757
-exon list size: 747


building trellis

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66.5    
66.6    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.6    
67.7    
67.8    
68.0    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.8    
70.9    
71.0    
71.2    
71.3    
71.4    
71.6    
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    
74.2    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
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    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
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    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 14409, rend_intergenic: 10710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21532, rend_intergenic: 14540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45337, rend_intergenic: 35980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50167, rend_intergenic: 49349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52914, rend_intergenic: 50307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59091, rend_intergenic: 53060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74906, rend_intergenic: 70089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80961, rend_intergenic: 77991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105031, rend_intergenic: 82394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109205, rend_intergenic: 105501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119383, rend_intergenic: 115787  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152090, rend_intergenic: 148075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167746, rend_intergenic: 155673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175895, rend_intergenic: 174474  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181510, rend_intergenic: 177816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support