-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_4186913-4357808

-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.47494_t
Valid prediction for Augustus_model.g18344.t1
Valid prediction for GeneMark_model.47548_t
Valid prediction for snap_scaffold_11-snap.1040-T1
Valid prediction for snap_scaffold_11-snap.1073-T1
Valid prediction for GeneMark_model.47519_t
Valid prediction for snap_scaffold_11-snap.1062-T1
Valid prediction for GeneMark_model.47496_t
Valid prediction for GeneMark_model.47504_t
Valid prediction for GlimmerHMM_glimmerT_27529-T1
Valid prediction for snap_scaffold_11-snap.1070-T1
Valid prediction for GeneMark_model.47522_t
Valid prediction for GeneMark_model.47508_t
Valid prediction for snap_scaffold_11-snap.1069-T1
Valid prediction for snap_scaffold_11-snap.1061-T1
Valid prediction for Augustus_model.g18350.t1
Valid prediction for GlimmerHMM_glimmerT_27515-T1
Valid prediction for snap_scaffold_11-snap.1037-T1
Valid prediction for GlimmerHMM_glimmerT_27522-T1
Valid prediction for GlimmerHMM_glimmerT_27519-T1
Valid prediction for snap_scaffold_11-snap.1044-T1
Valid prediction for GeneMark_model.47513_t
Valid prediction for snap_scaffold_11-snap.1041-T1
Valid prediction for snap_scaffold_11-snap.1064-T1
Valid prediction for snap_scaffold_11-snap.1045-T1
Valid prediction for snap_scaffold_11-snap.1056-T1
Valid prediction for GeneMark_model.47506_t
Valid prediction for snap_scaffold_11-snap.1060-T1
Valid prediction for Augustus_model.g18339.t1
Valid prediction for GlimmerHMM_glimmerT_27517-T1
Valid prediction for snap_scaffold_11-snap.1053-T1
Valid prediction for snap_scaffold_11-snap.1051-T1
Valid prediction for GeneMark_model.47546_t
Valid prediction for GeneMark_model.47532_t
Valid prediction for GlimmerHMM_glimmerT_27520-T1
Valid prediction for snap_scaffold_11-snap.1058-T1
Valid prediction for GeneMark_model.47541_t
Valid prediction for GeneMark_model.47545_t
Valid prediction for GeneMark_model.47515_t
Valid prediction for GeneMark_model.47539_t
Valid prediction for snap_scaffold_11-snap.1065-T1
Valid prediction for GeneMark_model.47534_t
Valid prediction for GlimmerHMM_glimmerT_27528-T1
Valid prediction for GeneMark_model.47536_t
Valid prediction for GeneMark_model.47530_t
Valid prediction for GlimmerHMM_glimmerT_27513-T1
Valid prediction for GeneMark_model.47520_t
Valid prediction for GeneMark_model.47490_t
Valid prediction for snap_scaffold_11-snap.1052-T1
Valid prediction for GeneMark_model.47528_t
Valid prediction for Augustus_model.g18346.t1
Valid prediction for snap_scaffold_11-snap.1050-T1
Valid prediction for Augustus_model.g18338.t1
Valid prediction for Augustus_model.g18340.t1
Valid prediction for GeneMark_model.47538_t
Valid prediction for GeneMark_model.47521_t
Valid prediction for snap_scaffold_11-snap.1063-T1
Valid prediction for snap_scaffold_11-snap.1072-T1
Valid prediction for GeneMark_model.47512_t
Valid prediction for GeneMark_model.47523_t
Valid prediction for GeneMark_model.47499_t
Valid prediction for GlimmerHMM_glimmerT_27512-T1
Valid prediction for GeneMark_model.47502_t
Valid prediction for snap_scaffold_11-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_27518-T1
Valid prediction for snap_scaffold_11-snap.1054-T1
Valid prediction for snap_scaffold_11-snap.1048-T1
Valid prediction for snap_scaffold_11-snap.1046-T1
Valid prediction for snap_scaffold_11-snap.1042-T1
Valid prediction for GlimmerHMM_glimmerT_27511-T1
Valid prediction for GeneMark_model.47517_t
Valid prediction for GeneMark_model.47510_t
Valid prediction for snap_scaffold_11-snap.1039-T1
Valid prediction for GeneMark_model.47544_t

-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_11-snap.1043-T1
Valid prediction for GeneMark_model.47497_t
Valid prediction for Augustus_model.g18342.t1
Valid prediction for snap_scaffold_11-snap.1068-T1
Valid prediction for GeneMark_model.47540_t
Valid prediction for Augustus_model.g18354.t1
Couldn't classify 60364, 60453
Couldn't classify 66308, 66441
Sorry, prediction pasa_asmbl_6572.p1 fails validation.
(GAT)	 AG	60364-60453	GT	AGG
(GAA)	 AG	61647-61718	GT	CTG
(AGG)	 AG	61895-61989	GT	AGG
(GTT)	 AG	62069-62288	GT	AGG
(GTG)	 AG	62438-62551	GT	AGG
(ACT)	 AG	62661-62771	GT	AGG
(TCC)	 AG	63098-63201	GT	CGG
(GCA)	 AG	63299-63365	GT	CCG
(GTC)	 AG	63477-63594	GT	TCG
(ACA)	 AG	64605-64743	GT	ATG
(GCT)	 AG	65619-65677	GT	AGG
(AGC)	 AG	66308-66441	GC	AGG
-recovered pasa_asmbl_6572.p1, internal, 60364, 60453
-recovered pasa_asmbl_6572.p1, internal, 61647, 61718
-recovered pasa_asmbl_6572.p1, internal, 61895, 61989
-recovered pasa_asmbl_6572.p1, internal, 62069, 62288
-recovered pasa_asmbl_6572.p1, internal, 62438, 62551
-recovered pasa_asmbl_6572.p1, internal, 62661, 62771
-recovered pasa_asmbl_6572.p1, internal, 63098, 63201
-recovered pasa_asmbl_6572.p1, internal, 63299, 63365
-recovered pasa_asmbl_6572.p1, internal, 63477, 63594
-recovered pasa_asmbl_6572.p1, internal, 64605, 64743
-recovered pasa_asmbl_6572.p1, internal, 65619, 65677
-recovered pasa_asmbl_6572.p1, internal, 66308, 66441
Valid prediction for GeneMark_model.47503_t
Valid prediction for GeneMark_model.47514_t
Couldn't classify 70152, 70198
Sorry, prediction pasa_asmbl_6571.p1 fails validation.
(GTC)	 CT	70152-70198	GT	AGG
(GCT)	 AG	71802-71886	GT	AGG
(TTG)	 AG	72771-72877	GT	AGG
(AAT)	 AG	73914-74002	GT	AGG
(CTC)	 AG	74411-74579	GT	AAG
(GAA)	 AG	75528-75635	GT	AAG
(TAT)	 AG	76076-76136	GT	CCG
(GAG)	 AG	76282-76413	GT	TGG
(TTC)	 AG	78294-78464	GT	AGG
(ATG)	 AG	78727-78936	TG	AAT
-recovered pasa_asmbl_6571.p1, terminal, 78727, 78936
-recovered pasa_asmbl_6571.p1, internal, 71802, 71886
-recovered pasa_asmbl_6571.p1, internal, 72771, 72877
-recovered pasa_asmbl_6571.p1, internal, 73914, 74002
-recovered pasa_asmbl_6571.p1, internal, 74411, 74579
-recovered pasa_asmbl_6571.p1, internal, 75528, 75635
-recovered pasa_asmbl_6571.p1, internal, 76076, 76136
-recovered pasa_asmbl_6571.p1, internal, 76282, 76413
-recovered pasa_asmbl_6571.p1, internal, 78294, 78464
Valid prediction for GlimmerHMM_glimmerT_27516-T1
Valid prediction for GlimmerHMM_glimmerT_27523-T1
Valid prediction for GeneMark_model.47498_t
Valid prediction for GeneMark_model.47500_t
Valid prediction for snap_scaffold_11-snap.1057-T1
Valid prediction for GlimmerHMM_glimmerT_27514-T1
Valid prediction for Augustus_model.g18351.t1
Valid prediction for snap_scaffold_11-snap.1038-T1
Valid prediction for snap_scaffold_11-snap.1055-T1
Valid prediction for GeneMark_model.47537_t
Valid prediction for CodingQuarry_transcript_8004-T1
Valid prediction for GeneMark_model.47507_t
Valid prediction for Augustus_model.g18348.t1
Valid prediction for GlimmerHMM_glimmerT_27530-T1
Valid prediction for GeneMark_model.47509_t
Valid prediction for GeneMark_model.47501_t
Valid prediction for GeneMark_model.47493_t
Valid prediction for GeneMark_model.47518_t
Valid prediction for GlimmerHMM_glimmerT_27524-T1
Valid prediction for GeneMark_model.47526_t
Valid prediction for GeneMark_model.47533_t
Valid prediction for pasa_asmbl_6570.p1
Valid prediction for Augustus_model.g18343.t1
Valid prediction for HiQ_model.g18352.t1
Valid prediction for GlimmerHMM_glimmerT_27527-T1
Valid prediction for snap_scaffold_11-snap.1071-T1
Valid prediction for CodingQuarry_transcript_8006-T1
Valid prediction for GeneMark_model.47535_t
Valid prediction for GlimmerHMM_glimmerT_27526-T1
Valid prediction for GlimmerHMM_glimmerT_27510-T1
Valid prediction for snap_scaffold_11-snap.1047-T1
Valid prediction for GeneMark_model.47489_t
Valid prediction for GeneMark_model.47527_t
Valid prediction for GlimmerHMM_glimmerT_27525-T1
Valid prediction for GeneMark_model.47505_t
Valid prediction for Augustus_model.g18349.t1
Couldn't classify 8384, 8647
Couldn't classify 15511, 15572
Sorry, prediction pasa_asmbl_7265.p1 fails validation.
(GCT)	 CC	8384-8647	GT	AGG
(ACC)	 AG	11598-11745	GT	TGG
(AGA)	 AG	13114-13233	GT	TGG
(AGA)	 AG	15511-15572	GT	AGG
-recovered pasa_asmbl_7265.p1, internal, 11598, 11745
-recovered pasa_asmbl_7265.p1, internal, 13114, 13233
-recovered pasa_asmbl_7265.p1, internal, 15511, 15572
Valid prediction for GlimmerHMM_glimmerT_27531-T1
Valid prediction for Augustus_model.g18347.t1
Valid prediction for snap_scaffold_11-snap.1067-T1
Valid prediction for GeneMark_model.47524_t
Valid prediction for GlimmerHMM_glimmerT_27532-T1
Valid prediction for Augustus_model.g18341.t1
Valid prediction for GlimmerHMM_glimmerT_27509-T1
Valid prediction for GeneMark_model.47547_t
Valid prediction for GeneMark_model.47542_t
Valid prediction for Augustus_model.g18353.t1
Valid prediction for GeneMark_model.47511_t
Valid prediction for CodingQuarry_transcript_8005-T1
Valid prediction for GeneMark_model.47491_t
Valid prediction for GeneMark_model.47495_t
Valid prediction for Augustus_model.g18336.t1
Valid prediction for GlimmerHMM_glimmerT_27521-T1
Valid prediction for HiQ_model.g18345.t1
Valid prediction for snap_scaffold_11-snap.1049-T1
Valid prediction for CodingQuarry_transcript_8003-T1
Valid prediction for GeneMark_model.47543_t
Valid prediction for snap_scaffold_11-snap.1066-T1
Valid prediction for GeneMark_model.47531_t
Valid prediction for GeneMark_model.47529_t
Valid prediction for GeneMark_model.47516_t
Valid prediction for Augustus_model.g18337.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 51042, rend_intergenic: 51039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9395, rend_intergenic: 6593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26444, rend_intergenic: 9873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40817, rend_intergenic: 27189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45796, rend_intergenic: 41133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60665, rend_intergenic: 52150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66464, rend_intergenic: 62393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76271, rend_intergenic: 68473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125219, rend_intergenic: 92443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151271, rend_intergenic: 139013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157452, rend_intergenic: 152610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164629, rend_intergenic: 157665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170896
-exon list size: 785


building trellis

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77.5    
77.6    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 51042, rend_intergenic: 51039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9395, rend_intergenic: 6593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26444, rend_intergenic: 9873  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40817, rend_intergenic: 27189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45796, rend_intergenic: 41133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60665, rend_intergenic: 52150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66464, rend_intergenic: 62393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76271, rend_intergenic: 68473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125219, rend_intergenic: 92443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151271, rend_intergenic: 139013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157452, rend_intergenic: 152610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164629, rend_intergenic: 157665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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