-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_15818192-16023475

-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.50064_t
Valid prediction for Augustus_model.g19379.t1
Valid prediction for GlimmerHMM_glimmerT_29037-T1
Valid prediction for GeneMark_model.50121_t
Valid prediction for GeneMark_model.50096_t
Valid prediction for snap_scaffold_11-snap.3261-T1
Valid prediction for GeneMark_model.50084_t
Valid prediction for GlimmerHMM_glimmerT_29018-T1
Valid prediction for CodingQuarry_transcript_8295-T1
Valid prediction for snap_scaffold_11-snap.3263-T1
Valid prediction for GlimmerHMM_glimmerT_29025-T1
Valid prediction for GlimmerHMM_glimmerT_29020-T1
Valid prediction for snap_scaffold_11-snap.3266-T1
Valid prediction for Augustus_model.g19384.t1
Valid prediction for snap_scaffold_11-snap.3270-T1
Valid prediction for Augustus_model.g19390.t1
Valid prediction for GeneMark_model.50082_t
Couldn't classify 11949, 12129
Sorry, prediction pasa_asmbl_6116.p1 fails validation.
(AGG)	 TC	11949-12129	GT	AGG
(ACG)	 AG	14055-14284	GT	GGG
(CCA)	 AG	14725-14847	GT	TTG
(GAT)	 AG	15411-15479	GT	TGG
(GGT)	 AG	18117-18251	GT	AGG
(GCC)	 AG	18474-18572	GT	CTG
(GTG)	 AG	19708-19923	GT	CGG
(GCG)	 AG	20564-20782	GT	AGG
(GCT)	 AG	21036-21965	GG	AAG
-recovered pasa_asmbl_6116.p1, terminal, 21036, 21965
-recovered pasa_asmbl_6116.p1, internal, 14055, 14284
-recovered pasa_asmbl_6116.p1, internal, 14725, 14847
-recovered pasa_asmbl_6116.p1, internal, 15411, 15479
-recovered pasa_asmbl_6116.p1, internal, 18117, 18251
-recovered pasa_asmbl_6116.p1, internal, 18474, 18572
-recovered pasa_asmbl_6116.p1, internal, 19708, 19923
-recovered pasa_asmbl_6116.p1, internal, 20564, 20782
Valid prediction for GlimmerHMM_glimmerT_29022-T1
Valid prediction for GeneMark_model.50104_t
Valid prediction for GeneMark_model.50067_t
Valid prediction for GeneMark_model.50070_t
Valid prediction for GlimmerHMM_glimmerT_29031-T1
Valid prediction for GeneMark_model.50088_t
Valid prediction for snap_scaffold_11-snap.3256-T1
Valid prediction for GeneMark_model.50115_t
Valid prediction for GlimmerHMM_glimmerT_29013-T1
Valid prediction for GeneMark_model.50068_t
Valid prediction for snap_scaffold_11-snap.3233-T1
Valid prediction for GeneMark_model.50079_t
Valid prediction for GeneMark_model.50118_t
Valid prediction for GlimmerHMM_glimmerT_29033-T1
Valid prediction for snap_scaffold_11-snap.3250-T1
Valid prediction for GeneMark_model.50098_t
Valid prediction for GeneMark_model.50086_t
Valid prediction for snap_scaffold_11-snap.3240-T1
Valid prediction for GeneMark_model.50059_t
Valid prediction for snap_scaffold_11-snap.3258-T1
Valid prediction for snap_scaffold_11-snap.3255-T1
Valid prediction for Augustus_model.g19386.t1
Valid prediction for GeneMark_model.50113_t
Valid prediction for GeneMark_model.50107_t
Valid prediction for GeneMark_model.50110_t
Valid prediction for Augustus_model.g19391.t1
Valid prediction for GlimmerHMM_glimmerT_29011-T1
Valid prediction for snap_scaffold_11-snap.3244-T1
Valid prediction for GlimmerHMM_glimmerT_29030-T1
Valid prediction for GeneMark_model.50061_t
Valid prediction for GlimmerHMM_glimmerT_29035-T1
Valid prediction for GeneMark_model.50081_t
Valid prediction for GeneMark_model.50119_t
Valid prediction for pasa_asmbl_6121.p1
Valid prediction for snap_scaffold_11-snap.3246-T1
Valid prediction for GeneMark_model.50116_t
Valid prediction for snap_scaffold_11-snap.3242-T1
Valid prediction for snap_scaffold_11-snap.3226-T1
Valid prediction for GeneMark_model.50108_t
Valid prediction for snap_scaffold_11-snap.3252-T1
Valid prediction for snap_scaffold_11-snap.3272-T1
Valid prediction for GeneMark_model.50112_t
Valid prediction for GeneMark_model.50102_t
Valid prediction for GeneMark_model.50094_t
Valid prediction for snap_scaffold_11-snap.3231-T1
Valid prediction for GlimmerHMM_glimmerT_29027-T1
Valid prediction for GeneMark_model.50100_t
Valid prediction for GeneMark_model.50091_t
Valid prediction for GlimmerHMM_glimmerT_29032-T1
Valid prediction for GeneMark_model.50074_t
Valid prediction for GeneMark_model.50077_t
Valid prediction for GeneMark_model.50072_t
Valid prediction for snap_scaffold_11-snap.3259-T1
Valid prediction for GlimmerHMM_glimmerT_29039-T1
Valid prediction for GeneMark_model.50089_t
Valid prediction for snap_scaffold_11-snap.3271-T1
Valid prediction for snap_scaffold_11-snap.3236-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_11-snap.3224-T1
Valid prediction for Augustus_model.g19383.t1
Valid prediction for snap_scaffold_11-snap.3247-T1
Valid prediction for GlimmerHMM_glimmerT_29029-T1
Valid prediction for GlimmerHMM_glimmerT_29040-T1
Valid prediction for GeneMark_model.50123_t
Valid prediction for GeneMark_model.50076_t
Valid prediction for snap_scaffold_11-snap.3227-T1
Valid prediction for Augustus_model.g19381.t1
Valid prediction for snap_scaffold_11-snap.3267-T1
Valid prediction for GeneMark_model.50109_t
Valid prediction for Augustus_model.g19389.t1
Valid prediction for GeneMark_model.50065_t
Valid prediction for Augustus_model.g19387.t1
Valid prediction for snap_scaffold_11-snap.3265-T1
Valid prediction for GlimmerHMM_glimmerT_29019-T1
Valid prediction for GlimmerHMM_glimmerT_29016-T1
Valid prediction for snap_scaffold_11-snap.3234-T1
Valid prediction for CodingQuarry_transcript_8297-T1
Valid prediction for CodingQuarry_transcript_8296-T1
Valid prediction for GeneMark_model.50071_t
Valid prediction for GeneMark_model.50122_t
Valid prediction for GlimmerHMM_glimmerT_29012-T1
Valid prediction for snap_scaffold_11-snap.3264-T1
Valid prediction for GeneMark_model.50090_t
Valid prediction for GeneMark_model.50054_t
Valid prediction for GeneMark_model.50106_t
Valid prediction for GeneMark_model.50060_t
Valid prediction for GlimmerHMM_glimmerT_29023-T1
Valid prediction for GeneMark_model.50073_t
Valid prediction for GeneMark_model.50093_t
Valid prediction for GlimmerHMM_glimmerT_29038-T1
Valid prediction for pasa_asmbl_7194.p1
Valid prediction for GlimmerHMM_glimmerT_29024-T1
Valid prediction for snap_scaffold_11-snap.3243-T1
Valid prediction for snap_scaffold_11-snap.3239-T1
Valid prediction for GeneMark_model.50063_t
Valid prediction for GlimmerHMM_glimmerT_29026-T1
Valid prediction for GeneMark_model.50078_t
Valid prediction for snap_scaffold_11-snap.3235-T1
Valid prediction for GeneMark_model.50066_t
Valid prediction for GlimmerHMM_glimmerT_29010-T1
Valid prediction for GeneMark_model.50101_t
Valid prediction for snap_scaffold_11-snap.3238-T1
Valid prediction for snap_scaffold_11-snap.3262-T1
Valid prediction for GeneMark_model.50103_t
Valid prediction for snap_scaffold_11-snap.3257-T1
Valid prediction for snap_scaffold_11-snap.3273-T1
Valid prediction for GeneMark_model.50062_t
Valid prediction for GeneMark_model.50083_t
Valid prediction for GeneMark_model.50120_t
Valid prediction for snap_scaffold_11-snap.3254-T1
Valid prediction for snap_scaffold_11-snap.3249-T1
Valid prediction for snap_scaffold_11-snap.3230-T1
Valid prediction for GeneMark_model.50087_t
Valid prediction for GeneMark_model.50075_t
Valid prediction for GeneMark_model.50111_t
Valid prediction for HiQ_model.g19380.t1
Valid prediction for GlimmerHMM_glimmerT_29036-T1
Valid prediction for GeneMark_model.50099_t
Valid prediction for Augustus_model.g19385.t1
Valid prediction for Augustus_model.g19392.t1
Valid prediction for GeneMark_model.50056_t
Valid prediction for Augustus_model.g19382.t1
Valid prediction for GlimmerHMM_glimmerT_29021-T1
Valid prediction for GeneMark_model.50117_t
Valid prediction for GeneMark_model.50055_t
Valid prediction for GlimmerHMM_glimmerT_29034-T1
Valid prediction for snap_scaffold_11-snap.3225-T1
Valid prediction for snap_scaffold_11-snap.3269-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.3237-T1
Valid prediction for snap_scaffold_11-snap.3232-T1
Valid prediction for GeneMark_model.50095_t
Valid prediction for snap_scaffold_11-snap.3229-T1
Valid prediction for Augustus_model.g19393.t1
Valid prediction for Augustus_model.g19388.t1
Valid prediction for snap_scaffold_11-snap.3228-T1
Valid prediction for GeneMark_model.50092_t
Valid prediction for snap_scaffold_11-snap.3260-T1
Valid prediction for snap_scaffold_11-snap.3241-T1
Valid prediction for GeneMark_model.50058_t
Valid prediction for GeneMark_model.50097_t
Valid prediction for snap_scaffold_11-snap.3251-T1
Valid prediction for snap_scaffold_11-snap.3268-T1
Valid prediction for GlimmerHMM_glimmerT_29028-T1
Valid prediction for GeneMark_model.50114_t
Valid prediction for GeneMark_model.50105_t
Valid prediction for GeneMark_model.50069_t
Valid prediction for snap_scaffold_11-snap.3253-T1
Valid prediction for snap_scaffold_11-snap.3248-T1
Valid prediction for snap_scaffold_11-snap.3245-T1
Valid prediction for GlimmerHMM_glimmerT_29017-T1
Valid prediction for GlimmerHMM_glimmerT_29014-T1
Valid prediction for GeneMark_model.50080_t
Valid prediction for GlimmerHMM_glimmerT_29015-T1
Valid prediction for GeneMark_model.50085_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13434, rend_intergenic: 4588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21965, rend_intergenic: 15288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42610, rend_intergenic: 35211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48687, rend_intergenic: 43050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58391, rend_intergenic: 49603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72733, rend_intergenic: 60385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82607, rend_intergenic: 75265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88537, rend_intergenic: 85545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93420, rend_intergenic: 89327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96737, rend_intergenic: 94728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101357, rend_intergenic: 98105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117231, rend_intergenic: 110268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125605, rend_intergenic: 123771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140365, rend_intergenic: 131554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143965, rend_intergenic: 142217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148478, rend_intergenic: 146614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158634, rend_intergenic: 153754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166718, rend_intergenic: 160378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197754, rend_intergenic: 177760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205284
-exon list size: 778


building trellis

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76.9    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 13434, rend_intergenic: 4588  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21965, rend_intergenic: 15288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42610, rend_intergenic: 35211  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48687, rend_intergenic: 43050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58391, rend_intergenic: 49603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72733, rend_intergenic: 60385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82607, rend_intergenic: 75265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88537, rend_intergenic: 85545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93420, rend_intergenic: 89327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96737, rend_intergenic: 94728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101357, rend_intergenic: 98105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117231, rend_intergenic: 110268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125605, rend_intergenic: 123771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140365, rend_intergenic: 131554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143965, rend_intergenic: 142217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148478, rend_intergenic: 146614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158634, rend_intergenic: 153754  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166718, rend_intergenic: 160378  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197754, rend_intergenic: 177760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support