-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_17105531-17271936

-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_8318-T1
Valid prediction for snap_scaffold_3-snap.3348-T1
Valid prediction for snap_scaffold_3-snap.3326-T1
Valid prediction for GlimmerHMM_glimmerT_8339-T1
Valid prediction for GeneMark_model.13521_t
Valid prediction for snap_scaffold_3-snap.3325-T1
Valid prediction for snap_scaffold_3-snap.3315-T1
Valid prediction for snap_scaffold_3-snap.3333-T1
Couldn't classify 36240, 36302
Couldn't classify 37504, 37665
Sorry, prediction pasa_asmbl_40614.p1 fails validation.
(AGA)	 CC	36240-36302	GT	CCG
(GAT)	 AG	36491-36586	GT	AGG
(GAG)	 AG	37504-37665	GT	AGG
-recovered pasa_asmbl_40614.p1, internal, 36491, 36586
-recovered pasa_asmbl_40614.p1, internal, 37504, 37665
Valid prediction for GlimmerHMM_glimmerT_8327-T1
Valid prediction for CodingQuarry_transcript_46326-T1
Valid prediction for GlimmerHMM_glimmerT_8323-T1
Valid prediction for snap_scaffold_3-snap.3340-T1
Valid prediction for GeneMark_model.13568_t
Valid prediction for GlimmerHMM_glimmerT_8342-T1
Valid prediction for GlimmerHMM_glimmerT_8321-T1
Valid prediction for snap_scaffold_3-snap.3329-T1
Valid prediction for GlimmerHMM_glimmerT_8340-T1
Valid prediction for GeneMark_model.13527_t
Valid prediction for snap_scaffold_3-snap.3346-T1
Valid prediction for snap_scaffold_3-snap.3328-T1
Valid prediction for GeneMark_model.13564_t
Valid prediction for Augustus_model.g5529.t1
Valid prediction for GeneMark_model.13560_t
Valid prediction for snap_scaffold_3-snap.3337-T1
Valid prediction for Augustus_model.g5528.t1
Valid prediction for GeneMark_model.13552_t
Valid prediction for Augustus_model.g5525.t1
Valid prediction for GeneMark_model.13562_t
Valid prediction for GlimmerHMM_glimmerT_8336-T1
Valid prediction for GeneMark_model.13551_t
Valid prediction for snap_scaffold_3-snap.3338-T1
Valid prediction for Augustus_model.g5521.t1
Valid prediction for snap_scaffold_3-snap.3332-T1
Valid prediction for GeneMark_model.13525_t
Valid prediction for GeneMark_model.13554_t
Valid prediction for GlimmerHMM_glimmerT_8341-T1
Couldn't classify 136205, 136279
Couldn't classify 137574, 137726
Sorry, prediction pasa_asmbl_40622.p1 fails validation.
(CCG)	 GA	136205-136279	GT	AGG
(AAT)	 AG	136703-136810	GT	AGG
(GAT)	 AG	137574-137726	TA	GGT
-recovered pasa_asmbl_40622.p1, internal, 136703, 136810
Couldn't classify 34061, 34480
Sorry, prediction pasa_asmbl_40612.p2 fails validation.
(ATG)	 CC	34061-34480	CG	TGC
Valid prediction for GeneMark_model.13558_t
Valid prediction for GeneMark_model.13542_t
Valid prediction for GeneMark_model.13534_t
Valid prediction for GlimmerHMM_glimmerT_8328-T1
Valid prediction for GeneMark_model.13571_t
Valid prediction for GeneMark_model.13536_t
Valid prediction for Augustus_model.g5532.t1
Valid prediction for GeneMark_model.13522_t
Valid prediction for GeneMark_model.13549_t
Valid prediction for snap_scaffold_3-snap.3342-T1
Couldn't classify 38724, 38899
Sorry, prediction pasa_asmbl_40617.p1 fails validation.
(TGG)	 AA	38724-38899	GT	AGG
(GAT)	 AG	39064-39128	GT	AGG
(AGA)	 AG	39683-39768	GT	AGG
(GTG)	 AG	40162-40203	CC	AAC
-recovered pasa_asmbl_40617.p1, terminal, 40162, 40203
-recovered pasa_asmbl_40617.p1, internal, 39064, 39128
-recovered pasa_asmbl_40617.p1, internal, 39683, 39768
Valid prediction for snap_scaffold_3-snap.3318-T1
Valid prediction for GlimmerHMM_glimmerT_8316-T1
Valid prediction for Augustus_model.g5527.t1
Valid prediction for GlimmerHMM_glimmerT_8344-T1
Valid prediction for snap_scaffold_3-snap.3320-T1
Valid prediction for snap_scaffold_3-snap.3317-T1
Valid prediction for GeneMark_model.13574_t
Valid prediction for GlimmerHMM_glimmerT_8319-T1
Valid prediction for snap_scaffold_3-snap.3341-T1
Valid prediction for GeneMark_model.13548_t
Valid prediction for GlimmerHMM_glimmerT_8338-T1
Valid prediction for GlimmerHMM_glimmerT_8343-T1
Valid prediction for Augustus_model.g5534.t1
Valid prediction for GeneMark_model.13523_t
Valid prediction for Augustus_model.g5538.t1
Valid prediction for snap_scaffold_3-snap.3336-T1
Valid prediction for GeneMark_model.13539_t
Valid prediction for GlimmerHMM_glimmerT_8322-T1
Valid prediction for GlimmerHMM_glimmerT_8314-T1
Valid prediction for snap_scaffold_3-snap.3355-T1
Valid prediction for GlimmerHMM_glimmerT_8326-T1
Valid prediction for Augustus_model.g5531.t1
Valid prediction for CodingQuarry_transcript_46325-T1
Valid prediction for GeneMark_model.13543_t
Valid prediction for GeneMark_model.13555_t
Valid prediction for snap_scaffold_3-snap.3322-T1
Valid prediction for GeneMark_model.13530_t
Valid prediction for snap_scaffold_3-snap.3353-T1
Valid prediction for GeneMark_model.13545_t
Valid prediction for pasa_asmbl_40609.p1
Valid prediction for GlimmerHMM_glimmerT_8330-T1
Valid prediction for GlimmerHMM_glimmerT_8324-T1
Valid prediction for Augustus_model.g5523.t1
Valid prediction for GlimmerHMM_glimmerT_8333-T1
Valid prediction for GlimmerHMM_glimmerT_8315-T1
Valid prediction for Augustus_model.g5533.t1
Valid prediction for GeneMark_model.13532_t
Valid prediction for snap_scaffold_3-snap.3350-T1
Valid prediction for GeneMark_model.13547_t
Valid prediction for GeneMark_model.13573_t
Valid prediction for GlimmerHMM_glimmerT_8348-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_3-snap.3345-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g5524.t1
Valid prediction for GeneMark_model.13556_t
Valid prediction for GeneMark_model.13572_t
Valid prediction for GlimmerHMM_glimmerT_8346-T1
Valid prediction for snap_scaffold_3-snap.3319-T1
Valid prediction for GeneMark_model.13550_t
Valid prediction for GeneMark_model.13528_t
Valid prediction for snap_scaffold_3-snap.3347-T1
Valid prediction for GeneMark_model.13569_t
Valid prediction for GlimmerHMM_glimmerT_8334-T1
Valid prediction for snap_scaffold_3-snap.3330-T1
Valid prediction for snap_scaffold_3-snap.3324-T1
Valid prediction for snap_scaffold_3-snap.3316-T1
Valid prediction for Augustus_model.g5536.t1
Valid prediction for Augustus_model.g5522.t1
Valid prediction for GlimmerHMM_glimmerT_8347-T1
Valid prediction for GlimmerHMM_glimmerT_8335-T1
Valid prediction for GeneMark_model.13541_t
Valid prediction for GeneMark_model.13533_t
Valid prediction for Augustus_model.g5530.t1
Valid prediction for snap_scaffold_3-snap.3351-T1
Valid prediction for GeneMark_model.13526_t
Valid prediction for GlimmerHMM_glimmerT_8325-T1
Valid prediction for GeneMark_model.13540_t
Valid prediction for GeneMark_model.13575_t
Valid prediction for GlimmerHMM_glimmerT_8332-T1
Valid prediction for GlimmerHMM_glimmerT_8320-T1
Valid prediction for GeneMark_model.13563_t
Valid prediction for GeneMark_model.13529_t
Valid prediction for GlimmerHMM_glimmerT_8331-T1
Valid prediction for snap_scaffold_3-snap.3352-T1
Valid prediction for snap_scaffold_3-snap.3356-T1
Valid prediction for snap_scaffold_3-snap.3321-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g5537.t1
Valid prediction for Augustus_model.g5535.t1
Valid prediction for GeneMark_model.13524_t
Valid prediction for snap_scaffold_3-snap.3334-T1
Valid prediction for snap_scaffold_3-snap.3331-T1
Valid prediction for GlimmerHMM_glimmerT_8329-T1
Valid prediction for snap_scaffold_3-snap.3344-T1
Valid prediction for GeneMark_model.13553_t
Valid prediction for GeneMark_model.13561_t
Valid prediction for snap_scaffold_3-snap.3349-T1
Valid prediction for GeneMark_model.13570_t
Valid prediction for GeneMark_model.13538_t
Valid prediction for GeneMark_model.13546_t
Valid prediction for GlimmerHMM_glimmerT_8345-T1
Valid prediction for GeneMark_model.13544_t
Valid prediction for GeneMark_model.13535_t
Valid prediction for GeneMark_model.13531_t
Valid prediction for snap_scaffold_3-snap.3343-T1
Valid prediction for GeneMark_model.13567_t
Valid prediction for GeneMark_model.13559_t
Valid prediction for snap_scaffold_3-snap.3323-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_3-snap.3354-T1
Valid prediction for snap_scaffold_3-snap.3335-T1
Valid prediction for snap_scaffold_3-snap.3339-T1
Valid prediction for GeneMark_model.13537_t
Valid prediction for snap_scaffold_3-snap.3327-T1
Valid prediction for Augustus_model.g5526.t1
Valid prediction for GeneMark_model.13557_t
Valid prediction for GeneMark_model.13565_t
Valid prediction for GlimmerHMM_glimmerT_8337-T1
Valid prediction for GlimmerHMM_glimmerT_8317-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16265, rend_intergenic: 7241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21962, rend_intergenic: 17090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28752, rend_intergenic: 26968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41160, rend_intergenic: 29095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42000, rend_intergenic: 41510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46342, rend_intergenic: 42085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61858, rend_intergenic: 59780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65933, rend_intergenic: 62133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74569, rend_intergenic: 73045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79264, rend_intergenic: 74776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85284, rend_intergenic: 82175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99969, rend_intergenic: 95859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121808, rend_intergenic: 109772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131319, rend_intergenic: 128129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136557, rend_intergenic: 131472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145256, rend_intergenic: 142095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156118, rend_intergenic: 148181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157295, rend_intergenic: 156171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166406
-exon list size: 844


building trellis

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74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.4    
76.5    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.6    
81.7    
81.8    
81.9    
82.0    
82.2    
82.3    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.5    
84.6    
84.8    
84.9    
85.0    
85.1    
85.2    
85.3    
85.5    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.6    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 44 predictions from path traversal
Error with prediction: snap lend_intergenic: 16265, rend_intergenic: 7241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21962, rend_intergenic: 17090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28752, rend_intergenic: 26968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41160, rend_intergenic: 29095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42000, rend_intergenic: 41510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46342, rend_intergenic: 42085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61858, rend_intergenic: 59780  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65933, rend_intergenic: 62133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74569, rend_intergenic: 73045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79264, rend_intergenic: 74776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85284, rend_intergenic: 82175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99969, rend_intergenic: 95859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121808, rend_intergenic: 109772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131319, rend_intergenic: 128129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136557, rend_intergenic: 131472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145256, rend_intergenic: 142095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156118, rend_intergenic: 148181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157295, rend_intergenic: 156171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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