-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_11443216-11665160

-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 snap_scaffold_10-snap.2272-T1
Valid prediction for GlimmerHMM_glimmerT_25943-T1
Valid prediction for snap_scaffold_10-snap.2245-T1
Valid prediction for GeneMark_model.44444_t
Valid prediction for Augustus_model.g17419.t1
Valid prediction for GlimmerHMM_glimmerT_25951-T1
Valid prediction for CodingQuarry_transcript_5561-T1
Valid prediction for HiQ_model.g17413.t1
Valid prediction for GeneMark_model.44463_t
Valid prediction for snap_scaffold_10-snap.2260-T1
Valid prediction for Augustus_model.g17407.t1
Valid prediction for GeneMark_model.44455_t
Valid prediction for snap_scaffold_10-snap.2257-T1
Valid prediction for snap_scaffold_10-snap.2253-T1
Valid prediction for pasa_asmbl_4749.p1
Valid prediction for snap_scaffold_10-snap.2249-T1
Valid prediction for GlimmerHMM_glimmerT_25959-T1
Valid prediction for snap_scaffold_10-snap.2266-T1
Valid prediction for snap_scaffold_10-snap.2246-T1
Valid prediction for GeneMark_model.44460_t
Valid prediction for HiQ_model.g17406.t1
Valid prediction for HiQ_model.g17411.t1
Valid prediction for snap_scaffold_10-snap.2239-T1
Valid prediction for snap_scaffold_10-snap.2258-T1
Valid prediction for snap_scaffold_10-snap.2263-T1
Valid prediction for GlimmerHMM_glimmerT_25938-T1
Valid prediction for GlimmerHMM_glimmerT_25948-T1
Valid prediction for snap_scaffold_10-snap.2264-T1
Valid prediction for GlimmerHMM_glimmerT_25957-T1
Valid prediction for GlimmerHMM_glimmerT_25945-T1
Valid prediction for GlimmerHMM_glimmerT_25950-T1
Couldn't classify 146439, 146509
Sorry, prediction pasa_asmbl_4750.p1 fails validation.
(GCG)	 AG	146439-146509	GT	GAG
(GCT)	 AG	146704-146773	GT	TTG
(GAC)	 AG	146928-147034	GT	AAG
(GGA)	 AG	147119-147149	GT	ATG
(GTG)	 AG	147562-147672	GT	CAG
(GAG)	 AG	148318-148442	GT	AGG
(CTT)	 AG	149043-149113	GT	TGG
(TTG)	 AG	149789-149978	GT	AGG
(CTG)	 AG	150305-150568	GT	AGG
(CGT)	 AG	151066-151392	GT	AGG
(TGA)	 AG	151615-151884	GT	AGG
(TGA)	 AG	152802-153059	GT	AGG
(ATT)	 AG	153598-154005	GT	AGG
(AGC)	 AG	154288-154629	GT	AGG
(CAG)	 AG	155113-155469	GT	ATG
(GAT)	 AG	156039-156077	GT	GAG
(GAG)	 AG	156579-156708	GT	ATG
(GAC)	 AG	156789-156946	GT	AAG
(GGA)	 AG	157136-157895	GT	AGG
(GTG)	 AG	158013-158324	GT	AGG
(GTC)	 AG	158443-158551	GT	AGG
(AAG)	 AG	158685-158710	GT	CTG
(ATT)	 AG	158901-159014	GT	AGG
(GAG)	 AG	159244-159336	GT	AGG
(GAG)	 AG	159446-159716	GT	AGG
(ATG)	 AG	159801-159894	GT	AGG
(GTC)	 AG	160314-160382	GT	AGG
(ATG)	 AG	160676-160784	GT	AGG
(TGT)	 AG	161064-161166	GT	TGG
(CAG)	 AG	161487-161512	TA	GAT
-recovered pasa_asmbl_4750.p1, initial, 159801, 159894
add_exon() Sorry, pasa_asmbl_4750.p1 160676-160784-initial-1 is invalid.
-recovered pasa_asmbl_4750.p1, initial, 160676, 160784
-recovered pasa_asmbl_4750.p1, terminal, 161487, 161512
-recovered pasa_asmbl_4750.p1, internal, 146439, 146509
-recovered pasa_asmbl_4750.p1, internal, 146704, 146773
-recovered pasa_asmbl_4750.p1, internal, 146928, 147034
-recovered pasa_asmbl_4750.p1, internal, 147119, 147149
-recovered pasa_asmbl_4750.p1, internal, 147562, 147672
-recovered pasa_asmbl_4750.p1, internal, 148318, 148442
-recovered pasa_asmbl_4750.p1, internal, 149043, 149113
-recovered pasa_asmbl_4750.p1, internal, 149789, 149978
-recovered pasa_asmbl_4750.p1, internal, 150305, 150568
-recovered pasa_asmbl_4750.p1, internal, 151066, 151392
-recovered pasa_asmbl_4750.p1, internal, 151615, 151884
-recovered pasa_asmbl_4750.p1, internal, 152802, 153059
-recovered pasa_asmbl_4750.p1, internal, 153598, 154005
-recovered pasa_asmbl_4750.p1, internal, 154288, 154629
-recovered pasa_asmbl_4750.p1, internal, 155113, 155469
-recovered pasa_asmbl_4750.p1, internal, 156039, 156077
-recovered pasa_asmbl_4750.p1, internal, 156579, 156708
-recovered pasa_asmbl_4750.p1, internal, 156789, 156946
-recovered pasa_asmbl_4750.p1, internal, 157136, 157895
-recovered pasa_asmbl_4750.p1, internal, 158013, 158324
-recovered pasa_asmbl_4750.p1, internal, 158443, 158551
-recovered pasa_asmbl_4750.p1, internal, 158685, 158710
-recovered pasa_asmbl_4750.p1, internal, 158901, 159014
-recovered pasa_asmbl_4750.p1, internal, 159244, 159336
-recovered pasa_asmbl_4750.p1, internal, 159446, 159716
-recovered pasa_asmbl_4750.p1, internal, 159801, 159894
-recovered pasa_asmbl_4750.p1, internal, 160314, 160382
-recovered pasa_asmbl_4750.p1, internal, 160676, 160784
-recovered pasa_asmbl_4750.p1, internal, 161064, 161166
Couldn't classify 195679, 195680
Sorry, prediction CodingQuarry_transcript_5563-T1 fails validation.
(ATG)	 CA	195679-195680	GT	ATG
(GCC)	 AG	196290-196366	GT	TGG
(ACT)	 AG	196725-196741	TC	AAT
-recovered CodingQuarry_transcript_5563-T1, terminal, 196725, 196741
-recovered CodingQuarry_transcript_5563-T1, internal, 196290, 196366
Valid prediction for pasa_asmbl_4735.p2
Valid prediction for GlimmerHMM_glimmerT_25956-T1
Valid prediction for snap_scaffold_10-snap.2243-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for HiQ_model.g17403.t1
Valid prediction for snap_scaffold_10-snap.2268-T1
Valid prediction for GeneMark_model.44468_t
Valid prediction for CodingQuarry_transcript_5560-T1
Valid prediction for GeneMark_model.44457_t
Valid prediction for GeneMark_model.44470_t
Valid prediction for GeneMark_model.44462_t
Valid prediction for GeneMark_model.44453_t
Valid prediction for GlimmerHMM_glimmerT_25942-T1
Valid prediction for GeneMark_model.44474_t
Valid prediction for Augustus_model.g17416.t1
Valid prediction for GlimmerHMM_glimmerT_25953-T1
Valid prediction for GlimmerHMM_glimmerT_25955-T1
Valid prediction for GlimmerHMM_glimmerT_25952-T1
Valid prediction for pasa_asmbl_4738.p1
Valid prediction for GeneMark_model.44465_t
Couldn't classify 195250, 195403
Sorry, prediction pasa_asmbl_4766.p1 fails validation.
(CTA)	 AG	195250-195403	GT	GGG
(AAA)	 AG	195629-195680	GT	ATG
(GCC)	 AG	196290-196366	GT	TGG
(ACT)	 AG	196725-196741	TC	AAT
-recovered pasa_asmbl_4766.p1, terminal, 196725, 196741
-recovered pasa_asmbl_4766.p1, internal, 195250, 195403
-recovered pasa_asmbl_4766.p1, internal, 195629, 195680
-recovered pasa_asmbl_4766.p1, internal, 196290, 196366
Valid prediction for snap_scaffold_10-snap.2255-T1
Valid prediction for GeneMark_model.44446_t
Valid prediction for GlimmerHMM_glimmerT_25947-T1
Valid prediction for snap_scaffold_10-snap.2271-T1
Couldn't classify 51013, 51118
Couldn't classify 55228, 55324
Sorry, prediction pasa_asmbl_4739.p1 fails validation.
(AAC)	 AT	51013-51118	GT	CAG
(TCA)	 AG	51506-51652	GT	AGG
(GTG)	 AG	51857-52008	GT	AGG
(GTG)	 AG	52292-52427	GT	AGG
(GTA)	 AG	52763-52854	GT	AGG
(GTT)	 AG	53057-53189	GT	AGG
(AGA)	 AG	54420-54498	GT	AGG
(GAA)	 AG	55228-55324	GT	AGG
-recovered pasa_asmbl_4739.p1, internal, 51506, 51652
-recovered pasa_asmbl_4739.p1, internal, 51857, 52008
-recovered pasa_asmbl_4739.p1, internal, 52292, 52427
-recovered pasa_asmbl_4739.p1, internal, 52763, 52854
-recovered pasa_asmbl_4739.p1, internal, 53057, 53189
-recovered pasa_asmbl_4739.p1, internal, 54420, 54498
-recovered pasa_asmbl_4739.p1, internal, 55228, 55324
Valid prediction for pasa_asmbl_4746.p1
Valid prediction for GeneMark_model.44448_t
Couldn't classify 56704, 56742
Sorry, prediction pasa_asmbl_4744.p1 fails validation.
(TGG)	 AC	56704-56742	GT	AGG
(GGG)	 AG	57201-57348	GT	CTG
(CTC)	 AG	57738-57890	GT	AGG
(ACA)	 AG	58451-58625	GT	GGG
(AGG)	 AG	59875-60015	GT	CGG
(GTC)	 AG	60490-60613	GT	AGG
(GTG)	 AG	61631-61699	GT	AGG
(GTG)	 AG	61831-62005	GT	AGG
(GTC)	 AG	62300-62398	GT	TCG
(CTC)	 AG	62521-62612	GT	AGG
(GGA)	 AG	63150-63197	AA	GAA
-recovered pasa_asmbl_4744.p1, terminal, 63150, 63197
-recovered pasa_asmbl_4744.p1, internal, 57201, 57348
-recovered pasa_asmbl_4744.p1, internal, 57738, 57890
-recovered pasa_asmbl_4744.p1, internal, 58451, 58625
-recovered pasa_asmbl_4744.p1, internal, 59875, 60015
-recovered pasa_asmbl_4744.p1, internal, 60490, 60613
-recovered pasa_asmbl_4744.p1, internal, 61631, 61699
-recovered pasa_asmbl_4744.p1, internal, 61831, 62005
-recovered pasa_asmbl_4744.p1, internal, 62300, 62398
-recovered pasa_asmbl_4744.p1, internal, 62521, 62612
Valid prediction for snap_scaffold_10-snap.2252-T1
Valid prediction for Augustus_model.g17410.t1
Valid prediction for pasa_asmbl_4758.p1
Valid prediction for CodingQuarry_transcript_5559-T1
Valid prediction for GeneMark_model.44451_t
Valid prediction for GlimmerHMM_glimmerT_25939-T1
Valid prediction for snap_scaffold_10-snap.2250-T1
Valid prediction for snap_scaffold_10-snap.2248-T1
Valid prediction for snap_scaffold_10-snap.2244-T1
Valid prediction for Augustus_model.g17408.t1
Valid prediction for GeneMark_model.44458_t
Valid prediction for GeneMark_model.44447_t
Valid prediction for snap_scaffold_10-snap.2269-T1
Valid prediction for Augustus_model.g17412.t1
Valid prediction for GeneMark_model.44466_t
Valid prediction for GeneMark_model.44469_t
Valid prediction for pasa_asmbl_4764.p1
Valid prediction for Augustus_model.g17418.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.44472_t
Valid prediction for snap_scaffold_10-snap.2261-T1
Valid prediction for GeneMark_model.44473_t
Valid prediction for snap_scaffold_10-snap.2240-T1
Valid prediction for Augustus_model.g17415.t1
Valid prediction for GeneMark_model.44452_t
Valid prediction for snap_scaffold_10-snap.2259-T1
Valid prediction for snap_scaffold_10-snap.2265-T1
Valid prediction for snap_scaffold_10-snap.2262-T1
Valid prediction for GeneMark_model.44459_t
Valid prediction for GeneMark_model.44450_t
Valid prediction for GlimmerHMM_glimmerT_25944-T1
Valid prediction for pasa_asmbl_3687.p1
Valid prediction for GeneMark_model.44476_t
Valid prediction for Augustus_model.g17404.t1
Valid prediction for snap_scaffold_10-snap.2242-T1
Valid prediction for snap_scaffold_10-snap.2241-T1
Valid prediction for GlimmerHMM_glimmerT_25949-T1
Valid prediction for snap_scaffold_10-snap.2251-T1
Valid prediction for snap_scaffold_10-snap.2267-T1
Valid prediction for GeneMark_model.44475_t
Valid prediction for GlimmerHMM_glimmerT_25941-T1
Valid prediction for HiQ_model.g17417.t1
Valid prediction for GlimmerHMM_glimmerT_25958-T1
Couldn't classify 208772, 209144
Couldn't classify 209559, 209587
Sorry, prediction pasa_asmbl_4093.p1 fails validation.
(GGG)	 AG	208772-209144	GT	AGG
(CCA)	 AG	209292-209399	GT	AAG
(TTT)	 AG	209559-209587	CC	CTC
-recovered pasa_asmbl_4093.p1, internal, 208772, 209144
-recovered pasa_asmbl_4093.p1, internal, 209292, 209399
Valid prediction for GlimmerHMM_glimmerT_25946-T1
Valid prediction for GlimmerHMM_glimmerT_25940-T1
Valid prediction for snap_scaffold_10-snap.2270-T1
Valid prediction for GlimmerHMM_glimmerT_25954-T1
Valid prediction for snap_scaffold_10-snap.2254-T1
Valid prediction for Augustus_model.g17414.t1
Valid prediction for GlimmerHMM_glimmerT_25961-T1
Valid prediction for CodingQuarry_transcript_5562-T1
Valid prediction for GeneMark_model.44467_t
Valid prediction for GeneMark_model.44477_t
Valid prediction for GeneMark_model.44464_t
Valid prediction for GeneMark_model.44461_t
Valid prediction for GeneMark_model.44471_t
Valid prediction for pasa_asmbl_3681.p1
Valid prediction for GlimmerHMM_glimmerT_25960-T1
Valid prediction for Augustus_model.g17405.t1
Valid prediction for snap_scaffold_10-snap.2247-T1
Valid prediction for Augustus_model.g17409.t1
Valid prediction for GeneMark_model.44456_t
Valid prediction for GeneMark_model.44449_t
Valid prediction for GlimmerHMM_glimmerT_25962-T1
Valid prediction for snap_scaffold_10-snap.2256-T1
Valid prediction for GeneMark_model.44454_t
Valid prediction for GeneMark_model.44445_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 54770, rend_intergenic: 52238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58178, rend_intergenic: 55205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103676, rend_intergenic: 102309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141767, rend_intergenic: 138272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161512, rend_intergenic: 143489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170730, rend_intergenic: 169679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177269, rend_intergenic: 173117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181037, rend_intergenic: 178511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182756, rend_intergenic: 181982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185063, rend_intergenic: 182801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 221945
-exon list size: 536


building trellis

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76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 54770, rend_intergenic: 52238  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58178, rend_intergenic: 55205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103676, rend_intergenic: 102309  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141767, rend_intergenic: 138272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161512, rend_intergenic: 143489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170730, rend_intergenic: 169679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177269, rend_intergenic: 173117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181037, rend_intergenic: 178511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182756, rend_intergenic: 181982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185063, rend_intergenic: 182801  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

-building DP trellis

-building trellis in range 211543 - 221945
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support