-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_3238009-3414538

-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.715-T1
Valid prediction for GeneMark_model.42580_t
Valid prediction for snap_scaffold_10-snap.712-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.42578_t
Valid prediction for GeneMark_model.42579_t
Valid prediction for snap_scaffold_10-snap.708-T1
Valid prediction for GeneMark_model.42597_t
Valid prediction for GlimmerHMM_glimmerT_24918-T1
Valid prediction for snap_scaffold_10-snap.724-T1
Valid prediction for snap_scaffold_10-snap.702-T1
Valid prediction for Augustus_model.g16706.t1
Valid prediction for GeneMark_model.42603_t
Valid prediction for GeneMark_model.42608_t
Valid prediction for Augustus_model.g16712.t1
Valid prediction for GeneMark_model.42589_t
Valid prediction for snap_scaffold_10-snap.696-T1
Valid prediction for snap_scaffold_10-snap.709-T1
Valid prediction for GlimmerHMM_glimmerT_24934-T1
Valid prediction for GeneMark_model.42591_t
Valid prediction for GlimmerHMM_glimmerT_24945-T1
Valid prediction for Augustus_model.g16724.t1
Valid prediction for snap_scaffold_10-snap.731-T1
Valid prediction for GeneMark_model.42600_t
Valid prediction for Augustus_model.g16721.t1
Valid prediction for snap_scaffold_10-snap.711-T1
Valid prediction for GeneMark_model.42605_t
Valid prediction for CodingQuarry_transcript_5325-T1
Valid prediction for GlimmerHMM_glimmerT_24942-T1
Valid prediction for GeneMark_model.42586_t
Valid prediction for Augustus_model.g16711.t1
Valid prediction for GlimmerHMM_glimmerT_24933-T1
Valid prediction for snap_scaffold_10-snap.723-T1
Valid prediction for GeneMark_model.42614_t
Valid prediction for Augustus_model.g16715.t1
Valid prediction for GlimmerHMM_glimmerT_24931-T1
Valid prediction for GeneMark_model.42593_t
Valid prediction for GeneMark_model.42612_t
Valid prediction for GlimmerHMM_glimmerT_24927-T1
Valid prediction for GeneMark_model.42607_t
Valid prediction for GeneMark_model.42617_t
Valid prediction for GlimmerHMM_glimmerT_24917-T1
Valid prediction for GeneMark_model.42570_t
Valid prediction for CodingQuarry_transcript_5324-T1
Valid prediction for pasa_asmbl_4314.p1
Valid prediction for GeneMark_model.42595_t
Valid prediction for GeneMark_model.42574_t
Valid prediction for snap_scaffold_10-snap.720-T1
Valid prediction for snap_scaffold_10-snap.706-T1
Valid prediction for snap_scaffold_10-snap.730-T1
Valid prediction for GlimmerHMM_glimmerT_24946-T1
Valid prediction for GeneMark_model.42610_t
Valid prediction for GeneMark_model.42572_t
Valid prediction for GlimmerHMM_glimmerT_24936-T1
Valid prediction for snap_scaffold_10-snap.728-T1
Valid prediction for snap_scaffold_10-snap.725-T1
Valid prediction for GlimmerHMM_glimmerT_24929-T1
Valid prediction for GeneMark_model.42619_t
Valid prediction for GeneMark_model.42582_t
Valid prediction for pasa_asmbl_4316.p1
Valid prediction for GlimmerHMM_glimmerT_24951-T1
Valid prediction for GlimmerHMM_glimmerT_24950-T1
Valid prediction for HiQ_model.g16726.t1
Valid prediction for snap_scaffold_10-snap.718-T1
Valid prediction for Augustus_model.g16705.t1
Valid prediction for Augustus_model.g16719.t1
Valid prediction for GeneMark_model.42576_t
Valid prediction for GlimmerHMM_glimmerT_24919-T1
Valid prediction for GeneMark_model.42587_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 GeneMark_model.42592_t
Valid prediction for GlimmerHMM_glimmerT_24940-T1
Valid prediction for Augustus_model.g16714.t1
Couldn't classify 99710, 99811
Couldn't classify 99996, 100173
Sorry, prediction CodingQuarry_transcript_5321-T1 fails validation.
(ATG)	 GG	96304-96319	GT	AGG
(GTG)	 AG	98954-99121	GT	TGG
(ACC)	 AG	99341-99480	GT	TGG
(ATC)	 AG	99710-99811	AT	TAA
(GAC)	 AC	99996-100173	GT	TGG
(AGC)	 AG	100349-100631	GT	CGG
(GTT)	 AG	100856-101117	TG	GAT
-recovered CodingQuarry_transcript_5321-T1, initial, 96304, 96319
-recovered CodingQuarry_transcript_5321-T1, terminal, 100856, 101117
-recovered CodingQuarry_transcript_5321-T1, internal, 98954, 99121
-recovered CodingQuarry_transcript_5321-T1, internal, 99341, 99480
-recovered CodingQuarry_transcript_5321-T1, internal, 100349, 100631
Valid prediction for snap_scaffold_10-snap.700-T1
Valid prediction for snap_scaffold_10-snap.710-T1
Valid prediction for GeneMark_model.42581_t
Valid prediction for pasa_asmbl_3095.p1
Valid prediction for snap_scaffold_10-snap.729-T1
Valid prediction for GeneMark_model.42613_t
Valid prediction for GeneMark_model.42616_t
Valid prediction for pasa_asmbl_3113.p1
Valid prediction for GeneMark_model.42596_t
Valid prediction for snap_scaffold_10-snap.726-T1
Valid prediction for snap_scaffold_10-snap.707-T1
Valid prediction for GeneMark_model.42577_t
Valid prediction for GlimmerHMM_glimmerT_24949-T1
Valid prediction for snap_scaffold_10-snap.705-T1
Valid prediction for GlimmerHMM_glimmerT_24926-T1
Valid prediction for snap_scaffold_10-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_24935-T1
Couldn't classify 122935, 122978
Sorry, prediction pasa_asmbl_3097.p1 fails validation.
(TAC)	 AG	122935-122978	GT	CGG
(GAT)	 AG	125241-125313	GT	AGG
(TAC)	 AG	125428-125541	GT	AGG
(AAC)	 AG	125673-125801	GT	AGG
(GCA)	 AG	126097-126407	GT	GGG
(AGG)	 AG	126666-126719	GT	AAG
(TGA)	 AG	127110-127149	GT	TGG
(AGT)	 AG	127722-127737	GT	TGG
(ACA)	 AG	127963-127995	GT	GGG
(GTG)	 AG	128146-128213	GT	ACG
(CTG)	 AG	128334-128503	GC	AGG
(TGT)	 AG	128925-128955	AG	AGA
-recovered pasa_asmbl_3097.p1, terminal, 128925, 128955
-recovered pasa_asmbl_3097.p1, internal, 122935, 122978
-recovered pasa_asmbl_3097.p1, internal, 125241, 125313
-recovered pasa_asmbl_3097.p1, internal, 125428, 125541
-recovered pasa_asmbl_3097.p1, internal, 125673, 125801
-recovered pasa_asmbl_3097.p1, internal, 126097, 126407
-recovered pasa_asmbl_3097.p1, internal, 126666, 126719
-recovered pasa_asmbl_3097.p1, internal, 127110, 127149
-recovered pasa_asmbl_3097.p1, internal, 127722, 127737
-recovered pasa_asmbl_3097.p1, internal, 127963, 127995
-recovered pasa_asmbl_3097.p1, internal, 128146, 128213
-recovered pasa_asmbl_3097.p1, internal, 128334, 128503
Valid prediction for GeneMark_model.42590_t
Valid prediction for snap_scaffold_10-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_24932-T1
Valid prediction for GeneMark_model.42604_t
Valid prediction for GeneMark_model.42575_t
Valid prediction for Augustus_model.g16716.t1
Valid prediction for GlimmerHMM_glimmerT_24920-T1
Valid prediction for GlimmerHMM_glimmerT_24938-T1
Valid prediction for GlimmerHMM_glimmerT_24925-T1
Valid prediction for GeneMark_model.42601_t
Valid prediction for GlimmerHMM_glimmerT_24943-T1
Valid prediction for GeneMark_model.42606_t
Valid prediction for Augustus_model.g16722.t1
Valid prediction for HiQ_model.g16709.t1
Valid prediction for GeneMark_model.42599_t
Valid prediction for GeneMark_model.42584_t
Valid prediction for snap_scaffold_10-snap.716-T1
Couldn't classify 72898, 72986
Couldn't classify 74378, 74426
Sorry, prediction pasa_asmbl_3106.p1 fails validation.
(ATC)	 TC	72898-72986	GT	AGG
(CGG)	 AG	73309-73417	GT	TGG
(GCC)	 AG	73535-73614	GT	TGG
(CCT)	 AG	74052-74159	GT	TGG
(GTC)	 AG	74378-74426	GA	CAG
-recovered pasa_asmbl_3106.p1, internal, 73309, 73417
-recovered pasa_asmbl_3106.p1, internal, 73535, 73614
-recovered pasa_asmbl_3106.p1, internal, 74052, 74159
Valid prediction for GlimmerHMM_glimmerT_24939-T1
Valid prediction for Augustus_model.g16707.t1
Valid prediction for Augustus_model.g16710.t1
Valid prediction for GlimmerHMM_glimmerT_24941-T1
Valid prediction for Augustus_model.g16725.t1
Valid prediction for GlimmerHMM_glimmerT_24923-T1
Valid prediction for GlimmerHMM_glimmerT_24948-T1
Valid prediction for GeneMark_model.42609_t
Valid prediction for GeneMark_model.42598_t
Valid prediction for CodingQuarry_transcript_5320-T1
Valid prediction for GlimmerHMM_glimmerT_24924-T1
Valid prediction for GeneMark_model.42602_t
Valid prediction for GlimmerHMM_glimmerT_24930-T1
Valid prediction for GlimmerHMM_glimmerT_24928-T1
Couldn't classify 62584, 62729
Sorry, prediction pasa_asmbl_3110.p1 fails validation.
(GAA)	 TG	62584-62729	GT	CGG
(GGA)	 AG	63205-63261	GT	GGG
(ATT)	 AG	63543-63600	GT	AGG
(AGC)	 AG	63907-64482	GT	GAG
-recovered pasa_asmbl_3110.p1, terminal, 63907, 64482
-recovered pasa_asmbl_3110.p1, internal, 63205, 63261
-recovered pasa_asmbl_3110.p1, internal, 63543, 63600
-recovered pasa_asmbl_3110.p1, internal, 63907, 64482
Valid prediction for snap_scaffold_10-snap.727-T1
Valid prediction for snap_scaffold_10-snap.717-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for pasa_asmbl_3116.p1
Valid prediction for snap_scaffold_10-snap.703-T1
Valid prediction for snap_scaffold_10-snap.721-T1
Valid prediction for Augustus_model.g16717.t1
Valid prediction for GlimmerHMM_glimmerT_24944-T1
Valid prediction for GlimmerHMM_glimmerT_24921-T1
Valid prediction for HiQ_model.g16718.t1
Valid prediction for GeneMark_model.42615_t
Valid prediction for GeneMark_model.42571_t
Valid prediction for snap_scaffold_10-snap.698-T1
Valid prediction for GeneMark_model.42588_t
Valid prediction for Augustus_model.g16708.t1
Valid prediction for Augustus_model.g16720.t1
Valid prediction for CodingQuarry_transcript_5322-T1
Valid prediction for GeneMark_model.42594_t
Valid prediction for snap_scaffold_10-snap.701-T1
Valid prediction for GeneMark_model.42618_t
Valid prediction for GlimmerHMM_glimmerT_24947-T1
Valid prediction for snap_scaffold_10-snap.713-T1
Valid prediction for snap_scaffold_10-snap.714-T1
Valid prediction for Augustus_model.g16713.t1
Valid prediction for GeneMark_model.42583_t
Valid prediction for GlimmerHMM_glimmerT_24922-T1
Valid prediction for Augustus_model.g16723.t1
Valid prediction for snap_scaffold_10-snap.719-T1
Valid prediction for GeneMark_model.42611_t
Valid prediction for GlimmerHMM_glimmerT_24937-T1
Valid prediction for snap_scaffold_10-snap.704-T1
Valid prediction for GeneMark_model.42585_t
Valid prediction for snap_scaffold_10-snap.697-T1
Valid prediction for GeneMark_model.42573_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25742, rend_intergenic: 3490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33622, rend_intergenic: 26826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53602, rend_intergenic: 50842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68886, rend_intergenic: 66677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78546, rend_intergenic: 75414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94678, rend_intergenic: 87037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108464, rend_intergenic: 100259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134659, rend_intergenic: 130659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169182, rend_intergenic: 168247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176530
-exon list size: 736


building trellis

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79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
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    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
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    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 25742, rend_intergenic: 3490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33622, rend_intergenic: 26826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53602, rend_intergenic: 50842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68886, rend_intergenic: 66677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78546, rend_intergenic: 75414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94678, rend_intergenic: 87037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108464, rend_intergenic: 100259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134659, rend_intergenic: 130659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169182, rend_intergenic: 168247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support