-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_15370631-15587309

-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_3-snap.2966-T1
Valid prediction for GlimmerHMM_glimmerT_8065-T1
Valid prediction for GlimmerHMM_glimmerT_8048-T1
Valid prediction for GlimmerHMM_glimmerT_8051-T1
Valid prediction for GlimmerHMM_glimmerT_8056-T1
Valid prediction for GlimmerHMM_glimmerT_8043-T1
Valid prediction for snap_scaffold_3-snap.2954-T1
Valid prediction for GeneMark_model.13112_t
Valid prediction for GeneMark_model.13131_t
Valid prediction for GlimmerHMM_glimmerT_8057-T1
Valid prediction for snap_scaffold_3-snap.2975-T1
Valid prediction for snap_scaffold_3-snap.2942-T1
Valid prediction for GeneMark_model.13105_t
Valid prediction for HiQ_model.g5354.t1
Valid prediction for GeneMark_model.13108_t
Valid prediction for GeneMark_model.13099_t
Valid prediction for Augustus_model.g5347.t1
Valid prediction for snap_scaffold_3-snap.2962-T1
Valid prediction for GeneMark_model.13097_t
Valid prediction for GeneMark_model.13117_t
Valid prediction for CodingQuarry_transcript_46280-T1
Valid prediction for GlimmerHMM_glimmerT_8068-T1
Valid prediction for pasa_asmbl_40530.p1
Valid prediction for GlimmerHMM_glimmerT_8060-T1
Valid prediction for snap_scaffold_3-snap.2948-T1
Valid prediction for GlimmerHMM_glimmerT_8037-T1
Valid prediction for CodingQuarry_transcript_46278-T1
Valid prediction for GlimmerHMM_glimmerT_8049-T1
Valid prediction for snap_scaffold_3-snap.2941-T1
Valid prediction for GeneMark_model.13090_t
Valid prediction for GlimmerHMM_glimmerT_8069-T1
Valid prediction for GeneMark_model.13123_t
Valid prediction for pasa_asmbl_40529.p1
Valid prediction for snap_scaffold_3-snap.2964-T1
Valid prediction for snap_scaffold_3-snap.2977-T1
Valid prediction for GlimmerHMM_glimmerT_8063-T1
Valid prediction for snap_scaffold_3-snap.2946-T1
Valid prediction for snap_scaffold_3-snap.2974-T1
Valid prediction for snap_scaffold_3-snap.2955-T1
Valid prediction for GeneMark_model.13093_t
Valid prediction for GlimmerHMM_glimmerT_8058-T1
Valid prediction for GlimmerHMM_glimmerT_8054-T1
Valid prediction for GlimmerHMM_glimmerT_8064-T1
Valid prediction for GeneMark_model.13130_t
Valid prediction for snap_scaffold_3-snap.2976-T1
Valid prediction for GeneMark_model.13095_t
Valid prediction for GeneMark_model.13100_t
Valid prediction for GeneMark_model.13136_t
Valid prediction for GeneMark_model.13129_t
Valid prediction for GeneMark_model.13132_t
Valid prediction for GeneMark_model.13127_t
Valid prediction for GlimmerHMM_glimmerT_8055-T1
Valid prediction for GlimmerHMM_glimmerT_8067-T1
Couldn't classify 201099, 201243
Couldn't classify 201360, 201374
Sorry, prediction CodingQuarry_transcript_46279-T1 fails validation.
(ATG)	 CC	199371-199463	GT	TGG
(GGT)	 AG	199804-199935	GT	GTG
(AAA)	 AG	200023-200070	GT	TGG
(ACA)	 AG	200158-200222	GT	AGG
(ACT)	 AG	200310-200374	GT	AGG
(ATG)	 AG	200517-200625	GT	ATG
(GGA)	 AG	201099-201243	CT	GCC
(AAG)	 AC	201360-201374	CC	AAC
-recovered CodingQuarry_transcript_46279-T1, initial, 199371, 199463
add_exon() Sorry, CodingQuarry_transcript_46279-T1 200517-200625-initial-1 is invalid.
-recovered CodingQuarry_transcript_46279-T1, initial, 200517, 200625
-recovered CodingQuarry_transcript_46279-T1, internal, 199804, 199935
-recovered CodingQuarry_transcript_46279-T1, internal, 200023, 200070
-recovered CodingQuarry_transcript_46279-T1, internal, 200158, 200222
-recovered CodingQuarry_transcript_46279-T1, internal, 200310, 200374
-recovered CodingQuarry_transcript_46279-T1, internal, 200517, 200625
Valid prediction for snap_scaffold_3-snap.2968-T1
Valid prediction for GeneMark_model.13133_t
Valid prediction for GlimmerHMM_glimmerT_8040-T1
Valid prediction for snap_scaffold_3-snap.2971-T1
Valid prediction for GlimmerHMM_glimmerT_8066-T1
Valid prediction for HiQ_model.g5358.t1
Valid prediction for snap_scaffold_3-snap.2961-T1
Valid prediction for Augustus_model.g5339.t1
Valid prediction for GlimmerHMM_glimmerT_8046-T1
Couldn't classify 47222, 47394
Couldn't classify 49504, 49708
Sorry, prediction pasa_asmbl_40527.p1 fails validation.
(TTT)	 CG	47222-47394	GT	AGG
(CAA)	 AG	49504-49708	AA	GTA
Valid prediction for GeneMark_model.13134_t
Valid prediction for GlimmerHMM_glimmerT_8044-T1
Couldn't classify 57956, 58103
Couldn't classify 62144, 62289
Sorry, prediction pasa_asmbl_40789.p1 fails validation.
(GGT)	 CA	57956-58103	GT	AGG
(GTT)	 AG	58802-58924	GT	AGG
(GGC)	 AG	59726-59866	GT	TGG
(GAA)	 AG	61272-61412	GT	AGG
(GTC)	 AG	62144-62289	GG	GAG
-recovered pasa_asmbl_40789.p1, internal, 58802, 58924
-recovered pasa_asmbl_40789.p1, internal, 59726, 59866
-recovered pasa_asmbl_40789.p1, internal, 61272, 61412
Valid prediction for GeneMark_model.13087_t
Valid prediction for snap_scaffold_3-snap.2978-T1
Valid prediction for GlimmerHMM_glimmerT_8038-T1
Valid prediction for Augustus_model.g5353.t1
Valid prediction for Augustus_model.g5359.t1
Valid prediction for snap_scaffold_3-snap.2973-T1
Valid prediction for snap_scaffold_3-snap.2950-T1
Valid prediction for GeneMark_model.13110_t
Valid prediction for GeneMark_model.13102_t
Couldn't classify 73623, 73770
Sorry, prediction pasa_asmbl_40528.p1 fails validation.
(GGT)	 CA	73623-73770	GT	AGG
(GAT)	 AG	74457-74570	GT	AGG
(GGA)	 AG	76432-76520	CA	GAC
-recovered pasa_asmbl_40528.p1, terminal, 76432, 76520
-recovered pasa_asmbl_40528.p1, internal, 74457, 74570
Valid prediction for snap_scaffold_3-snap.2943-T1
Valid prediction for snap_scaffold_3-snap.2972-T1
Valid prediction for HiQ_model.g5345.t1
Valid prediction for GeneMark_model.13107_t
Valid prediction for Augustus_model.g5349.t1
Valid prediction for Augustus_model.g5356.t1
Valid prediction for GeneMark_model.13084_t
Valid prediction for Augustus_model.g5346.t1
Valid prediction for Augustus_model.g5355.t1
Valid prediction for GlimmerHMM_glimmerT_8062-T1
Valid prediction for snap_scaffold_3-snap.2979-T1
Valid prediction for snap_scaffold_3-snap.2960-T1
Valid prediction for GeneMark_model.13125_t
Valid prediction for Augustus_model.g5357.t1
Valid prediction for GlimmerHMM_glimmerT_8070-T1
Valid prediction for snap_scaffold_3-snap.2959-T1
Valid prediction for Augustus_model.g5360.t1
Valid prediction for GeneMark_model.13083_t
Valid prediction for GeneMark_model.13121_t
Valid prediction for GeneMark_model.13115_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.13128_t
Valid prediction for Augustus_model.g5344.t1
Valid prediction for GeneMark_model.13116_t
Valid prediction for GeneMark_model.13119_t
Valid prediction for GeneMark_model.13094_t
Valid prediction for GeneMark_model.13092_t
Valid prediction for GeneMark_model.13111_t
Valid prediction for snap_scaffold_3-snap.2947-T1
Valid prediction for GeneMark_model.13114_t
Valid prediction for GlimmerHMM_glimmerT_8061-T1
Valid prediction for Augustus_model.g5350.t1
Valid prediction for GeneMark_model.13124_t
Valid prediction for Augustus_model.g5351.t1
Valid prediction for snap_scaffold_3-snap.2956-T1
Valid prediction for GeneMark_model.13082_t
Valid prediction for GeneMark_model.13085_t
Valid prediction for snap_scaffold_3-snap.2970-T1
Valid prediction for GlimmerHMM_glimmerT_8045-T1
Valid prediction for snap_scaffold_3-snap.2944-T1
Valid prediction for GeneMark_model.13109_t
Valid prediction for Augustus_model.g5341.t1
Valid prediction for GlimmerHMM_glimmerT_8052-T1
Valid prediction for GeneMark_model.13122_t
Valid prediction for snap_scaffold_3-snap.2965-T1
Valid prediction for GeneMark_model.13120_t
Valid prediction for snap_scaffold_3-snap.2951-T1
Valid prediction for GeneMark_model.13086_t
Valid prediction for GlimmerHMM_glimmerT_8059-T1
Valid prediction for Augustus_model.g5340.t1
Valid prediction for Augustus_model.g5343.t1
Valid prediction for snap_scaffold_3-snap.2949-T1
Valid prediction for GeneMark_model.13104_t
Valid prediction for GeneMark_model.13118_t
Valid prediction for snap_scaffold_3-snap.2952-T1
Valid prediction for snap_scaffold_3-snap.2969-T1
Valid prediction for GeneMark_model.13091_t
Valid prediction for GeneMark_model.13106_t
Valid prediction for snap_scaffold_3-snap.2967-T1
Valid prediction for Augustus_model.g5348.t1
Valid prediction for GeneMark_model.13113_t
Valid prediction for GeneMark_model.13101_t
Valid prediction for GlimmerHMM_glimmerT_8047-T1
Valid prediction for Augustus_model.g5352.t1
Valid prediction for GeneMark_model.13126_t
Valid prediction for GlimmerHMM_glimmerT_8042-T1
Valid prediction for GeneMark_model.13098_t
Valid prediction for snap_scaffold_3-snap.2945-T1
Valid prediction for GeneMark_model.13135_t
Valid prediction for GeneMark_model.13096_t
Valid prediction for snap_scaffold_3-snap.2958-T1
Valid prediction for GlimmerHMM_glimmerT_8053-T1
Valid prediction for snap_scaffold_3-snap.2963-T1
Valid prediction for GlimmerHMM_glimmerT_8041-T1
Valid prediction for Augustus_model.g5342.t1
Valid prediction for GeneMark_model.13088_t
Valid prediction for GeneMark_model.13089_t
Valid prediction for snap_scaffold_3-snap.2957-T1
Valid prediction for GlimmerHMM_glimmerT_8050-T1
Valid prediction for snap_scaffold_3-snap.2953-T1
Valid prediction for GeneMark_model.13103_t
Valid prediction for GlimmerHMM_glimmerT_8039-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 145337, rend_intergenic: 145334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17787, rend_intergenic: 15636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61794, rend_intergenic: 57423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108921, rend_intergenic: 90822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145743, rend_intergenic: 140028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153834, rend_intergenic: 152251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 216679
-exon list size: 616


building trellis

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99.8    
-found 33 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 145337, rend_intergenic: 145334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17787, rend_intergenic: 15636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61794, rend_intergenic: 57423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108921, rend_intergenic: 90822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145743, rend_intergenic: 140028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153834, rend_intergenic: 152251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support