-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_14666236-14824360

-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.8146_t
Valid prediction for snap_scaffold_2-snap.2848-T1
Valid prediction for GlimmerHMM_glimmerT_5078-T1
Valid prediction for GlimmerHMM_glimmerT_5081-T1
Valid prediction for GeneMark_model.8150_t
Valid prediction for snap_scaffold_2-snap.2841-T1
Valid prediction for GlimmerHMM_glimmerT_5077-T1
Valid prediction for snap_scaffold_2-snap.2846-T1
Valid prediction for GeneMark_model.8156_t
Valid prediction for snap_scaffold_2-snap.2859-T1
Valid prediction for snap_scaffold_2-snap.2862-T1
Valid prediction for GlimmerHMM_glimmerT_5080-T1
Valid prediction for GeneMark_model.8154_t
Valid prediction for snap_scaffold_2-snap.2834-T1
Valid prediction for snap_scaffold_2-snap.2853-T1
Valid prediction for snap_scaffold_2-snap.2854-T1
Valid prediction for Augustus_model.g3424.t1
Valid prediction for snap_scaffold_2-snap.2845-T1
Couldn't classify 50597, 50620
Couldn't classify 56317, 56322
Sorry, prediction pasa_asmbl_24997.p1 fails validation.
(CTG)	 CG	50597-50620	GT	AGG
(CCC)	 AG	50739-50854	GT	AGG
(GGA)	 AG	51157-51283	GT	AGG
(GTA)	 AG	51385-51478	GT	CGG
(ACC)	 AG	51726-51755	GT	AGG
(AGT)	 AG	52333-52480	GT	ATG
(TGA)	 AG	53327-53523	GT	AGG
(AAA)	 AG	53720-53838	GT	AGG
(GAC)	 AG	54046-54117	GT	ACG
(GAT)	 AG	54250-54426	GT	AGG
(GGA)	 AG	55749-55850	GT	AGG
(AAA)	 AG	56317-56322	AC	GCA
-recovered pasa_asmbl_24997.p1, internal, 50739, 50854
-recovered pasa_asmbl_24997.p1, internal, 51157, 51283
-recovered pasa_asmbl_24997.p1, internal, 51385, 51478
-recovered pasa_asmbl_24997.p1, internal, 51726, 51755
-recovered pasa_asmbl_24997.p1, internal, 52333, 52480
-recovered pasa_asmbl_24997.p1, internal, 53327, 53523
-recovered pasa_asmbl_24997.p1, internal, 53720, 53838
-recovered pasa_asmbl_24997.p1, internal, 54046, 54117
-recovered pasa_asmbl_24997.p1, internal, 54250, 54426
-recovered pasa_asmbl_24997.p1, internal, 55749, 55850
Valid prediction for Augustus_model.g3432.t1
Valid prediction for GlimmerHMM_glimmerT_5086-T1
Valid prediction for GeneMark_model.8180_t
Valid prediction for snap_scaffold_2-snap.2849-T1
Valid prediction for GeneMark_model.8183_t
Valid prediction for GeneMark_model.8177_t
Valid prediction for GeneMark_model.8161_t
Valid prediction for GeneMark_model.8185_t
Valid prediction for Augustus_model.g3419.t1
Valid prediction for HiQ_model.g3425.t1
Valid prediction for snap_scaffold_2-snap.2857-T1
Valid prediction for pasa_asmbl_25007.p1
Couldn't classify 79782, 79899
Sorry, prediction pasa_asmbl_25003.p1 fails validation.
(CTT)	 CC	79782-79899	GT	AGG
(GAA)	 AG	82319-82418	GT	TTG
(TGC)	 AG	82604-82677	GT	AGG
(ACC)	 AG	82786-82970	GG	GAG
-recovered pasa_asmbl_25003.p1, terminal, 82786, 82970
-recovered pasa_asmbl_25003.p1, internal, 82319, 82418
-recovered pasa_asmbl_25003.p1, internal, 82604, 82677
Valid prediction for GeneMark_model.8157_t
Valid prediction for snap_scaffold_2-snap.2839-T1
Valid prediction for GeneMark_model.8176_t
Valid prediction for snap_scaffold_2-snap.2836-T1
Valid prediction for GlimmerHMM_glimmerT_5089-T1
Valid prediction for GeneMark_model.8170_t
Couldn't classify 61098, 61184
Couldn't classify 62720, 62833
Sorry, prediction pasa_asmbl_24998.p1 fails validation.
(AGC)	 TG	61098-61184	GT	TGG
(GGC)	 AG	61624-61810	GT	CGG
(GGA)	 AG	62375-62469	GT	AGG
(GAC)	 AG	62720-62833	TT	CCT
-recovered pasa_asmbl_24998.p1, internal, 61624, 61810
-recovered pasa_asmbl_24998.p1, internal, 62375, 62469
Valid prediction for GlimmerHMM_glimmerT_5085-T1
Valid prediction for GlimmerHMM_glimmerT_5076-T1
Valid prediction for GeneMark_model.8166_t
Valid prediction for Augustus_model.g3423.t1
Valid prediction for Augustus_model.g3429.t1
Valid prediction for GeneMark_model.8151_t
Valid prediction for Augustus_model.g3420.t1
Valid prediction for snap_scaffold_2-snap.2863-T1
Valid prediction for Augustus_model.g3422.t1
Valid prediction for snap_scaffold_2-snap.2842-T1
Valid prediction for GeneMark_model.8168_t
Valid prediction for GeneMark_model.8149_t
Couldn't classify 58317, 58361
Couldn't classify 59406, 59555
Sorry, prediction pasa_asmbl_25455.p1 fails validation.
(GCC)	 CA	58317-58361	GT	AGG
(CCT)	 AG	58623-58715	GT	AGG
(GAG)	 AG	59114-59224	GT	AGG
(TCT)	 AG	59406-59555	AG	ACA
-recovered pasa_asmbl_25455.p1, internal, 58623, 58715
-recovered pasa_asmbl_25455.p1, internal, 59114, 59224
Valid prediction for GlimmerHMM_glimmerT_5073-T1
Valid prediction for GeneMark_model.8144_t
Couldn't classify 66952, 67045
Sorry, prediction pasa_asmbl_25000.p1 fails validation.
(GAG)	 TA	66952-67045	GT	AGG
(CCA)	 AG	67734-67877	GT	AGG
(AGC)	 AG	69352-69426	GT	GGG
(AGG)	 AG	69587-69700	GT	CGG
(AAC)	 AG	69885-69967	GT	AGG
(AAG)	 AG	70085-72077	GT	AGG
(ATC)	 AG	72252-72346	GT	AGG
(AAG)	 AG	75238-75345	GT	AGG
(ATC)	 AG	75756-75849	GT	AGG
(ACT)	 AG	77206-77256	GT	CGG
(TTG)	 AG	79834-79899	GT	AGG
(GAA)	 AG	82319-82418	GT	TTG
(TGC)	 AG	82604-82677	GT	AGG
(ACC)	 AG	82786-82970	GG	GAG
-recovered pasa_asmbl_25000.p1, terminal, 82786, 82970
-recovered pasa_asmbl_25000.p1, internal, 67734, 67877
-recovered pasa_asmbl_25000.p1, internal, 69352, 69426
-recovered pasa_asmbl_25000.p1, internal, 69587, 69700
-recovered pasa_asmbl_25000.p1, internal, 69885, 69967
-recovered pasa_asmbl_25000.p1, internal, 70085, 72077
-recovered pasa_asmbl_25000.p1, internal, 72252, 72346
-recovered pasa_asmbl_25000.p1, internal, 75238, 75345
-recovered pasa_asmbl_25000.p1, internal, 75756, 75849
-recovered pasa_asmbl_25000.p1, internal, 77206, 77256
-recovered pasa_asmbl_25000.p1, internal, 79834, 79899
-recovered pasa_asmbl_25000.p1, internal, 82319, 82418
-recovered pasa_asmbl_25000.p1, internal, 82604, 82677
Valid prediction for CodingQuarry_transcript_28696-T1
Valid prediction for GeneMark_model.8165_t
Valid prediction for GeneMark_model.8159_t
Valid prediction for snap_scaffold_2-snap.2844-T1
Valid prediction for Augustus_model.g3430.t1
Valid prediction for GeneMark_model.8174_t
Valid prediction for GeneMark_model.8147_t
Valid prediction for GeneMark_model.8162_t
Valid prediction for GlimmerHMM_glimmerT_5087-T1
Couldn't classify 47434, 47641
Couldn't classify 50363, 50533
Sorry, prediction pasa_asmbl_24996.p1 fails validation.
(TGT)	 AG	47434-47641	GT	CAG
(GTA)	 AG	47738-47854	GT	GAG
(GGA)	 AG	47966-48067	GT	AGG
(GGT)	 AG	48572-48727	GT	TGG
(GAA)	 AG	49135-49235	GT	ACG
(GAC)	 AG	50363-50533	AT	GCA
-recovered pasa_asmbl_24996.p1, internal, 47434, 47641
-recovered pasa_asmbl_24996.p1, internal, 47738, 47854
-recovered pasa_asmbl_24996.p1, internal, 47966, 48067
-recovered pasa_asmbl_24996.p1, internal, 48572, 48727
-recovered pasa_asmbl_24996.p1, internal, 49135, 49235
Valid prediction for GlimmerHMM_glimmerT_5071-T1
Sorry, intron length (8) is less than minimum required (10)

-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 GlimmerHMM_glimmerT_5083-T1
Valid prediction for snap_scaffold_2-snap.2860-T1
Valid prediction for GeneMark_model.8182_t
Valid prediction for GeneMark_model.8164_t
Valid prediction for GlimmerHMM_glimmerT_5084-T1
Valid prediction for snap_scaffold_2-snap.2833-T1
Couldn't classify 51031, 51132
Sorry, prediction pasa_asmbl_23626.p1 fails validation.
(GTC)	 AG	51031-51132	GT	AGG
(TGG)	 AG	51528-51659	GT	GGG
(GGC)	 AG	52799-52882	GT	AGG
(CTC)	 AG	54276-54347	CG	AGC
-recovered pasa_asmbl_23626.p1, terminal, 54276, 54347
-recovered pasa_asmbl_23626.p1, internal, 51031, 51132
-recovered pasa_asmbl_23626.p1, internal, 51528, 51659
-recovered pasa_asmbl_23626.p1, internal, 52799, 52882
Valid prediction for snap_scaffold_2-snap.2856-T1
Valid prediction for Augustus_model.g3428.t1
Valid prediction for snap_scaffold_2-snap.2838-T1
Valid prediction for GeneMark_model.8179_t
Valid prediction for GeneMark_model.8158_t
Valid prediction for snap_scaffold_2-snap.2847-T1
Valid prediction for GeneMark_model.8145_t
Valid prediction for GlimmerHMM_glimmerT_5090-T1
Valid prediction for snap_scaffold_2-snap.2837-T1
Valid prediction for snap_scaffold_2-snap.2855-T1
Valid prediction for snap_scaffold_2-snap.2851-T1
Valid prediction for GeneMark_model.8163_t
Valid prediction for Augustus_model.g3433.t1
Valid prediction for GeneMark_model.8175_t
Valid prediction for GeneMark_model.8178_t
Valid prediction for Augustus_model.g3431.t1
Valid prediction for GeneMark_model.8160_t
Valid prediction for GeneMark_model.8153_t
Valid prediction for GlimmerHMM_glimmerT_5074-T1
Valid prediction for GeneMark_model.8152_t
Valid prediction for GeneMark_model.8148_t
Valid prediction for GlimmerHMM_glimmerT_5079-T1
Valid prediction for GlimmerHMM_glimmerT_5088-T1
Valid prediction for CodingQuarry_transcript_28697-T1
Valid prediction for GeneMark_model.8173_t
Valid prediction for GeneMark_model.8184_t
Valid prediction for GlimmerHMM_glimmerT_5082-T1
Valid prediction for GeneMark_model.8169_t
Valid prediction for GeneMark_model.8172_t
Valid prediction for GeneMark_model.8171_t
Valid prediction for Augustus_model.g3426.t1
Valid prediction for snap_scaffold_2-snap.2858-T1
Valid prediction for snap_scaffold_2-snap.2835-T1
Valid prediction for GlimmerHMM_glimmerT_5075-T1
Valid prediction for snap_scaffold_2-snap.2852-T1
Valid prediction for GeneMark_model.8167_t
Valid prediction for snap_scaffold_2-snap.2850-T1
Valid prediction for snap_scaffold_2-snap.2840-T1
Valid prediction for GeneMark_model.8181_t
Valid prediction for snap_scaffold_2-snap.2861-T1
Valid prediction for GlimmerHMM_glimmerT_5072-T1
Valid prediction for snap_scaffold_2-snap.2843-T1
Valid prediction for GeneMark_model.8155_t
Valid prediction for Augustus_model.g3427.t1
Valid prediction for snap_scaffold_2-snap.2832-T1
Valid prediction for Augustus_model.g3421.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19134, rend_intergenic: 16075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59596, rend_intergenic: 56775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80285, rend_intergenic: 79578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83578, rend_intergenic: 80551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90093, rend_intergenic: 88455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108301, rend_intergenic: 101909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124483, rend_intergenic: 120613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135836, rend_intergenic: 131214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158125
-exon list size: 571


building trellis

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99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 19134, rend_intergenic: 16075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59596, rend_intergenic: 56775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80285, rend_intergenic: 79578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83578, rend_intergenic: 80551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90093, rend_intergenic: 88455  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108301, rend_intergenic: 101909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124483, rend_intergenic: 120613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135836, rend_intergenic: 131214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support