-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_14193732-14419130

-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_5011-T1
Valid prediction for pasa_asmbl_24953.p1
Valid prediction for CodingQuarry_transcript_28680-T1
Valid prediction for GeneMark_model.8088_t
Valid prediction for snap_scaffold_2-snap.2756-T1
Valid prediction for CodingQuarry_transcript_28677-T1
Valid prediction for HiQ_model.g3376.t1
Valid prediction for snap_scaffold_2-snap.2776-T1
Valid prediction for HiQ_model.g3387.t1
Valid prediction for CodingQuarry_transcript_28681-T1
Valid prediction for GeneMark_model.8105_t
Valid prediction for Augustus_model.g3375.t1
Valid prediction for snap_scaffold_2-snap.2772-T1
Valid prediction for GeneMark_model.8086_t
Valid prediction for GlimmerHMM_glimmerT_5012-T1
Valid prediction for GeneMark_model.8079_t
Valid prediction for CodingQuarry_transcript_28682-T1
Valid prediction for pasa_asmbl_24931.p2
Valid prediction for snap_scaffold_2-snap.2757-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.2771-T1
Valid prediction for GlimmerHMM_glimmerT_5021-T1
Valid prediction for CodingQuarry_transcript_28678-T1
Couldn't classify 159381, 160703
Sorry, prediction pasa_asmbl_24947.p1 fails validation.
(AAC)	 CT	159381-160703	GT	AAG
Valid prediction for HiQ_model.g3388.t1
Valid prediction for snap_scaffold_2-snap.2748-T1
Valid prediction for GeneMark_model.8103_t
Valid prediction for GlimmerHMM_glimmerT_5020-T1
Valid prediction for GeneMark_model.8087_t
Valid prediction for GeneMark_model.8072_t
Couldn't classify 113691, 113828
Couldn't classify 114976, 115085
Sorry, prediction pasa_asmbl_24938.p1 fails validation.
(GTC)	 CA	113691-113828	GT	AGG
(GAA)	 AG	113954-114135	GT	GCG
(CTT)	 AG	114553-114725	GT	TGG
(CTG)	 AG	114976-115085	GG	AGG
-recovered pasa_asmbl_24938.p1, internal, 113954, 114135
-recovered pasa_asmbl_24938.p1, internal, 114553, 114725
Valid prediction for CodingQuarry_transcript_28675-T1
Valid prediction for snap_scaffold_2-snap.2768-T1
Valid prediction for GeneMark_model.8093_t
Valid prediction for HiQ_model.g3385.t1
Valid prediction for snap_scaffold_2-snap.2780-T1
Valid prediction for pasa_asmbl_24926.p1
Valid prediction for pasa_asmbl_24959.p1
Valid prediction for GeneMark_model.8099_t
Valid prediction for CodingQuarry_transcript_28685-T1
Valid prediction for HiQ_model.g3383.t1
Valid prediction for HiQ_model.g3371.t1
Valid prediction for GlimmerHMM_glimmerT_5032-T1
Couldn't classify 189315, 189510
Sorry, prediction pasa_asmbl_24957.p1 fails validation.
(AAC)	 GC	189315-189510	GT	AGG
(GAT)	 AG	192069-192151	GT	GGG
(ATG)	 AG	193972-194020	GT	CGG
(CGG)	 AG	194608-194742	GT	AGG
(GCT)	 AG	195988-196067	GT	AGG
(GGC)	 AG	197287-197448	GT	CTG
(TTG)	 AG	197601-197664	GT	GGG
(CTG)	 AG	198734-198862	GT	CGG
(GTA)	 AG	199042-199218	GT	GGG
(GAC)	 AG	199358-199501	GT	CGG
(GGT)	 AG	199885-200012	TC	GAT
-recovered pasa_asmbl_24957.p1, initial, 193972, 194020
-recovered pasa_asmbl_24957.p1, terminal, 199885, 200012
-recovered pasa_asmbl_24957.p1, internal, 192069, 192151
-recovered pasa_asmbl_24957.p1, internal, 193972, 194020
-recovered pasa_asmbl_24957.p1, internal, 194608, 194742
-recovered pasa_asmbl_24957.p1, internal, 195988, 196067
-recovered pasa_asmbl_24957.p1, internal, 197287, 197448
-recovered pasa_asmbl_24957.p1, internal, 197601, 197664
-recovered pasa_asmbl_24957.p1, internal, 198734, 198862
-recovered pasa_asmbl_24957.p1, internal, 199042, 199218
-recovered pasa_asmbl_24957.p1, internal, 199358, 199501
Valid prediction for pasa_asmbl_24949.p1
Valid prediction for GlimmerHMM_glimmerT_5028-T1
Valid prediction for GlimmerHMM_glimmerT_5018-T1
Valid prediction for snap_scaffold_2-snap.2777-T1
Valid prediction for snap_scaffold_2-snap.2765-T1
Valid prediction for HiQ_model.g3379.t1
Valid prediction for GeneMark_model.8092_t
Valid prediction for snap_scaffold_2-snap.2769-T1
Valid prediction for snap_scaffold_2-snap.2781-T1
Valid prediction for GeneMark_model.8102_t
Valid prediction for GeneMark_model.8091_t
Valid prediction for pasa_asmbl_24940.p1
Valid prediction for pasa_asmbl_24925.p1
Couldn't classify 161622, 162230
Sorry, prediction pasa_asmbl_24948.p1 fails validation.
(GAG)	 GT	161622-162230	AA	GCA
Valid prediction for GlimmerHMM_glimmerT_5029-T1
Valid prediction for GlimmerHMM_glimmerT_5025-T1
Valid prediction for GlimmerHMM_glimmerT_5027-T1
Valid prediction for pasa_asmbl_24946.p1
Valid prediction for GlimmerHMM_glimmerT_5030-T1
Valid prediction for GeneMark_model.8081_t
Valid prediction for Augustus_model.g3369.t1
Valid prediction for GeneMark_model.8090_t
Valid prediction for GeneMark_model.8082_t
Valid prediction for GeneMark_model.8098_t
Valid prediction for GlimmerHMM_glimmerT_5031-T1
Valid prediction for GeneMark_model.8096_t
Valid prediction for snap_scaffold_2-snap.2766-T1
Valid prediction for CodingQuarry_transcript_28686-T1
Valid prediction for GlimmerHMM_glimmerT_5017-T1
Valid prediction for snap_scaffold_2-snap.2782-T1
Valid prediction for GlimmerHMM_glimmerT_5019-T1
Valid prediction for GeneMark_model.8089_t
Valid prediction for pasa_asmbl_24937.p1
Valid prediction for HiQ_model.g3378.t1
Valid prediction for snap_scaffold_2-snap.2755-T1
Valid prediction for CodingQuarry_transcript_28687-T1
Valid prediction for snap_scaffold_2-snap.2761-T1
Valid prediction for GeneMark_model.8084_t
Valid prediction for HiQ_model.g3374.t1
Valid prediction for GlimmerHMM_glimmerT_5022-T1
Valid prediction for Augustus_model.g3373.t1
Valid prediction for Augustus_model.g3386.t1
Valid prediction for snap_scaffold_2-snap.2759-T1
Valid prediction for Augustus_model.g3389.t1
Valid prediction for CodingQuarry_transcript_28676-T1
Valid prediction for GeneMark_model.8097_t
Valid prediction for snap_scaffold_2-snap.2767-T1
Valid prediction for snap_scaffold_2-snap.2773-T1
Valid prediction for Augustus_model.g3380.t1
Valid prediction for snap_scaffold_2-snap.2778-T1
Valid prediction for Augustus_model.g3382.t1
Valid prediction for GlimmerHMM_glimmerT_5010-T1
Valid prediction for GlimmerHMM_glimmerT_5015-T1
Valid prediction for snap_scaffold_2-snap.2758-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_2-snap.2751-T1
Valid prediction for GeneMark_model.8085_t
Valid prediction for GeneMark_model.8083_t
Valid prediction for CodingQuarry_transcript_28679-T1
Valid prediction for GeneMark_model.8080_t
Valid prediction for GlimmerHMM_glimmerT_5026-T1
Valid prediction for snap_scaffold_2-snap.2760-T1
Valid prediction for CodingQuarry_transcript_28674-T1
Valid prediction for GlimmerHMM_glimmerT_5013-T1
Couldn't classify 200037, 200116
Sorry, prediction pasa_asmbl_23594.p1 fails validation.
(AAA)	 AA	200037-200116	GT	GGG
(GTG)	 AG	200688-201307	GT	AGG
(GTA)	 AG	201833-202008	GT	GAG
-recovered pasa_asmbl_23594.p1, terminal, 201833, 202008
-recovered pasa_asmbl_23594.p1, internal, 200688, 201307
-recovered pasa_asmbl_23594.p1, internal, 201833, 202008
Valid prediction for Augustus_model.g3366.t1
Valid prediction for Augustus_model.g3370.t1
Valid prediction for snap_scaffold_2-snap.2747-T1
Valid prediction for GlimmerHMM_glimmerT_5016-T1
Valid prediction for snap_scaffold_2-snap.2754-T1
Valid prediction for Augustus_model.g3372.t1
Valid prediction for HiQ_model.g3381.t1
Valid prediction for pasa_asmbl_23610.p1
Valid prediction for HiQ_model.g3367.t1
Valid prediction for snap_scaffold_2-snap.2763-T1
Valid prediction for pasa_asmbl_23613.p1
Valid prediction for CodingQuarry_transcript_28673-T1
Valid prediction for snap_scaffold_2-snap.2762-T1
Valid prediction for snap_scaffold_2-snap.2764-T1
Valid prediction for Augustus_model.g3365.t1
Valid prediction for HiQ_model.g3368.t1
Valid prediction for snap_scaffold_2-snap.2774-T1
Valid prediction for CodingQuarry_transcript_28684-T1
Valid prediction for GlimmerHMM_glimmerT_5008-T1
Valid prediction for GeneMark_model.8071_t
Valid prediction for CodingQuarry_transcript_28683-T1
Valid prediction for CodingQuarry_transcript_28671-T1
Valid prediction for snap_scaffold_2-snap.2770-T1
Valid prediction for HiQ_model.g3377.t1
Valid prediction for GlimmerHMM_glimmerT_5024-T1
Valid prediction for GeneMark_model.8076_t
Valid prediction for pasa_asmbl_23988.p1
Valid prediction for GeneMark_model.8075_t
Valid prediction for snap_scaffold_2-snap.2775-T1
Valid prediction for GeneMark_model.8101_t
Valid prediction for GlimmerHMM_glimmerT_5009-T1
Valid prediction for GlimmerHMM_glimmerT_5014-T1
Valid prediction for snap_scaffold_2-snap.2779-T1
Valid prediction for GeneMark_model.8095_t
Valid prediction for pasa_asmbl_23601.p1
Valid prediction for pasa_asmbl_23597.p1
Valid prediction for GeneMark_model.8100_t
Valid prediction for snap_scaffold_2-snap.2750-T1
Valid prediction for GlimmerHMM_glimmerT_5023-T1
Valid prediction for snap_scaffold_2-snap.2753-T1
Valid prediction for snap_scaffold_2-snap.2752-T1
Valid prediction for GeneMark_model.8104_t
Valid prediction for HiQ_model.g3384.t1
Valid prediction for snap_scaffold_2-snap.2749-T1
Valid prediction for pasa_asmbl_23603.p1
Valid prediction for GeneMark_model.8077_t
Couldn't classify 214090, 214223
Sorry, prediction pasa_asmbl_23587.p1 fails validation.
(AGC)	 TG	214090-214223	GT	AGG
(TGT)	 AG	214344-214782	GT	AGG
(GTT)	 AG	215994-216035	GT	AGG
(CAG)	 AG	216230-216288	GT	AGG
(CCC)	 AG	216626-216875	GT	AGG
(GAG)	 AG	217111-217245	GT	AGG
(ATT)	 AG	218078-218121	GT	AGG
(CAG)	 AG	218276-218354	GT	AGG
(AGC)	 AG	218504-218635	GT	AGG
(GAT)	 AG	218876-218971	GT	GGG
(GAC)	 AG	220173-220244	GT	AGG
(TAG)	 AG	220340-220342	AC	AGA
-recovered pasa_asmbl_23587.p1, terminal, 220340, 220342
-recovered pasa_asmbl_23587.p1, internal, 214344, 214782
-recovered pasa_asmbl_23587.p1, internal, 215994, 216035
-recovered pasa_asmbl_23587.p1, internal, 216230, 216288
-recovered pasa_asmbl_23587.p1, internal, 216626, 216875
-recovered pasa_asmbl_23587.p1, internal, 217111, 217245
-recovered pasa_asmbl_23587.p1, internal, 218078, 218121
-recovered pasa_asmbl_23587.p1, internal, 218276, 218354
-recovered pasa_asmbl_23587.p1, internal, 218504, 218635
-recovered pasa_asmbl_23587.p1, internal, 218876, 218971
-recovered pasa_asmbl_23587.p1, internal, 220173, 220244
Valid prediction for GeneMark_model.8078_t
Valid prediction for CodingQuarry_transcript_28672-T1
Valid prediction for HiQ_model.g3363.t1
Valid prediction for GeneMark_model.8074_t
Valid prediction for pasa_asmbl_23609.p1
Valid prediction for Augustus_model.g3364.t1
Valid prediction for GeneMark_model.8073_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11313, rend_intergenic: 6562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200012, rend_intergenic: 191680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225399
-exon list size: 504


building trellis

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98.8    
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99.2    
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99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 11313, rend_intergenic: 6562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200012, rend_intergenic: 191680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support