-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_15710532-15921243

-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_4-snap.3186-T1
Valid prediction for GlimmerHMM_glimmerT_11007-T1
Valid prediction for GlimmerHMM_glimmerT_11010-T1
Valid prediction for snap_scaffold_4-snap.3212-T1
Valid prediction for snap_scaffold_4-snap.3214-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3201-T1
Valid prediction for GlimmerHMM_glimmerT_11018-T1
Valid prediction for GeneMark_model.17895_t
Valid prediction for GlimmerHMM_glimmerT_11017-T1
Valid prediction for GlimmerHMM_glimmerT_11012-T1
Valid prediction for snap_scaffold_4-snap.3182-T1
Valid prediction for GeneMark_model.17913_t
Valid prediction for snap_scaffold_4-snap.3199-T1
Valid prediction for snap_scaffold_4-snap.3185-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3183-T1
Valid prediction for GeneMark_model.17893_t
Valid prediction for GeneMark_model.17888_t
Valid prediction for GeneMark_model.17899_t
Valid prediction for GeneMark_model.17892_t
Valid prediction for snap_scaffold_4-snap.3194-T1
Valid prediction for GeneMark_model.17886_t
Valid prediction for GeneMark_model.17906_t
Valid prediction for GeneMark_model.17887_t
Valid prediction for GlimmerHMM_glimmerT_11011-T1
Valid prediction for snap_scaffold_4-snap.3207-T1
Valid prediction for GeneMark_model.17885_t
Valid prediction for snap_scaffold_4-snap.3181-T1
Valid prediction for GeneMark_model.17921_t
Valid prediction for GlimmerHMM_glimmerT_11016-T1
Valid prediction for GeneMark_model.17911_t
Valid prediction for GeneMark_model.17931_t
Valid prediction for snap_scaffold_4-snap.3187-T1
Valid prediction for GeneMark_model.17880_t
Valid prediction for GeneMark_model.17930_t
Valid prediction for snap_scaffold_4-snap.3191-T1
Valid prediction for snap_scaffold_4-snap.3198-T1
Valid prediction for GeneMark_model.17919_t
Valid prediction for GeneMark_model.17897_t
Valid prediction for snap_scaffold_4-snap.3189-T1
Valid prediction for snap_scaffold_4-snap.3208-T1
Valid prediction for GeneMark_model.17896_t
Valid prediction for Augustus_model.g7285.t1
Valid prediction for snap_scaffold_4-snap.3180-T1
Valid prediction for snap_scaffold_4-snap.3193-T1
Valid prediction for GeneMark_model.17901_t
Valid prediction for GeneMark_model.17909_t
Valid prediction for snap_scaffold_4-snap.3202-T1
Valid prediction for snap_scaffold_4-snap.3195-T1
Valid prediction for GeneMark_model.17884_t
Valid prediction for snap_scaffold_4-snap.3210-T1
Valid prediction for Augustus_model.g7284.t1
Valid prediction for GeneMark_model.17890_t
Valid prediction for GeneMark_model.17904_t
Valid prediction for GeneMark_model.17925_t
Valid prediction for GeneMark_model.17929_t
Valid prediction for GeneMark_model.17923_t
Valid prediction for GeneMark_model.17927_t
Valid prediction for GeneMark_model.17903_t
Valid prediction for GlimmerHMM_glimmerT_11013-T1
Valid prediction for GeneMark_model.17917_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.17891_t
Valid prediction for GlimmerHMM_glimmerT_11020-T1
Valid prediction for Augustus_model.g7280.t1
Valid prediction for snap_scaffold_4-snap.3177-T1
Valid prediction for GeneMark_model.17924_t
Valid prediction for Augustus_model.g7279.t1
Valid prediction for snap_scaffold_4-snap.3197-T1
Valid prediction for Augustus_model.g7275.t1
Valid prediction for snap_scaffold_4-snap.3205-T1
Valid prediction for CodingQuarry_transcript_49163-T1
Valid prediction for snap_scaffold_4-snap.3204-T1
Valid prediction for Augustus_model.g7276.t1
Valid prediction for GlimmerHMM_glimmerT_11025-T1
Valid prediction for GeneMark_model.17926_t
Valid prediction for snap_scaffold_4-snap.3175-T1
Valid prediction for snap_scaffold_4-snap.3200-T1
Valid prediction for snap_scaffold_4-snap.3206-T1
Valid prediction for GlimmerHMM_glimmerT_11009-T1
Valid prediction for GeneMark_model.17915_t
Valid prediction for GeneMark_model.17932_t
Valid prediction for GeneMark_model.17907_t
Couldn't classify 205474, 205696
Sorry, prediction pasa_asmbl_41868.p1 fails validation.
(TCT)	 AC	205474-205696	GT	TGG
(GAA)	 AG	205851-205948	GG	GAG
-recovered pasa_asmbl_41868.p1, terminal, 205851, 205948
Valid prediction for GlimmerHMM_glimmerT_11014-T1
Valid prediction for snap_scaffold_4-snap.3190-T1
Valid prediction for snap_scaffold_4-snap.3178-T1
Valid prediction for GeneMark_model.17933_t
Valid prediction for snap_scaffold_4-snap.3213-T1
Valid prediction for Augustus_model.g7281.t1
Valid prediction for snap_scaffold_4-snap.3184-T1
Valid prediction for GeneMark_model.17900_t
Valid prediction for Augustus_model.g7288.t1
Valid prediction for GeneMark_model.17881_t
Valid prediction for snap_scaffold_4-snap.3211-T1
Valid prediction for GeneMark_model.17905_t
Couldn't classify 30912, 31226
Sorry, prediction pasa_asmbl_41874.p2 fails validation.
(TGC)	 AG	30912-31226	GA	GAG
Valid prediction for GeneMark_model.17898_t
Valid prediction for GlimmerHMM_glimmerT_11019-T1
Valid prediction for GlimmerHMM_glimmerT_11006-T1
Valid prediction for Augustus_model.g7278.t1
Valid prediction for GeneMark_model.17916_t
Valid prediction for GeneMark_model.17922_t
Valid prediction for Augustus_model.g7283.t1
Valid prediction for Augustus_model.g7282.t1
Valid prediction for Augustus_model.g7287.t1
Valid prediction for Augustus_model.g7274.t1
Valid prediction for Augustus_model.g7291.t1
Valid prediction for snap_scaffold_4-snap.3173-T1
Valid prediction for snap_scaffold_4-snap.3176-T1
Valid prediction for GeneMark_model.17920_t
Valid prediction for GlimmerHMM_glimmerT_11004-T1
Valid prediction for GeneMark_model.17918_t
Couldn't classify 8826, 8863
Couldn't classify 9737, 9763
Sorry, prediction pasa_asmbl_42385.p1 fails validation.
(CCT)	 AC	8826-8863	GT	AGG
(TGC)	 AG	9150-9354	GT	AGG
(GTT)	 AG	9507-9602	GT	AGG
(GTG)	 AG	9737-9763	GC	AGG
-recovered pasa_asmbl_42385.p1, internal, 9150, 9354
-recovered pasa_asmbl_42385.p1, internal, 9507, 9602
-recovered pasa_asmbl_42385.p1, internal, 9737, 9763
Valid prediction for GeneMark_model.17908_t
Valid prediction for snap_scaffold_4-snap.3188-T1
Valid prediction for GeneMark_model.17928_t
Valid prediction for snap_scaffold_4-snap.3196-T1
Valid prediction for GeneMark_model.17912_t
Valid prediction for Augustus_model.g7277.t1
Valid prediction for GeneMark_model.17914_t
Valid prediction for CodingQuarry_transcript_49162-T1
Valid prediction for GeneMark_model.17883_t
Couldn't classify 23350, 23418
Couldn't classify 24098, 24190
Sorry, prediction pasa_asmbl_41875.p2 fails validation.
(TTC)	 CC	23350-23418	GT	AGG
(GTG)	 AG	23598-23783	GT	CGG
(AGA)	 AG	24098-24190	AG	ACA
-recovered pasa_asmbl_41875.p2, internal, 23598, 23783
Valid prediction for GlimmerHMM_glimmerT_11015-T1
Valid prediction for snap_scaffold_4-snap.3179-T1
Valid prediction for Augustus_model.g7290.t1
Valid prediction for GlimmerHMM_glimmerT_11024-T1
Valid prediction for GlimmerHMM_glimmerT_11005-T1
Valid prediction for GeneMark_model.17894_t
Valid prediction for Augustus_model.g7289.t1
Valid prediction for Augustus_model.g7286.t1
Valid prediction for snap_scaffold_4-snap.3203-T1
Valid prediction for snap_scaffold_4-snap.3174-T1
Valid prediction for snap_scaffold_4-snap.3215-T1
Valid prediction for GeneMark_model.17879_t
Valid prediction for snap_scaffold_4-snap.3192-T1
Valid prediction for GeneMark_model.17889_t
Valid prediction for GlimmerHMM_glimmerT_11008-T1
Valid prediction for snap_scaffold_4-snap.3209-T1
Valid prediction for GeneMark_model.17902_t
Valid prediction for GlimmerHMM_glimmerT_11021-T1
Valid prediction for pasa_asmbl_41869.p1
Valid prediction for GlimmerHMM_glimmerT_11022-T1
Valid prediction for GeneMark_model.17882_t
Couldn't classify 203610, 203709
Couldn't classify 204459, 204562
Sorry, prediction pasa_asmbl_42322.p1 fails validation.
(GGC)	 TT	203610-203709	GT	CCG
(ATC)	 AG	203978-204253	GT	CTG
(ATG)	 AG	204459-204562	TG	CCT
-recovered pasa_asmbl_42322.p1, internal, 203978, 204253
Valid prediction for GlimmerHMM_glimmerT_11023-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 110379, rend_intergenic: 101552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118153, rend_intergenic: 112231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142415, rend_intergenic: 128687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146084, rend_intergenic: 142473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150710, rend_intergenic: 147205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155551, rend_intergenic: 152056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164189, rend_intergenic: 159845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170350, rend_intergenic: 167848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180056, rend_intergenic: 179208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186062, rend_intergenic: 180436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206236, rend_intergenic: 202388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 210712
-exon list size: 681


building trellis

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99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 110379, rend_intergenic: 101552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118153, rend_intergenic: 112231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142415, rend_intergenic: 128687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146084, rend_intergenic: 142473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150710, rend_intergenic: 147205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155551, rend_intergenic: 152056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164189, rend_intergenic: 159845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170350, rend_intergenic: 167848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180056, rend_intergenic: 179208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186062, rend_intergenic: 180436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206236, rend_intergenic: 202388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support