-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_16100406-16299128

-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 pasa_asmbl_25144.p1
Valid prediction for GeneMark_model.8491_t
Valid prediction for GeneMark_model.8482_t
Valid prediction for pasa_asmbl_25127.p1
Valid prediction for GeneMark_model.8525_t
Valid prediction for GeneMark_model.8486_t
Valid prediction for CodingQuarry_transcript_28742-T1
Valid prediction for CodingQuarry_transcript_28741-T1
Valid prediction for GeneMark_model.8485_t
Valid prediction for Augustus_model.g3606.t1
Valid prediction for GeneMark_model.8498_t
Valid prediction for GeneMark_model.8502_t
Valid prediction for GeneMark_model.8510_t
Valid prediction for GeneMark_model.8528_t
Valid prediction for GeneMark_model.8520_t
Valid prediction for Augustus_model.g3596.t1
Valid prediction for Augustus_model.g3604.t1
Valid prediction for GlimmerHMM_glimmerT_5328-T1
Valid prediction for GlimmerHMM_glimmerT_5310-T1
Valid prediction for snap_scaffold_2-snap.3138-T1
Valid prediction for GlimmerHMM_glimmerT_5323-T1
Valid prediction for pasa_asmbl_25126.p1
Valid prediction for GlimmerHMM_glimmerT_5321-T1
Valid prediction for GlimmerHMM_glimmerT_5311-T1
Valid prediction for GlimmerHMM_glimmerT_5314-T1
Valid prediction for Augustus_model.g3594.t1
Valid prediction for GeneMark_model.8514_t
Valid prediction for snap_scaffold_2-snap.3132-T1
Valid prediction for GlimmerHMM_glimmerT_5331-T1
Valid prediction for snap_scaffold_2-snap.3146-T1
Valid prediction for CodingQuarry_transcript_28739-T1
Valid prediction for GeneMark_model.8513_t
Valid prediction for snap_scaffold_2-snap.3121-T1
Valid prediction for GeneMark_model.8488_t
Valid prediction for snap_scaffold_2-snap.3117-T1
Valid prediction for snap_scaffold_2-snap.3149-T1
Valid prediction for GeneMark_model.8524_t
Valid prediction for GeneMark_model.8503_t
Valid prediction for Augustus_model.g3595.t1
Valid prediction for GlimmerHMM_glimmerT_5315-T1
Valid prediction for GeneMark_model.8494_t
Valid prediction for GlimmerHMM_glimmerT_5332-T1
Couldn't classify 186233, 186295
Sorry, prediction pasa_asmbl_25140.p1 fails validation.
(CCA)	 GT	186233-186295	GT	AGG
(GAC)	 AG	186404-186523	GT	AGG
(GGA)	 AG	186660-186791	GT	AGG
(GAT)	 AG	186881-186992	GT	GGG
(GTG)	 AG	187198-187270	GT	AGG
(TCT)	 AG	187337-187473	GT	AGG
(GGC)	 AG	187662-187795	GT	GGG
(GCT)	 AG	187905-187919	GA	AGG
-recovered pasa_asmbl_25140.p1, terminal, 187905, 187919
-recovered pasa_asmbl_25140.p1, internal, 186404, 186523
-recovered pasa_asmbl_25140.p1, internal, 186660, 186791
-recovered pasa_asmbl_25140.p1, internal, 186881, 186992
-recovered pasa_asmbl_25140.p1, internal, 187198, 187270
-recovered pasa_asmbl_25140.p1, internal, 187337, 187473
-recovered pasa_asmbl_25140.p1, internal, 187662, 187795
Valid prediction for snap_scaffold_2-snap.3124-T1
Valid prediction for GeneMark_model.8531_t
Valid prediction for GeneMark_model.8526_t
Valid prediction for snap_scaffold_2-snap.3127-T1
Valid prediction for CodingQuarry_transcript_28740-T1
Valid prediction for Augustus_model.g3598.t1
Valid prediction for GlimmerHMM_glimmerT_5329-T1
Valid prediction for GeneMark_model.8530_t
Valid prediction for GeneMark_model.8484_t
Valid prediction for GlimmerHMM_glimmerT_5312-T1
Valid prediction for snap_scaffold_2-snap.3145-T1
Valid prediction for GeneMark_model.8515_t
Valid prediction for snap_scaffold_2-snap.3140-T1
Valid prediction for GeneMark_model.8508_t
Valid prediction for snap_scaffold_2-snap.3135-T1
Valid prediction for GlimmerHMM_glimmerT_5330-T1
Valid prediction for HiQ_model.g3610.t1
Valid prediction for GeneMark_model.8500_t
Valid prediction for snap_scaffold_2-snap.3120-T1
Valid prediction for GlimmerHMM_glimmerT_5317-T1
Valid prediction for GlimmerHMM_glimmerT_5324-T1
Valid prediction for snap_scaffold_2-snap.3141-T1
Valid prediction for snap_scaffold_2-snap.3148-T1
Valid prediction for GeneMark_model.8512_t
Valid prediction for GeneMark_model.8489_t
Valid prediction for GlimmerHMM_glimmerT_5316-T1
Valid prediction for HiQ_model.g3611.t1
Valid prediction for HiQ_model.g3612.t1
Couldn't classify 185860, 186214
Sorry, prediction pasa_asmbl_25139.p1 fails validation.
(ATG)	 AC	185024-185273	GT	AGG
(GTG)	 AG	185509-185719	GT	AGG
(GTA)	 AG	185860-186214	AA	CCA
-recovered pasa_asmbl_25139.p1, initial, 185024, 185273
-recovered pasa_asmbl_25139.p1, internal, 185509, 185719
Valid prediction for snap_scaffold_2-snap.3136-T1
Valid prediction for HiQ_model.g3609.t1
Valid prediction for GlimmerHMM_glimmerT_5322-T1
Valid prediction for GeneMark_model.8522_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 Augustus_model.g3600.t1
Valid prediction for GeneMark_model.8529_t
Valid prediction for GeneMark_model.8516_t
Valid prediction for snap_scaffold_2-snap.3130-T1
Valid prediction for GeneMark_model.8511_t
Valid prediction for snap_scaffold_2-snap.3119-T1
Valid prediction for snap_scaffold_2-snap.3125-T1
Valid prediction for GeneMark_model.8517_t
Valid prediction for GeneMark_model.8499_t
Valid prediction for GeneMark_model.8506_t
Valid prediction for GeneMark_model.8493_t
Valid prediction for Augustus_model.g3603.t1
Valid prediction for Augustus_model.g3608.t1
Valid prediction for Augustus_model.g3607.t1
Valid prediction for GlimmerHMM_glimmerT_5327-T1
Valid prediction for GeneMark_model.8509_t
Valid prediction for GeneMark_model.8481_t
Valid prediction for snap_scaffold_2-snap.3147-T1
Valid prediction for snap_scaffold_2-snap.3144-T1
Valid prediction for GeneMark_model.8495_t
Valid prediction for snap_scaffold_2-snap.3131-T1
Valid prediction for Augustus_model.g3597.t1
Valid prediction for GlimmerHMM_glimmerT_5313-T1
Valid prediction for GeneMark_model.8504_t
Valid prediction for GeneMark_model.8523_t
Valid prediction for snap_scaffold_2-snap.3116-T1
Valid prediction for snap_scaffold_2-snap.3118-T1
Couldn't classify 40213, 40234
Couldn't classify 41029, 41181
Sorry, prediction pasa_asmbl_23693.p1 fails validation.
(CGG)	 AA	40213-40234	GT	AGG
(ACA)	 AG	40346-40461	GT	AGG
(GTG)	 AG	40608-40715	GT	CTG
(GCT)	 AG	41029-41181	AT	GAA
-recovered pasa_asmbl_23693.p1, internal, 40346, 40461
-recovered pasa_asmbl_23693.p1, internal, 40608, 40715
Valid prediction for GeneMark_model.8519_t
Valid prediction for GlimmerHMM_glimmerT_5319-T1
Valid prediction for snap_scaffold_2-snap.3137-T1
Valid prediction for snap_scaffold_2-snap.3126-T1
Valid prediction for GlimmerHMM_glimmerT_5308-T1
Valid prediction for GlimmerHMM_glimmerT_5325-T1
Valid prediction for Augustus_model.g3602.t1
Valid prediction for GeneMark_model.8507_t
Valid prediction for snap_scaffold_2-snap.3123-T1
Valid prediction for GeneMark_model.8505_t
Valid prediction for snap_scaffold_2-snap.3133-T1
Valid prediction for GlimmerHMM_glimmerT_5326-T1
Valid prediction for GeneMark_model.8501_t
Valid prediction for Augustus_model.g3593.t1
Valid prediction for snap_scaffold_2-snap.3134-T1
Valid prediction for GeneMark_model.8490_t
Valid prediction for Augustus_model.g3601.t1
Valid prediction for Augustus_model.g3599.t1
Valid prediction for GeneMark_model.8487_t
Valid prediction for GeneMark_model.8521_t
Valid prediction for snap_scaffold_2-snap.3143-T1
Valid prediction for snap_scaffold_2-snap.3128-T1
Valid prediction for GeneMark_model.8518_t
Valid prediction for GlimmerHMM_glimmerT_5309-T1
Valid prediction for Augustus_model.g3605.t1
Valid prediction for snap_scaffold_2-snap.3142-T1
Valid prediction for HiQ_model.g3592.t1
Valid prediction for snap_scaffold_2-snap.3129-T1
Valid prediction for GeneMark_model.8527_t
Valid prediction for GeneMark_model.8496_t
Valid prediction for GeneMark_model.8483_t
Valid prediction for snap_scaffold_2-snap.3122-T1
Valid prediction for GlimmerHMM_glimmerT_5320-T1
Valid prediction for GeneMark_model.8497_t
Valid prediction for GlimmerHMM_glimmerT_5318-T1
Valid prediction for snap_scaffold_2-snap.3139-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16341, rend_intergenic: 10806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87063, rend_intergenic: 75646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99099, rend_intergenic: 98323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102002, rend_intergenic: 99628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116140, rend_intergenic: 109333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129795, rend_intergenic: 123966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183319, rend_intergenic: 173298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 198723
-exon list size: 662


building trellis

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99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 16341, rend_intergenic: 10806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87063, rend_intergenic: 75646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99099, rend_intergenic: 98323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102002, rend_intergenic: 99628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116140, rend_intergenic: 109333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129795, rend_intergenic: 123966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183319, rend_intergenic: 173298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support