-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_672313-886758

-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_53537-T1
Valid prediction for GlimmerHMM_glimmerT_53530-T1
Valid prediction for GlimmerHMM_glimmerT_53520-T1
Valid prediction for GlimmerHMM_glimmerT_53535-T1
Valid prediction for GlimmerHMM_glimmerT_53522-T1
Valid prediction for snap_scaffold_25-snap.173-T1
Valid prediction for snap_scaffold_25-snap.145-T1
Valid prediction for GlimmerHMM_glimmerT_53540-T1
Valid prediction for snap_scaffold_25-snap.174-T1
Valid prediction for snap_scaffold_25-snap.168-T1
Valid prediction for Augustus_model.g35592.t1
Couldn't classify 119896, 120062
Sorry, prediction pasa_asmbl_33900.p1 fails validation.
(CAG)	 CT	119896-120062	GT	AGG
(GCT)	 AG	120435-120575	GT	AGG
(GAG)	 AG	120961-121162	GT	AGG
(GTC)	 AG	121448-121558	GT	AGG
(CGC)	 AG	121719-121806	GT	AGG
(GGA)	 AG	121898-121958	GT	AAG
(GGA)	 AG	122579-122719	GT	AGG
(GCT)	 AG	123176-123263	GT	ATG
(TCT)	 AG	123384-123415	GT	ATG
(GGT)	 AG	123723-123805	GT	ATG
(CTT)	 AG	124534-124634	GT	ACG
(GTG)	 AG	124888-124989	GT	AGG
(CGT)	 AG	125406-125474	GT	AGG
(AGC)	 AG	125562-125720	GC	AAG
-recovered pasa_asmbl_33900.p1, terminal, 125562, 125720
-recovered pasa_asmbl_33900.p1, internal, 120435, 120575
-recovered pasa_asmbl_33900.p1, internal, 120961, 121162
-recovered pasa_asmbl_33900.p1, internal, 121448, 121558
-recovered pasa_asmbl_33900.p1, internal, 121719, 121806
-recovered pasa_asmbl_33900.p1, internal, 121898, 121958
-recovered pasa_asmbl_33900.p1, internal, 122579, 122719
-recovered pasa_asmbl_33900.p1, internal, 123176, 123263
-recovered pasa_asmbl_33900.p1, internal, 123384, 123415
-recovered pasa_asmbl_33900.p1, internal, 123723, 123805
-recovered pasa_asmbl_33900.p1, internal, 124534, 124634
-recovered pasa_asmbl_33900.p1, internal, 124888, 124989
-recovered pasa_asmbl_33900.p1, internal, 125406, 125474
-recovered pasa_asmbl_33900.p1, internal, 125562, 125720
Valid prediction for snap_scaffold_25-snap.131-T1
Valid prediction for snap_scaffold_25-snap.161-T1
Valid prediction for Augustus_model.g35591.t1
Valid prediction for GlimmerHMM_glimmerT_53533-T1
Valid prediction for snap_scaffold_25-snap.149-T1
Valid prediction for Augustus_model.g35598.t1
Valid prediction for GlimmerHMM_glimmerT_53545-T1
Valid prediction for snap_scaffold_25-snap.159-T1
Couldn't classify 69091, 69118
Sorry, prediction pasa_asmbl_33863.p1 fails validation.
(CTG)	 GT	69091-69118	GT	TGG
(GAA)	 AG	69515-69573	GT	TTG
(ACG)	 AG	69711-69800	GT	AGG
(GGT)	 AG	70414-70595	GT	AGG
(AGA)	 AG	71919-72015	CC	GAC
-recovered pasa_asmbl_33863.p1, terminal, 71919, 72015
-recovered pasa_asmbl_33863.p1, internal, 69515, 69573
-recovered pasa_asmbl_33863.p1, internal, 69711, 69800
-recovered pasa_asmbl_33863.p1, internal, 70414, 70595
Valid prediction for GlimmerHMM_glimmerT_53546-T1
Valid prediction for Augustus_model.g35585.t1
Valid prediction for Augustus_model.g35596.t1
Couldn't classify 16861, 16965
Couldn't classify 18514, 18659
Sorry, prediction pasa_asmbl_33350.p1 fails validation.
(TGT)	 TG	16861-16965	GT	AGG
(ACG)	 AG	17289-17389	GT	AGG
(GGT)	 AG	17791-17876	GT	AGG
(CAG)	 AG	18514-18659	GG	CTG
-recovered pasa_asmbl_33350.p1, internal, 17289, 17389
-recovered pasa_asmbl_33350.p1, internal, 17791, 17876
Valid prediction for snap_scaffold_25-snap.151-T1
Valid prediction for snap_scaffold_25-snap.153-T1
Valid prediction for snap_scaffold_25-snap.166-T1
Valid prediction for GlimmerHMM_glimmerT_53526-T1
Valid prediction for Augustus_model.g35593.t1
Valid prediction for GlimmerHMM_glimmerT_53523-T1
Valid prediction for snap_scaffold_25-snap.163-T1
Valid prediction for GlimmerHMM_glimmerT_53541-T1
Valid prediction for Augustus_model.g35587.t1
Valid prediction for snap_scaffold_25-snap.135-T1
Valid prediction for GlimmerHMM_glimmerT_53528-T1
Valid prediction for GlimmerHMM_glimmerT_53527-T1
Valid prediction for snap_scaffold_25-snap.141-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_53538-T1
Valid prediction for GlimmerHMM_glimmerT_53524-T1
Valid prediction for snap_scaffold_25-snap.171-T1
Valid prediction for Augustus_model.g35600.t1
Valid prediction for snap_scaffold_25-snap.176-T1
Valid prediction for snap_scaffold_25-snap.177-T1
Valid prediction for GlimmerHMM_glimmerT_53529-T1
Valid prediction for snap_scaffold_25-snap.139-T1
Valid prediction for snap_scaffold_25-snap.133-T1
Valid prediction for snap_scaffold_25-snap.146-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.156-T1
Valid prediction for Augustus_model.g35599.t1
Valid prediction for Augustus_model.g35590.t1
Valid prediction for snap_scaffold_25-snap.169-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_25-snap.150-T1
Valid prediction for snap_scaffold_25-snap.138-T1
Valid prediction for CodingQuarry_transcript_38636-T1
Valid prediction for Augustus_model.g35589.t1
Valid prediction for GlimmerHMM_glimmerT_53543-T1
Valid prediction for snap_scaffold_25-snap.162-T1
Valid prediction for GlimmerHMM_glimmerT_53525-T1
Couldn't classify 82771, 82803
Sorry, prediction pasa_asmbl_34001.p1 fails validation.
(CTG)	 CA	82771-82803	GT	TGG
(GTC)	 AG	83827-84024	GT	AGG
(CTG)	 AG	84120-84282	GT	CGG
(GCA)	 AG	84508-84657	GT	TGG
(GAA)	 AG	84766-84926	GT	AGG
(CTG)	 AG	85035-85211	GT	AGG
(AGG)	 AG	85500-85641	GT	AGG
(AGA)	 AG	85765-85952	GT	AGG
(GGC)	 AG	86511-86652	GT	AGG
(GCA)	 AG	86817-86992	TC	GAT
-recovered pasa_asmbl_34001.p1, terminal, 86817, 86992
-recovered pasa_asmbl_34001.p1, internal, 83827, 84024
-recovered pasa_asmbl_34001.p1, internal, 84120, 84282
-recovered pasa_asmbl_34001.p1, internal, 84508, 84657
-recovered pasa_asmbl_34001.p1, internal, 84766, 84926
-recovered pasa_asmbl_34001.p1, internal, 85035, 85211
-recovered pasa_asmbl_34001.p1, internal, 85500, 85641
-recovered pasa_asmbl_34001.p1, internal, 85765, 85952
-recovered pasa_asmbl_34001.p1, internal, 86511, 86652
Valid prediction for snap_scaffold_25-snap.152-T1
Valid prediction for GlimmerHMM_glimmerT_53534-T1
Valid prediction for snap_scaffold_25-snap.164-T1
Valid prediction for GlimmerHMM_glimmerT_53542-T1
Valid prediction for GlimmerHMM_glimmerT_53521-T1
Valid prediction for CodingQuarry_transcript_38635-T1
Valid prediction for snap_scaffold_25-snap.147-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g35586.t1
Valid prediction for snap_scaffold_25-snap.134-T1
Valid prediction for snap_scaffold_25-snap.140-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g35602.t1
Valid prediction for snap_scaffold_25-snap.170-T1
Valid prediction for pasa_asmbl_34007.p1
Valid prediction for Augustus_model.g35597.t1
Valid prediction for Augustus_model.g35588.t1
Valid prediction for snap_scaffold_25-snap.154-T1
Valid prediction for snap_scaffold_25-snap.142-T1
Valid prediction for snap_scaffold_25-snap.136-T1
Valid prediction for GlimmerHMM_glimmerT_53539-T1
Valid prediction for GlimmerHMM_glimmerT_53536-T1
Valid prediction for snap_scaffold_25-snap.165-T1
Valid prediction for snap_scaffold_25-snap.143-T1
Valid prediction for pasa_asmbl_33998.p1
Valid prediction for snap_scaffold_25-snap.175-T1
Valid prediction for snap_scaffold_25-snap.137-T1
Valid prediction for GlimmerHMM_glimmerT_53544-T1
Valid prediction for snap_scaffold_25-snap.158-T1
Couldn't classify 183728, 183762
Sorry, prediction pasa_asmbl_33996.p1 fails validation.
(ATG)	 AG	180519-180585	GT	AGG
(GCC)	 AG	182522-182836	GT	AGG
(ACG)	 AG	183728-183762	CA	CCC
-recovered pasa_asmbl_33996.p1, initial, 180519, 180585
add_exon() Sorry, pasa_asmbl_33996.p1 180519-180585-terminal-3 is invalid.
-recovered pasa_asmbl_33996.p1, terminal, 180519, 180585
-recovered pasa_asmbl_33996.p1, internal, 180519, 180585
-recovered pasa_asmbl_33996.p1, internal, 182522, 182836
Valid prediction for GlimmerHMM_glimmerT_53532-T1
Valid prediction for snap_scaffold_25-snap.155-T1
Valid prediction for GlimmerHMM_glimmerT_53531-T1
Valid prediction for GlimmerHMM_glimmerT_53519-T1
Valid prediction for snap_scaffold_25-snap.167-T1
Valid prediction for Augustus_model.g35594.t1
Valid prediction for HiQ_model.g35601.t1
Valid prediction for snap_scaffold_25-snap.172-T1
Valid prediction for pasa_asmbl_34609.p1
Valid prediction for snap_scaffold_25-snap.144-T1
Valid prediction for snap_scaffold_25-snap.148-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.132-T1
Valid prediction for snap_scaffold_25-snap.160-T1
Valid prediction for HiQ_model.g35595.t1
Valid prediction for CodingQuarry_transcript_38634-T1
Valid prediction for snap_scaffold_25-snap.157-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4338, rend_intergenic: 2518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10570, rend_intergenic: 4560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12938, rend_intergenic: 10589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33555, rend_intergenic: 14862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50275, rend_intergenic: 36822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51767, rend_intergenic: 51153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53280, rend_intergenic: 52523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66280, rend_intergenic: 53356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87496, rend_intergenic: 68070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101041, rend_intergenic: 88034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110687, rend_intergenic: 105299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119120, rend_intergenic: 112491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125720, rend_intergenic: 119929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137822, rend_intergenic: 133858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144023, rend_intergenic: 137839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146740, rend_intergenic: 144325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154658, rend_intergenic: 150840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157325, rend_intergenic: 154863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165603, rend_intergenic: 158914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171089, rend_intergenic: 167125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185720, rend_intergenic: 181518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187706, rend_intergenic: 186260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188064, rend_intergenic: 187794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203764, rend_intergenic: 188305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213447, rend_intergenic: 205949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214446
-exon list size: 490


building trellis

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99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 4338, rend_intergenic: 2518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10570, rend_intergenic: 4560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12938, rend_intergenic: 10589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33555, rend_intergenic: 14862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50275, rend_intergenic: 36822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51767, rend_intergenic: 51153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53280, rend_intergenic: 52523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66280, rend_intergenic: 53356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87496, rend_intergenic: 68070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101041, rend_intergenic: 88034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110687, rend_intergenic: 105299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119120, rend_intergenic: 112491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125720, rend_intergenic: 119929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137822, rend_intergenic: 133858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144023, rend_intergenic: 137839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146740, rend_intergenic: 144325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154658, rend_intergenic: 150840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157325, rend_intergenic: 154863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165603, rend_intergenic: 158914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171089, rend_intergenic: 167125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185720, rend_intergenic: 181518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187706, rend_intergenic: 186260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188064, rend_intergenic: 187794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203764, rend_intergenic: 188305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213447, rend_intergenic: 205949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support