-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_12180491-12367453

-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_12784-T1
Valid prediction for CodingQuarry_transcript_52275-T1
Valid prediction for GlimmerHMM_glimmerT_12785-T1
Valid prediction for snap_scaffold_5-snap.2263-T1
Valid prediction for snap_scaffold_5-snap.2279-T1
Valid prediction for Augustus_model.g8452.t1
Valid prediction for Augustus_model.g8463.t1
Valid prediction for snap_scaffold_5-snap.2248-T1
Valid prediction for Augustus_model.g8454.t1
Valid prediction for GlimmerHMM_glimmerT_12774-T1
Valid prediction for snap_scaffold_5-snap.2257-T1
Valid prediction for HiQ_model.g8461.t1
Valid prediction for snap_scaffold_5-snap.2277-T1
Valid prediction for Augustus_model.g8458.t1
Valid prediction for GlimmerHMM_glimmerT_12770-T1
Valid prediction for GlimmerHMM_glimmerT_12788-T1
Valid prediction for snap_scaffold_5-snap.2273-T1
Valid prediction for HiQ_model.g8469.t1
Valid prediction for snap_scaffold_5-snap.2282-T1
Valid prediction for GlimmerHMM_glimmerT_12782-T1
Valid prediction for CodingQuarry_transcript_52280-T1
Valid prediction for CodingQuarry_transcript_52282-T1
Valid prediction for snap_scaffold_5-snap.2251-T1
Valid prediction for GlimmerHMM_glimmerT_12777-T1
Valid prediction for Augustus_model.g8468.t1
Valid prediction for pasa_asmbl_45792.p1
Valid prediction for CodingQuarry_transcript_52279-T1
Valid prediction for GlimmerHMM_glimmerT_12771-T1
Valid prediction for pasa_asmbl_45790.p1
Valid prediction for HiQ_model.g8464.t1
Couldn't classify 173160, 173672
Sorry, prediction pasa_asmbl_45795.p1 fails validation.
(TTA)	 AG	173160-173672	AC	AGA
Valid prediction for snap_scaffold_5-snap.2270-T1
Valid prediction for CodingQuarry_transcript_52281-T1
Valid prediction for GlimmerHMM_glimmerT_12778-T1
Valid prediction for pasa_asmbl_45785.p1
Valid prediction for snap_scaffold_5-snap.2253-T1
Valid prediction for GlimmerHMM_glimmerT_12786-T1
Valid prediction for Augustus_model.g8467.t1
Valid prediction for snap_scaffold_5-snap.2261-T1
Valid prediction for snap_scaffold_5-snap.2266-T1
Valid prediction for GlimmerHMM_glimmerT_12775-T1
Valid prediction for snap_scaffold_5-snap.2269-T1
Valid prediction for snap_scaffold_5-snap.2260-T1
Valid prediction for Augustus_model.g8457.t1
Valid prediction for snap_scaffold_5-snap.2275-T1
Valid prediction for snap_scaffold_5-snap.2274-T1
Valid prediction for snap_scaffold_5-snap.2268-T1
Valid prediction for GlimmerHMM_glimmerT_12772-T1
Valid prediction for GlimmerHMM_glimmerT_12765-T1
Valid prediction for snap_scaffold_5-snap.2283-T1
Valid prediction for GlimmerHMM_glimmerT_12783-T1
Valid prediction for pasa_asmbl_45793.p1
Valid prediction for GlimmerHMM_glimmerT_12767-T1
Valid prediction for snap_scaffold_5-snap.2250-T1
Couldn't classify 173793, 174098
Couldn't classify 179380, 179481
Sorry, prediction pasa_asmbl_45796.p1 fails validation.
(GCG)	 GC	173793-174098	GT	TTG
(CTG)	 AG	175714-175890	GT	AGG
(CTG)	 AG	178658-178789	GT	ATG
(CTG)	 AG	179380-179481	TG	GGT
-recovered pasa_asmbl_45796.p1, internal, 175714, 175890
-recovered pasa_asmbl_45796.p1, internal, 178658, 178789

-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_5-snap.2264-T1
Valid prediction for snap_scaffold_5-snap.2267-T1
Valid prediction for CodingQuarry_transcript_52274-T1
Valid prediction for snap_scaffold_5-snap.2249-T1
Valid prediction for snap_scaffold_5-snap.2259-T1
Valid prediction for snap_scaffold_5-snap.2278-T1
Valid prediction for Augustus_model.g8462.t1
Valid prediction for HiQ_model.g8456.t1
Valid prediction for pasa_asmbl_44438.p1
Valid prediction for pasa_asmbl_44444.p1
Valid prediction for GlimmerHMM_glimmerT_12764-T1
Valid prediction for snap_scaffold_5-snap.2252-T1
Valid prediction for snap_scaffold_5-snap.2254-T1
Valid prediction for Augustus_model.g8466.t1
Valid prediction for GlimmerHMM_glimmerT_12780-T1
Valid prediction for snap_scaffold_5-snap.2262-T1
Couldn't classify 77178, 77311
Sorry, prediction pasa_asmbl_44448.p1 fails validation.
(ATG)	 CC	76834-76996	GT	GAG
(GTC)	 AG	77178-77311	GG	TGG
-recovered pasa_asmbl_44448.p1, initial, 76834, 76996
Valid prediction for GlimmerHMM_glimmerT_12773-T1
Valid prediction for CodingQuarry_transcript_52276-T1
Valid prediction for GlimmerHMM_glimmerT_12766-T1
Valid prediction for HiQ_model.g8453.t1
Valid prediction for GlimmerHMM_glimmerT_12787-T1
Valid prediction for CodingQuarry_transcript_52278-T1
Valid prediction for pasa_asmbl_44441.p1
Valid prediction for Augustus_model.g8455.t1
Couldn't classify 77539, 77631
Sorry, prediction pasa_asmbl_44447.p1 fails validation.
(AGA)	 CC	77539-77631	GT	AGG
(TTG)	 AG	77740-77785	GT	AGG
(CAA)	 AG	77895-78056	GT	TTG
(ATA)	 AG	78307-78569	GT	AGG
(AGG)	 AG	78788-78858	GT	AAG
(TGC)	 AG	78966-79052	GT	AGG
(TAA)	 AG	79166-79268	GT	AGG
(GAG)	 AG	79483-79587	GT	TGG
(GCT)	 AG	79683-80795	CA	GAC
add_exon() Sorry, pasa_asmbl_44447.p1 78788-78858-terminal-2 is invalid.
-recovered pasa_asmbl_44447.p1, terminal, 78788, 78858
-recovered pasa_asmbl_44447.p1, terminal, 79683, 80795
-recovered pasa_asmbl_44447.p1, internal, 77740, 77785
-recovered pasa_asmbl_44447.p1, internal, 77895, 78056
-recovered pasa_asmbl_44447.p1, internal, 78307, 78569
-recovered pasa_asmbl_44447.p1, internal, 78788, 78858
-recovered pasa_asmbl_44447.p1, internal, 78966, 79052
-recovered pasa_asmbl_44447.p1, internal, 79166, 79268
-recovered pasa_asmbl_44447.p1, internal, 79483, 79587
Valid prediction for GlimmerHMM_glimmerT_12781-T1
Valid prediction for snap_scaffold_5-snap.2276-T1
Valid prediction for snap_scaffold_5-snap.2284-T1
Valid prediction for snap_scaffold_5-snap.2255-T1
Valid prediction for snap_scaffold_5-snap.2272-T1
Valid prediction for snap_scaffold_5-snap.2258-T1
Couldn't classify 94038, 94547
Sorry, prediction pasa_asmbl_44446.p1 fails validation.
(TTC)	 AC	94038-94547	TG	AAT
Valid prediction for GlimmerHMM_glimmerT_12768-T1
Valid prediction for snap_scaffold_5-snap.2280-T1
Valid prediction for GlimmerHMM_glimmerT_12779-T1
Valid prediction for pasa_asmbl_44443.p1
Valid prediction for snap_scaffold_5-snap.2281-T1
Valid prediction for snap_scaffold_5-snap.2265-T1
Valid prediction for CodingQuarry_transcript_52273-T1
Valid prediction for HiQ_model.g8459.t1
Valid prediction for Augustus_model.g8460.t1
Valid prediction for snap_scaffold_5-snap.2271-T1
Valid prediction for GlimmerHMM_glimmerT_12776-T1
Valid prediction for CodingQuarry_transcript_52277-T1
Valid prediction for snap_scaffold_5-snap.2256-T1
Valid prediction for GlimmerHMM_glimmerT_12769-T1
Couldn't classify 139731, 139830
Sorry, prediction pasa_asmbl_44440.p1 fails validation.
(CTG)	 CC	139731-139830	GT	ACG
(GTC)	 AG	139919-140073	GT	AAG
(TAT)	 AG	140171-140285	GT	GGG
(GTT)	 AG	140389-140497	GT	AAG
(GTA)	 AG	140579-140727	GT	AGG
(TGA)	 AG	140835-140925	GT	TGG
(TCC)	 AG	141038-141227	CT	AGC
-recovered pasa_asmbl_44440.p1, terminal, 141038, 141227
-recovered pasa_asmbl_44440.p1, internal, 139919, 140073
-recovered pasa_asmbl_44440.p1, internal, 140171, 140285
-recovered pasa_asmbl_44440.p1, internal, 140389, 140497
-recovered pasa_asmbl_44440.p1, internal, 140579, 140727
-recovered pasa_asmbl_44440.p1, internal, 140835, 140925
Valid prediction for HiQ_model.g8465.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16125, rend_intergenic: 8608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26889, rend_intergenic: 26080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29927, rend_intergenic: 28142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32562, rend_intergenic: 30603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73515, rend_intergenic: 70986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110136, rend_intergenic: 106169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145106, rend_intergenic: 132651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151344, rend_intergenic: 148114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163927, rend_intergenic: 160241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186257, rend_intergenic: 175654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186963
-exon list size: 332


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 16125, rend_intergenic: 8608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26889, rend_intergenic: 26080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29927, rend_intergenic: 28142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32562, rend_intergenic: 30603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73515, rend_intergenic: 70986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110136, rend_intergenic: 106169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145106, rend_intergenic: 132651  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151344, rend_intergenic: 148114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163927, rend_intergenic: 160241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186257, rend_intergenic: 175654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 1 - 10286
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support