-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_15119497-15314557

-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: +)Couldn't classify 157077, 157215
Sorry, prediction pasa_asmbl_8120.p1 fails validation.
(AGG)	 TC	157077-157215	GT	AGG
(TCT)	 AG	157973-158010	GT	AGG
(GCC)	 AG	158296-158405	GT	ATG
(GGC)	 AG	158936-158987	TC	AGT
-recovered pasa_asmbl_8120.p1, terminal, 158936, 158987
-recovered pasa_asmbl_8120.p1, internal, 157973, 158010
-recovered pasa_asmbl_8120.p1, internal, 158296, 158405
Valid prediction for Augustus_model.g20272.t1
Couldn't classify 174836, 174845
Couldn't classify 175567, 175679
Sorry, prediction pasa_asmbl_8123.p1 fails validation.
(GAG)	 TG	174836-174845	GT	AGG
(AGT)	 AG	175003-175425	GT	AGG
(ACT)	 AG	175567-175679	AG	TGA
-recovered pasa_asmbl_8123.p1, internal, 175003, 175425
Valid prediction for HiQ_model.g20277.t1
Valid prediction for snap_scaffold_12-snap.2899-T1
Valid prediction for snap_scaffold_12-snap.2893-T1
Valid prediction for pasa_asmbl_8111.p1
Valid prediction for GlimmerHMM_glimmerT_30645-T1
Valid prediction for Augustus_model.g20274.t1
Valid prediction for snap_scaffold_12-snap.2888-T1
Valid prediction for Augustus_model.g20283.t1
Valid prediction for GlimmerHMM_glimmerT_30629-T1
Valid prediction for snap_scaffold_12-snap.2895-T1
Valid prediction for snap_scaffold_12-snap.2907-T1
Valid prediction for GlimmerHMM_glimmerT_30641-T1
Valid prediction for snap_scaffold_12-snap.2891-T1
Valid prediction for Augustus_model.g20273.t1
Valid prediction for snap_scaffold_12-snap.2910-T1
Valid prediction for GlimmerHMM_glimmerT_30626-T1
Couldn't classify 160428, 160566
Sorry, prediction pasa_asmbl_8121.p1 fails validation.
(AGG)	 TC	160428-160566	GT	AGG
(TCT)	 AG	161506-161543	GT	AGG
(GCC)	 AG	161801-161910	GT	ATG
(GGC)	 AG	162491-162542	TC	AGT
-recovered pasa_asmbl_8121.p1, terminal, 162491, 162542
-recovered pasa_asmbl_8121.p1, internal, 161506, 161543
-recovered pasa_asmbl_8121.p1, internal, 161801, 161910
Valid prediction for GlimmerHMM_glimmerT_30639-T1
Valid prediction for snap_scaffold_12-snap.2880-T1
Valid prediction for HiQ_model.g20268.t1
Valid prediction for CodingQuarry_transcript_10493-T1
Valid prediction for GlimmerHMM_glimmerT_30634-T1
Valid prediction for GlimmerHMM_glimmerT_30628-T1
Valid prediction for GlimmerHMM_glimmerT_30627-T1
Valid prediction for snap_scaffold_12-snap.2911-T1
Valid prediction for Augustus_model.g20269.t1
Valid prediction for snap_scaffold_12-snap.2903-T1
Valid prediction for snap_scaffold_12-snap.2876-T1
Valid prediction for Augustus_model.g20262.t1
Valid prediction for snap_scaffold_12-snap.2898-T1
Valid prediction for Augustus_model.g20282.t1
Valid prediction for Augustus_model.g20270.t1
Valid prediction for snap_scaffold_12-snap.2896-T1
Valid prediction for Augustus_model.g20279.t1
Couldn't classify 113311, 113328
Couldn't classify 113812, 114062
Sorry, prediction pasa_asmbl_8211.p1 fails validation.
(GCT)	 AG	113311-113328	GT	TGG
(GGT)	 AG	113445-113610	GT	CGG
(GGG)	 AG	113812-114062	GT	ATG
-recovered pasa_asmbl_8211.p1, internal, 113311, 113328
-recovered pasa_asmbl_8211.p1, internal, 113445, 113610
-recovered pasa_asmbl_8211.p1, internal, 113812, 114062
Valid prediction for CodingQuarry_transcript_10492-T1
Valid prediction for HiQ_model.g20276.t1
Valid prediction for snap_scaffold_12-snap.2874-T1
Valid prediction for GlimmerHMM_glimmerT_30647-T1
Valid prediction for GlimmerHMM_glimmerT_30636-T1
Valid prediction for snap_scaffold_12-snap.2879-T1
Valid prediction for snap_scaffold_12-snap.2883-T1
Valid prediction for Augustus_model.g20271.t1
Valid prediction for GlimmerHMM_glimmerT_30635-T1
Valid prediction for HiQ_model.g20284.t1
Couldn't classify 118024, 118420
Couldn't classify 120030, 120142
Sorry, prediction pasa_asmbl_8117.p1 fails validation.
(GCA)	 GG	118024-118420	GT	TGG
(ATC)	 AG	118518-118618	GT	AGG
(GTC)	 AG	118727-118829	GT	TGG
(CAA)	 AG	119012-119178	GT	AGG
(ATC)	 AG	119371-119516	GT	CAG
(GGA)	 AG	119767-119870	GT	GGG
(GTG)	 AG	120030-120142	AG	GCA
-recovered pasa_asmbl_8117.p1, internal, 118518, 118618
-recovered pasa_asmbl_8117.p1, internal, 118727, 118829
-recovered pasa_asmbl_8117.p1, internal, 119012, 119178
-recovered pasa_asmbl_8117.p1, internal, 119371, 119516
-recovered pasa_asmbl_8117.p1, internal, 119767, 119870
Valid prediction for CodingQuarry_transcript_10488-T1
Couldn't classify 187907, 188011
Sorry, prediction pasa_asmbl_8124.p1 fails validation.
(ATG)	 AG	184038-184134	GT	CGG
(GTC)	 AG	186544-186739	GT	TGG
(CGG)	 AG	186977-187129	GT	AAG
(GTT)	 AG	187641-187824	GT	AGG
(TGC)	 AG	187907-188011	CA	AGC
-recovered pasa_asmbl_8124.p1, initial, 184038, 184134
-recovered pasa_asmbl_8124.p1, internal, 184038, 184134
-recovered pasa_asmbl_8124.p1, internal, 186544, 186739
-recovered pasa_asmbl_8124.p1, internal, 186977, 187129
-recovered pasa_asmbl_8124.p1, internal, 187641, 187824

-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 HiQ_model.g20278.t1
Valid prediction for CodingQuarry_transcript_10487-T1
Valid prediction for CodingQuarry_transcript_10491-T1
Valid prediction for CodingQuarry_transcript_10494-T1
Valid prediction for snap_scaffold_12-snap.2894-T1
Valid prediction for Augustus_model.g20267.t1
Valid prediction for CodingQuarry_transcript_10485-T1
Valid prediction for GlimmerHMM_glimmerT_30633-T1
Valid prediction for snap_scaffold_12-snap.2885-T1
Valid prediction for snap_scaffold_12-snap.2889-T1
Valid prediction for CodingQuarry_transcript_10490-T1
Valid prediction for GlimmerHMM_glimmerT_30622-T1
Valid prediction for HiQ_model.g20258.t1
Valid prediction for pasa_asmbl_9051.p1
Valid prediction for GlimmerHMM_glimmerT_30623-T1
Valid prediction for Augustus_model.g20264.t1
Valid prediction for Augustus_model.g20263.t1
Valid prediction for Augustus_model.g20281.t1
Valid prediction for GlimmerHMM_glimmerT_30630-T1
Valid prediction for snap_scaffold_12-snap.2900-T1
Valid prediction for Augustus_model.g20265.t1
Valid prediction for snap_scaffold_12-snap.2882-T1
Valid prediction for GlimmerHMM_glimmerT_30624-T1
Valid prediction for snap_scaffold_12-snap.2875-T1
Valid prediction for Augustus_model.g20261.t1
Couldn't classify 154769, 155176
Sorry, prediction pasa_asmbl_9058.p1 fails validation.
(TCC)	 CC	154769-155176	CT	TCC
Valid prediction for snap_scaffold_12-snap.2886-T1
Valid prediction for snap_scaffold_12-snap.2912-T1
Valid prediction for pasa_asmbl_9062.p1
Valid prediction for GlimmerHMM_glimmerT_30644-T1
Valid prediction for GlimmerHMM_glimmerT_30640-T1
Valid prediction for pasa_asmbl_9054.p1
Valid prediction for GlimmerHMM_glimmerT_30637-T1
Valid prediction for GlimmerHMM_glimmerT_30646-T1
Valid prediction for pasa_asmbl_9068.p1
Couldn't classify 24212, 24277
Couldn't classify 25533, 25641
Sorry, prediction pasa_asmbl_9069.p1 fails validation.
(TTG)	 TG	24212-24277	GT	AGG
(TTA)	 AG	24404-24501	GT	GTG
(GAA)	 AG	24642-24829	GT	TGG
(AGT)	 AG	25030-25324	GT	AGG
(GGA)	 AG	25533-25641	GG	GGG
-recovered pasa_asmbl_9069.p1, internal, 24404, 24501
-recovered pasa_asmbl_9069.p1, internal, 24642, 24829
-recovered pasa_asmbl_9069.p1, internal, 25030, 25324
Valid prediction for snap_scaffold_12-snap.2878-T1
Valid prediction for snap_scaffold_12-snap.2902-T1
Valid prediction for GlimmerHMM_glimmerT_30642-T1
Valid prediction for snap_scaffold_12-snap.2884-T1
Valid prediction for snap_scaffold_12-snap.2897-T1
Valid prediction for snap_scaffold_12-snap.2892-T1
Valid prediction for snap_scaffold_12-snap.2887-T1
Valid prediction for snap_scaffold_12-snap.2873-T1
Valid prediction for CodingQuarry_transcript_10486-T1
Valid prediction for GlimmerHMM_glimmerT_30638-T1
Valid prediction for GlimmerHMM_glimmerT_30625-T1
Couldn't classify 177240, 177295
Couldn't classify 178242, 178340
Sorry, prediction pasa_asmbl_9238.p1 fails validation.
(AGT)	 CA	177240-177295	GT	AGG
(GAA)	 AG	177450-177600	GT	AGG
(TAC)	 AG	178242-178340	CT	CCC
-recovered pasa_asmbl_9238.p1, internal, 177450, 177600
Valid prediction for GlimmerHMM_glimmerT_30632-T1
Valid prediction for snap_scaffold_12-snap.2905-T1
Valid prediction for snap_scaffold_12-snap.2901-T1
Valid prediction for Augustus_model.g20280.t1
Valid prediction for snap_scaffold_12-snap.2906-T1
Valid prediction for snap_scaffold_12-snap.2890-T1
Valid prediction for HiQ_model.g20275.t1
Valid prediction for snap_scaffold_12-snap.2877-T1
Valid prediction for snap_scaffold_12-snap.2904-T1
Valid prediction for snap_scaffold_12-snap.2908-T1
Valid prediction for Augustus_model.g20266.t1
Valid prediction for Augustus_model.g20260.t1
Valid prediction for Augustus_model.g20259.t1
Valid prediction for snap_scaffold_12-snap.2909-T1
Valid prediction for GlimmerHMM_glimmerT_30643-T1
Valid prediction for GlimmerHMM_glimmerT_30631-T1
Valid prediction for snap_scaffold_12-snap.2881-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5794, rend_intergenic: 2542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29536, rend_intergenic: 22614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35865, rend_intergenic: 31214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61740, rend_intergenic: 45555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74999, rend_intergenic: 69456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90530, rend_intergenic: 87182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107664, rend_intergenic: 98646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114719, rend_intergenic: 113759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132934, rend_intergenic: 115075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182218, rend_intergenic: 176056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187345, rend_intergenic: 182738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191842, rend_intergenic: 187543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195061
-exon list size: 508


building trellis

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99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 5794, rend_intergenic: 2542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29536, rend_intergenic: 22614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35865, rend_intergenic: 31214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61740, rend_intergenic: 45555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74999, rend_intergenic: 69456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90530, rend_intergenic: 87182  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107664, rend_intergenic: 98646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114719, rend_intergenic: 113759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132934, rend_intergenic: 115075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182218, rend_intergenic: 176056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187345, rend_intergenic: 182738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191842, rend_intergenic: 187543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support