-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_11226379-11428671

-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_15-snap.2348-T1
Valid prediction for snap_scaffold_15-snap.2335-T1
Valid prediction for snap_scaffold_15-snap.2314-T1
Valid prediction for Augustus_model.g24610.t1
Valid prediction for snap_scaffold_15-snap.2305-T1
Valid prediction for snap_scaffold_15-snap.2341-T1
Valid prediction for GlimmerHMM_glimmerT_36975-T1
Valid prediction for Augustus_model.g24612.t1
Valid prediction for GlimmerHMM_glimmerT_36955-T1
Valid prediction for snap_scaffold_15-snap.2306-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.2324-T1
Valid prediction for snap_scaffold_15-snap.2326-T1
Valid prediction for HiQ_model.g24616.t1
Valid prediction for GlimmerHMM_glimmerT_36971-T1
Valid prediction for snap_scaffold_15-snap.2308-T1
Valid prediction for Augustus_model.g24613.t1
Valid prediction for Augustus_model.g24622.t1
Valid prediction for snap_scaffold_15-snap.2309-T1
Valid prediction for snap_scaffold_15-snap.2320-T1
Valid prediction for GlimmerHMM_glimmerT_36957-T1
Valid prediction for snap_scaffold_15-snap.2347-T1
Valid prediction for snap_scaffold_15-snap.2337-T1
Valid prediction for GlimmerHMM_glimmerT_36953-T1
Valid prediction for GlimmerHMM_glimmerT_36961-T1
Valid prediction for Augustus_model.g24615.t1
Valid prediction for snap_scaffold_15-snap.2328-T1
Valid prediction for GlimmerHMM_glimmerT_36977-T1
Valid prediction for snap_scaffold_15-snap.2318-T1
Valid prediction for GlimmerHMM_glimmerT_36956-T1
Valid prediction for snap_scaffold_15-snap.2344-T1
Valid prediction for GlimmerHMM_glimmerT_36979-T1
Valid prediction for snap_scaffold_15-snap.2313-T1
Valid prediction for snap_scaffold_15-snap.2338-T1
Valid prediction for Augustus_model.g24624.t1
Valid prediction for Augustus_model.g24617.t1
Valid prediction for Augustus_model.g24611.t1
Valid prediction for snap_scaffold_15-snap.2316-T1
Valid prediction for GlimmerHMM_glimmerT_36958-T1
Valid prediction for GlimmerHMM_glimmerT_36965-T1
Valid prediction for snap_scaffold_15-snap.2323-T1
Valid prediction for snap_scaffold_15-snap.2333-T1
Valid prediction for GlimmerHMM_glimmerT_36972-T1
Valid prediction for snap_scaffold_15-snap.2321-T1
Valid prediction for snap_scaffold_15-snap.2331-T1
Valid prediction for GlimmerHMM_glimmerT_36978-T1
Couldn't classify 77898, 78018
Couldn't classify 78539, 78713
Couldn't classify 79082, 79142
Sorry, prediction pasa_asmbl_15491.p1 fails validation.
(ATG)	 GA	71118-71287	GT	AGG
(GAA)	 AG	74252-74315	GT	AGG
(AAA)	 AG	74772-74882	GT	AGG
(AAA)	 AG	75116-75176	GT	CCG
(ACG)	 AG	75630-75754	GT	AGG
(GTC)	 AG	76041-76108	GT	GAG
(CGT)	 AG	76884-76986	GT	AGG
(GTT)	 AG	77617-77727	GT	GGG
(GAC)	 AG	77898-78018	AT	AAA
(CGC)	 AC	78539-78713	GT	AAG
(CGT)	 AG	79082-79142	TT	TGT
-recovered pasa_asmbl_15491.p1, initial, 71118, 71287
add_exon() Sorry, pasa_asmbl_15491.p1 76041-76108-terminal-2 is invalid.
-recovered pasa_asmbl_15491.p1, terminal, 76041, 76108
-recovered pasa_asmbl_15491.p1, internal, 74252, 74315
-recovered pasa_asmbl_15491.p1, internal, 74772, 74882
-recovered pasa_asmbl_15491.p1, internal, 75116, 75176
-recovered pasa_asmbl_15491.p1, internal, 75630, 75754
-recovered pasa_asmbl_15491.p1, internal, 76041, 76108
-recovered pasa_asmbl_15491.p1, internal, 76884, 76986
-recovered pasa_asmbl_15491.p1, internal, 77617, 77727
Valid prediction for GlimmerHMM_glimmerT_36960-T1
Valid prediction for GlimmerHMM_glimmerT_36964-T1
Valid prediction for snap_scaffold_15-snap.2334-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_15-snap.2322-T1
Valid prediction for GlimmerHMM_glimmerT_36983-T1
Valid prediction for GlimmerHMM_glimmerT_36985-T1
Valid prediction for GlimmerHMM_glimmerT_36966-T1
Valid prediction for Augustus_model.g24618.t1
Valid prediction for snap_scaffold_15-snap.2325-T1
Valid prediction for GlimmerHMM_glimmerT_36952-T1
Valid prediction for snap_scaffold_15-snap.2304-T1
Valid prediction for snap_scaffold_15-snap.2332-T1
Valid prediction for snap_scaffold_15-snap.2342-T1
Valid prediction for GlimmerHMM_glimmerT_36963-T1
Valid prediction for snap_scaffold_15-snap.2319-T1
Valid prediction for GlimmerHMM_glimmerT_36969-T1
Valid prediction for HiQ_model.g24627.t1
Valid prediction for snap_scaffold_15-snap.2343-T1
Valid prediction for snap_scaffold_15-snap.2349-T1
Valid prediction for GlimmerHMM_glimmerT_36954-T1
Valid prediction for snap_scaffold_15-snap.2329-T1
Valid prediction for snap_scaffold_15-snap.2311-T1
Valid prediction for GlimmerHMM_glimmerT_36970-T1
Couldn't classify 114056, 114442
Sorry, prediction pasa_asmbl_14492.p1 fails validation.
(CTC)	 CC	114056-114442	CA	CTC
Valid prediction for GlimmerHMM_glimmerT_36982-T1
Couldn't classify 114536, 114733
Sorry, prediction pasa_asmbl_14491.p1 fails validation.
(GGT)	 GG	114536-114733	GT	GGG
(ACG)	 AG	115968-116105	GT	GGG
(TGT)	 AG	117119-117337	GT	AGG
(GTG)	 AG	118086-118214	GT	AGG
(GAG)	 AG	118790-119024	GT	CTG
(CGT)	 AG	119185-119348	GT	AGG
(AGG)	 AG	119497-119625	CC	GAC
-recovered pasa_asmbl_14491.p1, terminal, 119497, 119625
-recovered pasa_asmbl_14491.p1, internal, 115968, 116105
-recovered pasa_asmbl_14491.p1, internal, 117119, 117337
-recovered pasa_asmbl_14491.p1, internal, 118086, 118214
-recovered pasa_asmbl_14491.p1, internal, 118790, 119024
-recovered pasa_asmbl_14491.p1, internal, 119185, 119348
Valid prediction for snap_scaffold_15-snap.2336-T1
Valid prediction for GlimmerHMM_glimmerT_36973-T1
Valid prediction for snap_scaffold_15-snap.2307-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_18145-T1
Valid prediction for snap_scaffold_15-snap.2312-T1
Valid prediction for GlimmerHMM_glimmerT_36974-T1
Valid prediction for Augustus_model.g24619.t1
Valid prediction for GlimmerHMM_glimmerT_36984-T1
Valid prediction for GlimmerHMM_glimmerT_36959-T1
Valid prediction for Augustus_model.g24614.t1
Valid prediction for GlimmerHMM_glimmerT_36980-T1
Valid prediction for snap_scaffold_15-snap.2345-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_15-snap.2327-T1
Valid prediction for Augustus_model.g24621.t1
Valid prediction for Augustus_model.g24625.t1
Valid prediction for snap_scaffold_15-snap.2340-T1
Valid prediction for snap_scaffold_15-snap.2339-T1
Valid prediction for GlimmerHMM_glimmerT_36976-T1
Valid prediction for GlimmerHMM_glimmerT_36981-T1
Valid prediction for snap_scaffold_15-snap.2310-T1
Valid prediction for snap_scaffold_15-snap.2330-T1
Valid prediction for Augustus_model.g24626.t1
Couldn't classify 3812, 3861
Sorry, prediction pasa_asmbl_14501.p1 fails validation.
(GTG)	 AG	3812-3861	GT	AGG
(GTC)	 AG	5538-5656	GT	AGG
(GAG)	 AG	7500-7577	GT	TGG
(TCA)	 AG	8139-8216	GT	AGG
(TGA)	 AG	9450-9516	GT	AAG
(ACC)	 AG	9692-9834	GT	CGG
(ATC)	 AG	9941-10084	GT	AGG
(GTT)	 AG	10335-10417	GT	AGG
(GAG)	 AG	12352-12526	GT	AGG
(GGG)	 AG	14191-14327	GT	AGG
(CGA)	 AG	14523-14606	GT	AGG
(GAT)	 AG	17428-17517	GT	AGG
(GAG)	 AG	17890-17948	GT	AGG
(TAC)	 AG	18332-18492	GT	GGG
(GTC)	 AG	18765-18879	GT	AGG
(GAG)	 AG	19142-19263	GT	AGG
(GCA)	 AG	20952-21052	GT	AGG
(CAC)	 AG	21893-21973	CT	AAC
add_exon() Sorry, pasa_asmbl_14501.p1 19142-19263-terminal-2 is invalid.
-recovered pasa_asmbl_14501.p1, terminal, 19142, 19263
-recovered pasa_asmbl_14501.p1, terminal, 21893, 21973
-recovered pasa_asmbl_14501.p1, internal, 3812, 3861
-recovered pasa_asmbl_14501.p1, internal, 5538, 5656
-recovered pasa_asmbl_14501.p1, internal, 7500, 7577
-recovered pasa_asmbl_14501.p1, internal, 8139, 8216
-recovered pasa_asmbl_14501.p1, internal, 9450, 9516
-recovered pasa_asmbl_14501.p1, internal, 9692, 9834
-recovered pasa_asmbl_14501.p1, internal, 9941, 10084
-recovered pasa_asmbl_14501.p1, internal, 10335, 10417
-recovered pasa_asmbl_14501.p1, internal, 12352, 12526
-recovered pasa_asmbl_14501.p1, internal, 14191, 14327
-recovered pasa_asmbl_14501.p1, internal, 14523, 14606
-recovered pasa_asmbl_14501.p1, internal, 17428, 17517
-recovered pasa_asmbl_14501.p1, internal, 17890, 17948
-recovered pasa_asmbl_14501.p1, internal, 18332, 18492
-recovered pasa_asmbl_14501.p1, internal, 18765, 18879
-recovered pasa_asmbl_14501.p1, internal, 19142, 19263
-recovered pasa_asmbl_14501.p1, internal, 20952, 21052
Valid prediction for Augustus_model.g24620.t1
Valid prediction for GlimmerHMM_glimmerT_36968-T1
Valid prediction for snap_scaffold_15-snap.2346-T1
Valid prediction for GlimmerHMM_glimmerT_36962-T1
Valid prediction for GlimmerHMM_glimmerT_36967-T1
Valid prediction for Augustus_model.g24623.t1
Valid prediction for snap_scaffold_15-snap.2315-T1
Couldn't classify 28243, 28331
Sorry, prediction pasa_asmbl_14497.p1 fails validation.
(AAC)	 CC	28243-28331	GT	GGG
(CAT)	 AG	29126-29299	GT	AAG
(GCA)	 AG	29474-29522	GT	AGG
(GCG)	 AG	29659-29824	GT	TGG
(CCA)	 AG	29985-30190	AG	GAA
-recovered pasa_asmbl_14497.p1, terminal, 29985, 30190
-recovered pasa_asmbl_14497.p1, internal, 29126, 29299
-recovered pasa_asmbl_14497.p1, internal, 29474, 29522
-recovered pasa_asmbl_14497.p1, internal, 29659, 29824
Valid prediction for CodingQuarry_transcript_18144-T1
Valid prediction for snap_scaffold_15-snap.2317-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4852, rend_intergenic: 2003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14555, rend_intergenic: 6303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50382, rend_intergenic: 31509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61841, rend_intergenic: 58220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67227, rend_intergenic: 63193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78083, rend_intergenic: 72289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86908, rend_intergenic: 82669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94862, rend_intergenic: 88264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96944, rend_intergenic: 95492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102995, rend_intergenic: 96992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112993, rend_intergenic: 106595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132134, rend_intergenic: 126727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147715, rend_intergenic: 144536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169085, rend_intergenic: 168149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186048, rend_intergenic: 180321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200049, rend_intergenic: 190275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202293
-exon list size: 432


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 4852, rend_intergenic: 2003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14555, rend_intergenic: 6303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50382, rend_intergenic: 31509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61841, rend_intergenic: 58220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67227, rend_intergenic: 63193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78083, rend_intergenic: 72289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86908, rend_intergenic: 82669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94862, rend_intergenic: 88264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96944, rend_intergenic: 95492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102995, rend_intergenic: 96992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112993, rend_intergenic: 106595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132134, rend_intergenic: 126727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147715, rend_intergenic: 144536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169085, rend_intergenic: 168149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186048, rend_intergenic: 180321  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200049, rend_intergenic: 190275  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