-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_7333443-7491672

-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 GeneMark_model.52095_t
Valid prediction for GlimmerHMM_glimmerT_30171-T1
Valid prediction for GlimmerHMM_glimmerT_30167-T1
Valid prediction for CodingQuarry_transcript_10246-T1
Valid prediction for snap_scaffold_12-snap.1362-T1
Valid prediction for GeneMark_model.52114_t
Valid prediction for pasa_asmbl_8718.p2
Valid prediction for snap_scaffold_12-snap.1370-T1
Valid prediction for GeneMark_model.52097_t
Valid prediction for GeneMark_model.52117_t
Valid prediction for snap_scaffold_12-snap.1364-T1
Valid prediction for CodingQuarry_transcript_10254-T1
Valid prediction for snap_scaffold_12-snap.1361-T1
Valid prediction for CodingQuarry_transcript_10248-T1
Valid prediction for GeneMark_model.52093_t
Valid prediction for GlimmerHMM_glimmerT_30168-T1
Valid prediction for Augustus_model.g20077.t1
Valid prediction for GeneMark_model.52091_t
Couldn't classify 34812, 35384
Couldn't classify 37417, 37460
Sorry, prediction pasa_asmbl_8715.p1 fails validation.
(GCT)	 CA	34812-35384	GT	AGG
(GTG)	 AG	35599-35873	GT	CGG
(GAT)	 AG	36017-37014	GT	AGG
(GTT)	 AG	37417-37460	AG	TGA
-recovered pasa_asmbl_8715.p1, internal, 35599, 35873
-recovered pasa_asmbl_8715.p1, internal, 36017, 37014
Valid prediction for HiQ_model.g20088.t1
Valid prediction for GlimmerHMM_glimmerT_30173-T1
Valid prediction for Augustus_model.g20094.t1
Valid prediction for Augustus_model.g20081.t1
Couldn't classify 28024, 28261
Couldn't classify 32159, 32206
Sorry, prediction pasa_asmbl_8713.p1 fails validation.
(CCC)	 GT	28024-28261	GT	AAG
(TGT)	 AG	29194-29402	GT	GGG
(GTG)	 AG	29598-29723	GT	GGG
(GAC)	 AG	30034-30162	GT	AGG
(CTG)	 AG	31687-31809	GT	CGG
(GAG)	 AG	32159-32206	AG	GCA
-recovered pasa_asmbl_8713.p1, internal, 29194, 29402
-recovered pasa_asmbl_8713.p1, internal, 29598, 29723
-recovered pasa_asmbl_8713.p1, internal, 30034, 30162
-recovered pasa_asmbl_8713.p1, internal, 31687, 31809
Valid prediction for GeneMark_model.52111_t
Valid prediction for snap_scaffold_12-snap.1379-T1
Valid prediction for snap_scaffold_12-snap.1388-T1
Valid prediction for pasa_asmbl_8717.p1
Valid prediction for GeneMark_model.52099_t
Valid prediction for GlimmerHMM_glimmerT_30172-T1
Valid prediction for snap_scaffold_12-snap.1387-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_30183-T1
Valid prediction for GeneMark_model.52108_t
Valid prediction for pasa_asmbl_8708.p1
Valid prediction for snap_scaffold_12-snap.1374-T1
Valid prediction for HiQ_model.g20076.t1
Valid prediction for HiQ_model.g20078.t1
Valid prediction for GeneMark_model.52087_t
Valid prediction for GeneMark_model.52089_t
Valid prediction for GeneMark_model.52086_t
Valid prediction for GeneMark_model.52101_t
Valid prediction for snap_scaffold_12-snap.1382-T1
Valid prediction for GeneMark_model.52106_t
Valid prediction for GlimmerHMM_glimmerT_30180-T1
Valid prediction for GeneMark_model.52084_t
Valid prediction for GeneMark_model.52119_t
Valid prediction for CodingQuarry_transcript_10247-T1
Couldn't classify 125587, 126498
Sorry, prediction pasa_asmbl_8722.p1 fails validation.
(GGT)	 GT	125587-126498	CT	GAC
Valid prediction for snap_scaffold_12-snap.1393-T1
Couldn't classify 33015, 34484
Sorry, prediction pasa_asmbl_8714.p1 fails validation.
(AGC)	 CA	33015-34484	GA	GAG
Valid prediction for HiQ_model.g20089.t1
Valid prediction for GlimmerHMM_glimmerT_30179-T1
Valid prediction for CodingQuarry_transcript_10253-T1
Valid prediction for Augustus_model.g20080.t1
Valid prediction for pasa_asmbl_8711.p1
Valid prediction for snap_scaffold_12-snap.1384-T1
Valid prediction for snap_scaffold_12-snap.1359-T1
Valid prediction for GeneMark_model.52082_t
Valid prediction for snap_scaffold_12-snap.1368-T1
Valid prediction for GeneMark_model.52113_t
Valid prediction for snap_scaffold_12-snap.1381-T1
Valid prediction for GlimmerHMM_glimmerT_30169-T1
Valid prediction for snap_scaffold_12-snap.1373-T1
Valid prediction for GeneMark_model.52110_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 GeneMark_model.52105_t
Valid prediction for CodingQuarry_transcript_10250-T1
Valid prediction for CodingQuarry_transcript_10251-T1
Valid prediction for snap_scaffold_12-snap.1377-T1
Valid prediction for snap_scaffold_12-snap.1378-T1
Valid prediction for Augustus_model.g20092.t1
Valid prediction for GeneMark_model.52102_t
Valid prediction for GeneMark_model.52109_t
Valid prediction for snap_scaffold_12-snap.1372-T1
Valid prediction for CodingQuarry_transcript_10252-T1
Valid prediction for GeneMark_model.52104_t
Valid prediction for snap_scaffold_12-snap.1390-T1
Valid prediction for CodingQuarry_transcript_10249-T1
Valid prediction for GlimmerHMM_glimmerT_30185-T1
Valid prediction for snap_scaffold_12-snap.1366-T1
Valid prediction for snap_scaffold_12-snap.1385-T1
Valid prediction for snap_scaffold_12-snap.1360-T1
Valid prediction for pasa_asmbl_7705.p1
Valid prediction for Augustus_model.g20091.t1
Valid prediction for snap_scaffold_12-snap.1386-T1
Couldn't classify 20685, 20745
Couldn't classify 21782, 21872
Sorry, prediction CodingQuarry_transcript_10256-T1 fails validation.
(ATG)	 CA	17205-17254	GT	CTG
(CGA)	 AG	19114-19308	GT	AAG
(TAA)	 AG	19513-19593	GT	AGG
(GTC)	 AG	20087-20250	GT	TGG
(ACG)	 AG	20685-20745	AT	GTA
(GAA)	 TA	21782-21872	GT	AGG
(GTG)	 AG	22049-22092	GT	GTG
(TGA)	 AG	22186-22376	GT	CAG
(CCC)	 AG	22540-22610	GT	AGG
(GAT)	 AG	22869-23026	GT	CCG
(GAG)	 AG	23353-23497	GT	AGG
(GAG)	 AG	23763-23906	GT	AGG
(AAG)	 AG	24204-24425	GG	GAG
-recovered CodingQuarry_transcript_10256-T1, initial, 17205, 17254
-recovered CodingQuarry_transcript_10256-T1, terminal, 24204, 24425
-recovered CodingQuarry_transcript_10256-T1, internal, 19114, 19308
-recovered CodingQuarry_transcript_10256-T1, internal, 19513, 19593
-recovered CodingQuarry_transcript_10256-T1, internal, 20087, 20250
-recovered CodingQuarry_transcript_10256-T1, internal, 22049, 22092
-recovered CodingQuarry_transcript_10256-T1, internal, 22186, 22376
-recovered CodingQuarry_transcript_10256-T1, internal, 22540, 22610
-recovered CodingQuarry_transcript_10256-T1, internal, 22869, 23026
-recovered CodingQuarry_transcript_10256-T1, internal, 23353, 23497
-recovered CodingQuarry_transcript_10256-T1, internal, 23763, 23906
Valid prediction for Augustus_model.g20083.t1
Valid prediction for GeneMark_model.52090_t
Valid prediction for GeneMark_model.52103_t
Valid prediction for snap_scaffold_12-snap.1369-T1
Valid prediction for GlimmerHMM_glimmerT_30170-T1
Valid prediction for GeneMark_model.52094_t
Valid prediction for snap_scaffold_12-snap.1363-T1
Valid prediction for snap_scaffold_12-snap.1365-T1
Valid prediction for pasa_asmbl_7708.p1
Valid prediction for GlimmerHMM_glimmerT_30177-T1
Valid prediction for HiQ_model.g20085.t1
Valid prediction for snap_scaffold_12-snap.1371-T1
Valid prediction for snap_scaffold_12-snap.1367-T1
Valid prediction for GeneMark_model.52120_t
Valid prediction for GlimmerHMM_glimmerT_30174-T1
Valid prediction for GeneMark_model.52096_t
Valid prediction for Augustus_model.g20090.t1
Valid prediction for snap_scaffold_12-snap.1391-T1
Valid prediction for snap_scaffold_12-snap.1383-T1
Valid prediction for pasa_asmbl_7712.p1
Valid prediction for snap_scaffold_12-snap.1375-T1
Valid prediction for Augustus_model.g20079.t1
Valid prediction for GlimmerHMM_glimmerT_30178-T1
Valid prediction for GeneMark_model.52098_t
Valid prediction for HiQ_model.g20087.t1
Valid prediction for GlimmerHMM_glimmerT_30181-T1
Valid prediction for snap_scaffold_12-snap.1380-T1
Valid prediction for GlimmerHMM_glimmerT_30182-T1
Valid prediction for GeneMark_model.52085_t
Valid prediction for GlimmerHMM_glimmerT_30175-T1
Valid prediction for GeneMark_model.52083_t
Valid prediction for Augustus_model.g20093.t1
Valid prediction for snap_scaffold_12-snap.1389-T1
Valid prediction for snap_scaffold_12-snap.1376-T1
Valid prediction for GeneMark_model.52118_t
Valid prediction for HiQ_model.g20095.t1
Valid prediction for Augustus_model.g20096.t1
Valid prediction for GlimmerHMM_glimmerT_30184-T1
Valid prediction for HiQ_model.g20084.t1
Valid prediction for GlimmerHMM_glimmerT_30176-T1
Valid prediction for GeneMark_model.52088_t
Valid prediction for Augustus_model.g20086.t1
Valid prediction for snap_scaffold_12-snap.1392-T1
Valid prediction for GeneMark_model.52100_t
Valid prediction for GeneMark_model.52115_t
Valid prediction for Augustus_model.g20082.t1
Valid prediction for GeneMark_model.52092_t
Valid prediction for GeneMark_model.52112_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11938, rend_intergenic: 8522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41430, rend_intergenic: 26868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44774, rend_intergenic: 43514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48549, rend_intergenic: 45460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50433, rend_intergenic: 49013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70166, rend_intergenic: 61069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84831, rend_intergenic: 82506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109178, rend_intergenic: 106492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123403, rend_intergenic: 115679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150958, rend_intergenic: 141444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158230
-exon list size: 548


building trellis

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-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 11938, rend_intergenic: 8522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41430, rend_intergenic: 26868  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44774, rend_intergenic: 43514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48549, rend_intergenic: 45460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50433, rend_intergenic: 49013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70166, rend_intergenic: 61069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84831, rend_intergenic: 82506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109178, rend_intergenic: 106492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123403, rend_intergenic: 115679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150958, rend_intergenic: 141444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 147675 - 158230
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
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-found 1 predictions from path traversal

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