-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_5975217-6143158

-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_26-snap.1384-T1
Valid prediction for snap_scaffold_26-snap.1395-T1
Valid prediction for GeneMark_model.99679_t
Valid prediction for snap_scaffold_26-snap.1388-T1
Valid prediction for GlimmerHMM_glimmerT_57129-T1
Valid prediction for GeneMark_model.99709_t
Valid prediction for Augustus_model.g38090.t1
Valid prediction for GlimmerHMM_glimmerT_57145-T1
Valid prediction for GeneMark_model.99693_t
Valid prediction for snap_scaffold_26-snap.1390-T1
Valid prediction for snap_scaffold_26-snap.1386-T1
Valid prediction for GeneMark_model.99687_t
Valid prediction for GeneMark_model.99674_t
Valid prediction for GlimmerHMM_glimmerT_57153-T1
Valid prediction for snap_scaffold_26-snap.1382-T1
Valid prediction for GeneMark_model.99707_t
Valid prediction for CodingQuarry_transcript_40287-T1
Couldn't classify 8110, 8186
Sorry, prediction pasa_asmbl_35592.p1 fails validation.
(CTC)	 CT	8110-8186	GT	GTG
(GTT)	 AG	8297-8510	GT	AGG
(CTC)	 AG	8766-8873	AA	AGA
-recovered pasa_asmbl_35592.p1, terminal, 8766, 8873
-recovered pasa_asmbl_35592.p1, internal, 8297, 8510
Valid prediction for snap_scaffold_26-snap.1402-T1
Valid prediction for snap_scaffold_26-snap.1401-T1
Valid prediction for Augustus_model.g38087.t1
Valid prediction for CodingQuarry_transcript_40286-T1
Valid prediction for GeneMark_model.99701_t
Valid prediction for CodingQuarry_transcript_40284-T1
Valid prediction for GeneMark_model.99712_t
Valid prediction for snap_scaffold_26-snap.1370-T1
Valid prediction for GlimmerHMM_glimmerT_57144-T1
Valid prediction for snap_scaffold_26-snap.1392-T1
Valid prediction for GlimmerHMM_glimmerT_57134-T1
Valid prediction for GeneMark_model.99713_t
Valid prediction for GeneMark_model.99688_t
Valid prediction for Augustus_model.g38088.t1
Valid prediction for GeneMark_model.99717_t
Valid prediction for pasa_asmbl_35587.p1
Valid prediction for GeneMark_model.99696_t
Valid prediction for snap_scaffold_26-snap.1381-T1
Valid prediction for Augustus_model.g38084.t1
Valid prediction for Augustus_model.g38071.t1
Valid prediction for snap_scaffold_26-snap.1376-T1
Valid prediction for pasa_asmbl_35597.p1
Valid prediction for snap_scaffold_26-snap.1393-T1
Valid prediction for GeneMark_model.99698_t
Valid prediction for GeneMark_model.99684_t
Valid prediction for snap_scaffold_26-snap.1377-T1
Valid prediction for GlimmerHMM_glimmerT_57138-T1
Valid prediction for HiQ_model.g38074.t1
Valid prediction for Augustus_model.g38083.t1
Valid prediction for snap_scaffold_26-snap.1397-T1
Valid prediction for GlimmerHMM_glimmerT_57157-T1
Valid prediction for GlimmerHMM_glimmerT_57128-T1
Valid prediction for GeneMark_model.99676_t
Valid prediction for GlimmerHMM_glimmerT_57156-T1
Valid prediction for GeneMark_model.99681_t
Valid prediction for Augustus_model.g38081.t1
Valid prediction for GeneMark_model.99677_t
Valid prediction for HiQ_model.g38075.t1
Valid prediction for GlimmerHMM_glimmerT_57148-T1
Valid prediction for snap_scaffold_26-snap.1380-T1
Valid prediction for snap_scaffold_26-snap.1366-T1
Valid prediction for GlimmerHMM_glimmerT_57154-T1
Valid prediction for GeneMark_model.99703_t
Valid prediction for GlimmerHMM_glimmerT_57137-T1
Valid prediction for GeneMark_model.99691_t
Valid prediction for GlimmerHMM_glimmerT_57141-T1
Valid prediction for snap_scaffold_26-snap.1365-T1
Valid prediction for GlimmerHMM_glimmerT_57136-T1
Valid prediction for Augustus_model.g38082.t1
Valid prediction for Augustus_model.g38073.t1
Valid prediction for snap_scaffold_26-snap.1369-T1
Valid prediction for GlimmerHMM_glimmerT_57131-T1
Valid prediction for pasa_asmbl_35596.p1
Valid prediction for snap_scaffold_26-snap.1398-T1
Valid prediction for GeneMark_model.99705_t
Valid prediction for GlimmerHMM_glimmerT_57152-T1
Valid prediction for GeneMark_model.99689_t
Valid prediction for Augustus_model.g38089.t1
Valid prediction for GeneMark_model.99704_t
Valid prediction for GeneMark_model.99715_t
Valid prediction for HiQ_model.g38067.t1
Valid prediction for snap_scaffold_26-snap.1362-T1
Valid prediction for snap_scaffold_26-snap.1368-T1
Valid prediction for pasa_asmbl_35593.p1
Valid prediction for GlimmerHMM_glimmerT_57149-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 Augustus_model.g38080.t1
Couldn't classify 147714, 147840
Couldn't classify 150463, 150497
Sorry, prediction pasa_asmbl_34933.p1 fails validation.
(AAC)	 AT	147714-147840	GT	TGG
(ATG)	 AG	150063-150332	GT	AGG
(CAA)	 AG	150463-150497	AC	CCA
add_exon() Sorry, pasa_asmbl_34933.p1 150063-150332-initial-1 is invalid.
-recovered pasa_asmbl_34933.p1, initial, 150063, 150332
-recovered pasa_asmbl_34933.p1, internal, 150063, 150332
Valid prediction for GlimmerHMM_glimmerT_57155-T1
Valid prediction for snap_scaffold_26-snap.1400-T1
Valid prediction for GlimmerHMM_glimmerT_57139-T1
Valid prediction for GeneMark_model.99716_t
Valid prediction for GeneMark_model.99711_t
Valid prediction for GeneMark_model.99686_t
Valid prediction for GlimmerHMM_glimmerT_57130-T1
Valid prediction for snap_scaffold_26-snap.1396-T1
Valid prediction for Augustus_model.g38076.t1
Valid prediction for snap_scaffold_26-snap.1363-T1
Valid prediction for GeneMark_model.99699_t
Valid prediction for GeneMark_model.99682_t
Valid prediction for Augustus_model.g38079.t1
Valid prediction for snap_scaffold_26-snap.1364-T1
Valid prediction for GlimmerHMM_glimmerT_57143-T1
Valid prediction for GeneMark_model.99708_t
Valid prediction for GeneMark_model.99678_t
Valid prediction for snap_scaffold_26-snap.1399-T1
Valid prediction for Augustus_model.g38070.t1
Valid prediction for GeneMark_model.99690_t
Valid prediction for snap_scaffold_26-snap.1391-T1
Valid prediction for Augustus_model.g38068.t1
Valid prediction for snap_scaffold_26-snap.1387-T1
Valid prediction for snap_scaffold_26-snap.1383-T1
Valid prediction for GeneMark_model.99695_t
Valid prediction for snap_scaffold_26-snap.1374-T1
Valid prediction for GeneMark_model.99700_t
Valid prediction for Augustus_model.g38085.t1
Valid prediction for GeneMark_model.99692_t
Valid prediction for Augustus_model.g38086.t1
Valid prediction for snap_scaffold_26-snap.1378-T1
Valid prediction for snap_scaffold_26-snap.1375-T1
Valid prediction for Augustus_model.g38078.t1
Valid prediction for GeneMark_model.99685_t
Valid prediction for GlimmerHMM_glimmerT_57147-T1
Valid prediction for GeneMark_model.99697_t
Valid prediction for GeneMark_model.99694_t
Valid prediction for snap_scaffold_26-snap.1379-T1
Valid prediction for GeneMark_model.99683_t
Valid prediction for snap_scaffold_26-snap.1389-T1
Valid prediction for Augustus_model.g38069.t1
Valid prediction for GlimmerHMM_glimmerT_57132-T1
Valid prediction for snap_scaffold_26-snap.1385-T1
Valid prediction for pasa_asmbl_34937.p1
Valid prediction for GlimmerHMM_glimmerT_57151-T1
Valid prediction for GeneMark_model.99672_t
Valid prediction for snap_scaffold_26-snap.1372-T1
Valid prediction for GeneMark_model.99671_t
Valid prediction for GlimmerHMM_glimmerT_57140-T1
Valid prediction for Augustus_model.g38077.t1
Valid prediction for GlimmerHMM_glimmerT_57133-T1
Valid prediction for GeneMark_model.99680_t
Valid prediction for GeneMark_model.99714_t
Valid prediction for snap_scaffold_26-snap.1394-T1
Valid prediction for snap_scaffold_26-snap.1367-T1
Valid prediction for GeneMark_model.99673_t
Valid prediction for snap_scaffold_26-snap.1373-T1
Valid prediction for snap_scaffold_26-snap.1371-T1
Valid prediction for GeneMark_model.99706_t
Valid prediction for GlimmerHMM_glimmerT_57146-T1
Valid prediction for GlimmerHMM_glimmerT_57135-T1
Valid prediction for Augustus_model.g38072.t1
Valid prediction for GeneMark_model.99675_t
Valid prediction for GeneMark_model.99710_t
Couldn't classify 95675, 95851
Sorry, prediction pasa_asmbl_34935.p1 fails validation.
(ACC)	 AG	95675-95851	GT	AGG
(GAC)	 AG	95950-96205	GT	AGG
(ACC)	 AG	98318-98626	GT	AGG
(GGC)	 AG	98854-99039	GT	GGG
(GTC)	 AG	100147-100751	GC	GAG
-recovered pasa_asmbl_34935.p1, terminal, 100147, 100751
-recovered pasa_asmbl_34935.p1, internal, 95675, 95851
-recovered pasa_asmbl_34935.p1, internal, 95950, 96205
-recovered pasa_asmbl_34935.p1, internal, 98318, 98626
-recovered pasa_asmbl_34935.p1, internal, 98854, 99039
-recovered pasa_asmbl_34935.p1, internal, 100147, 100751
Valid prediction for GlimmerHMM_glimmerT_57142-T1
Valid prediction for GlimmerHMM_glimmerT_57150-T1
Valid prediction for GeneMark_model.99702_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19789, rend_intergenic: 18406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70805, rend_intergenic: 67192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92109, rend_intergenic: 90214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100088, rend_intergenic: 95688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106825, rend_intergenic: 100848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110460, rend_intergenic: 107523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149646, rend_intergenic: 147781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153071, rend_intergenic: 151157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165636, rend_intergenic: 154972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167942
-exon list size: 639


building trellis

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-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 19789, rend_intergenic: 18406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70805, rend_intergenic: 67192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92109, rend_intergenic: 90214  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100088, rend_intergenic: 95688  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106825, rend_intergenic: 100848  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110460, rend_intergenic: 107523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149646, rend_intergenic: 147781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153071, rend_intergenic: 151157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165636, rend_intergenic: 154972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support