-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_15/scaffold_15_6685448-6908840

-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 Augustus_model.g24896.t1
Valid prediction for HiQ_model.g24903.t1
Valid prediction for HiQ_model.g24899.t1
Valid prediction for GlimmerHMM_glimmerT_37138-T1
Valid prediction for Augustus_model.g24894.t1
Valid prediction for GeneMark_model.63942_t
Valid prediction for snap_scaffold_15-snap.1447-T1
Valid prediction for GlimmerHMM_glimmerT_37133-T1
Valid prediction for snap_scaffold_15-snap.1426-T1
Valid prediction for snap_scaffold_15-snap.1457-T1
Valid prediction for GeneMark_model.63922_t
Valid prediction for snap_scaffold_15-snap.1452-T1
Valid prediction for snap_scaffold_15-snap.1423-T1
Valid prediction for GeneMark_model.63933_t
Valid prediction for GlimmerHMM_glimmerT_37150-T1
Valid prediction for GlimmerHMM_glimmerT_37152-T1
Valid prediction for GlimmerHMM_glimmerT_37149-T1
Valid prediction for GlimmerHMM_glimmerT_37137-T1
Valid prediction for GlimmerHMM_glimmerT_37140-T1
Valid prediction for GeneMark_model.63940_t
Valid prediction for GeneMark_model.63927_t
Valid prediction for GlimmerHMM_glimmerT_37145-T1
Couldn't classify 68669, 68715
Sorry, prediction pasa_asmbl_14202.p1 fails validation.
(ATG)	 TC	67928-68056	GT	AGG
(GGT)	 AG	68254-68578	GT	TGG
(GTA)	 AG	68669-68715	TA	TCT
-recovered pasa_asmbl_14202.p1, initial, 67928, 68056
-recovered pasa_asmbl_14202.p1, internal, 68254, 68578
Valid prediction for snap_scaffold_15-snap.1446-T1
Valid prediction for HiQ_model.g24900.t1
Valid prediction for Augustus_model.g24910.t1
Valid prediction for Augustus_model.g24912.t1
Valid prediction for GlimmerHMM_glimmerT_37139-T1
Valid prediction for GeneMark_model.63905_t
Valid prediction for GeneMark_model.63917_t
Couldn't classify 68961, 69138
Sorry, prediction pasa_asmbl_14203.p1 fails validation.
(GTC)	 TT	68961-69138	GT	TGG
(GCA)	 AG	69329-69510	GT	AGG
(ATC)	 AG	69647-69790	AC	AAA
-recovered pasa_asmbl_14203.p1, terminal, 69647, 69790
-recovered pasa_asmbl_14203.p1, internal, 69329, 69510
Valid prediction for snap_scaffold_15-snap.1444-T1
Valid prediction for snap_scaffold_15-snap.1424-T1
Valid prediction for Augustus_model.g24914.t1
Valid prediction for snap_scaffold_15-snap.1435-T1
Valid prediction for snap_scaffold_15-snap.1438-T1
Valid prediction for GeneMark_model.63909_t
Valid prediction for snap_scaffold_15-snap.1419-T1
Valid prediction for snap_scaffold_15-snap.1427-T1
Couldn't classify 57714, 58166
Sorry, prediction pasa_asmbl_14200.p1 fails validation.
(CAG)	 GA	57714-58166	AT	AGA
Valid prediction for Augustus_model.g24897.t1
Valid prediction for snap_scaffold_15-snap.1434-T1
Valid prediction for snap_scaffold_15-snap.1445-T1
Valid prediction for GeneMark_model.63918_t
Valid prediction for CodingQuarry_transcript_17987-T1
Valid prediction for GeneMark_model.63924_t
Valid prediction for GeneMark_model.63906_t
Valid prediction for GeneMark_model.63911_t
Valid prediction for snap_scaffold_15-snap.1449-T1
Valid prediction for Augustus_model.g24898.t1
Valid prediction for GeneMark_model.63937_t
Valid prediction for snap_scaffold_15-snap.1441-T1
Valid prediction for snap_scaffold_15-snap.1429-T1
Valid prediction for snap_scaffold_15-snap.1428-T1
Valid prediction for CodingQuarry_transcript_17985-T1
Valid prediction for snap_scaffold_15-snap.1454-T1
Valid prediction for pasa_asmbl_14204.p1
Valid prediction for Augustus_model.g24908.t1
Valid prediction for GeneMark_model.63920_t
Valid prediction for Augustus_model.g24913.t1
Valid prediction for snap_scaffold_15-snap.1451-T1
Valid prediction for GeneMark_model.63931_t
Valid prediction for GlimmerHMM_glimmerT_37147-T1
Valid prediction for GlimmerHMM_glimmerT_37159-T1
Valid prediction for GeneMark_model.63930_t
Valid prediction for pasa_asmbl_14206.p1
Valid prediction for pasa_asmbl_14201.p1
Valid prediction for snap_scaffold_15-snap.1443-T1
Valid prediction for snap_scaffold_15-snap.1422-T1
Valid prediction for GeneMark_model.63914_t
Valid prediction for GeneMark_model.63934_t
Valid prediction for GlimmerHMM_glimmerT_37135-T1
Valid prediction for GeneMark_model.63913_t
Valid prediction for snap_scaffold_15-snap.1415-T1
Valid prediction for HiQ_model.g24906.t1
Valid prediction for GeneMark_model.63912_t
Valid prediction for Augustus_model.g24911.t1
Valid prediction for snap_scaffold_15-snap.1414-T1
Valid prediction for GlimmerHMM_glimmerT_37153-T1
Valid prediction for snap_scaffold_15-snap.1430-T1
Valid prediction for snap_scaffold_15-snap.1448-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.1420-T1
Valid prediction for GlimmerHMM_glimmerT_37146-T1
Valid prediction for Augustus_model.g24909.t1
Valid prediction for GlimmerHMM_glimmerT_37151-T1
Valid prediction for CodingQuarry_transcript_17988-T1
Valid prediction for snap_scaffold_15-snap.1421-T1
Valid prediction for GeneMark_model.63923_t
Valid prediction for GlimmerHMM_glimmerT_37142-T1
Valid prediction for GeneMark_model.63939_t
Valid prediction for GeneMark_model.63910_t
Valid prediction for Augustus_model.g24917.t1
Valid prediction for HiQ_model.g24904.t1
Valid prediction for GlimmerHMM_glimmerT_37156-T1
Couldn't classify 126320, 126459
Sorry, prediction pasa_asmbl_15266.p1 fails validation.
(ATC)	 TC	126320-126459	GT	AGG
(GTT)	 AG	126578-126653	GT	AGG
(GTG)	 AG	126760-126909	GT	TGG
(GCA)	 AG	127011-127075	GT	TGG
(GTA)	 AG	127193-127371	GT	GGG
(GTG)	 AG	127876-128106	GT	ATG
(TGG)	 AG	128192-128376	CA	AAC
-recovered pasa_asmbl_15266.p1, terminal, 128192, 128376
-recovered pasa_asmbl_15266.p1, internal, 126578, 126653
-recovered pasa_asmbl_15266.p1, internal, 126760, 126909
-recovered pasa_asmbl_15266.p1, internal, 127011, 127075
-recovered pasa_asmbl_15266.p1, internal, 127193, 127371
-recovered pasa_asmbl_15266.p1, internal, 127876, 128106
Valid prediction for GlimmerHMM_glimmerT_37148-T1
Valid prediction for snap_scaffold_15-snap.1425-T1
Valid prediction for snap_scaffold_15-snap.1455-T1
Valid prediction for GlimmerHMM_glimmerT_37141-T1
Valid prediction for snap_scaffold_15-snap.1431-T1
Valid prediction for GeneMark_model.63928_t
Valid prediction for GlimmerHMM_glimmerT_37136-T1
Valid prediction for GlimmerHMM_glimmerT_37154-T1
Valid prediction for snap_scaffold_15-snap.1453-T1
Valid prediction for GeneMark_model.63921_t
Valid prediction for GeneMark_model.63925_t
Valid prediction for CodingQuarry_transcript_17986-T1
Valid prediction for snap_scaffold_15-snap.1437-T1
Valid prediction for GeneMark_model.63929_t
Valid prediction for snap_scaffold_15-snap.1416-T1
Valid prediction for GeneMark_model.63938_t
Couldn't classify 125962, 125999
Sorry, prediction pasa_asmbl_15268.p1 fails validation.
(ATG)	 AT	123802-124561	GT	CCG
(AGC)	 AG	124702-124899	GT	GGG
(CTG)	 AG	125270-125398	GT	GGG
(CCT)	 AG	125503-125650	GT	ATG
(GAT)	 AG	125756-125865	GT	AGG
(ACA)	 AG	125962-125999	CT	GGC
-recovered pasa_asmbl_15268.p1, initial, 123802, 124561
-recovered pasa_asmbl_15268.p1, internal, 124702, 124899
-recovered pasa_asmbl_15268.p1, internal, 125270, 125398
-recovered pasa_asmbl_15268.p1, internal, 125503, 125650
-recovered pasa_asmbl_15268.p1, internal, 125756, 125865
Valid prediction for GeneMark_model.63941_t
Valid prediction for Augustus_model.g24915.t1
Valid prediction for GeneMark_model.63915_t
Valid prediction for GlimmerHMM_glimmerT_37144-T1
Valid prediction for GlimmerHMM_glimmerT_37158-T1
Valid prediction for HiQ_model.g24905.t1
Couldn't classify 18510, 18647
Sorry, prediction pasa_asmbl_15279.p1 fails validation.
(GGT)	 AT	18510-18647	GT	AGG
(GCG)	 AG	18961-19014	GT	AGG
(AAT)	 AG	19204-19258	GT	TGG
(GAC)	 AG	19364-19452	GT	CGG
(CTC)	 AG	19636-19767	GT	AGG
(GGA)	 AG	20098-20124	GT	AGG
(GAC)	 AG	20596-20652	GT	AGG
(GAC)	 AG	20777-20847	GT	AAG
(AAA)	 AG	20973-21034	GT	ATG
(CTG)	 AG	21150-21211	GT	TGG
(GTC)	 AG	21322-21396	GT	AGG
(GGG)	 AG	24155-24381	GT	TGG
(TAT)	 AG	24698-24766	GT	AAG
(CCT)	 AG	25211-25285	GT	GAG
(CCT)	 AG	25659-25742	GT	AGG
(GAG)	 AG	25940-26127	GT	TGG
(ACG)	 AG	26206-26239	GT	AGG
(CCA)	 AG	26388-26475	GT	AGG
(TTT)	 AG	26859-26933	CC	AAC
add_exon() Sorry, pasa_asmbl_15279.p1 25211-25285-terminal-1 is invalid.
-recovered pasa_asmbl_15279.p1, terminal, 25211, 25285
-recovered pasa_asmbl_15279.p1, terminal, 26859, 26933
-recovered pasa_asmbl_15279.p1, internal, 18961, 19014
-recovered pasa_asmbl_15279.p1, internal, 19204, 19258
-recovered pasa_asmbl_15279.p1, internal, 19364, 19452
-recovered pasa_asmbl_15279.p1, internal, 19636, 19767
-recovered pasa_asmbl_15279.p1, internal, 20098, 20124
-recovered pasa_asmbl_15279.p1, internal, 20596, 20652
-recovered pasa_asmbl_15279.p1, internal, 20777, 20847
-recovered pasa_asmbl_15279.p1, internal, 20973, 21034
-recovered pasa_asmbl_15279.p1, internal, 21150, 21211
-recovered pasa_asmbl_15279.p1, internal, 21322, 21396
-recovered pasa_asmbl_15279.p1, internal, 24155, 24381
-recovered pasa_asmbl_15279.p1, internal, 24698, 24766
-recovered pasa_asmbl_15279.p1, internal, 25211, 25285
-recovered pasa_asmbl_15279.p1, internal, 25659, 25742
-recovered pasa_asmbl_15279.p1, internal, 25940, 26127
-recovered pasa_asmbl_15279.p1, internal, 26206, 26239
-recovered pasa_asmbl_15279.p1, internal, 26388, 26475
Valid prediction for pasa_asmbl_15270.p1
Valid prediction for Augustus_model.g24901.t1
Valid prediction for GeneMark_model.63908_t
Valid prediction for snap_scaffold_15-snap.1418-T1
Valid prediction for GlimmerHMM_glimmerT_37155-T1
Valid prediction for GeneMark_model.63919_t
Valid prediction for snap_scaffold_15-snap.1442-T1
Valid prediction for snap_scaffold_15-snap.1432-T1
Valid prediction for snap_scaffold_15-snap.1439-T1
Valid prediction for snap_scaffold_15-snap.1417-T1
Valid prediction for GeneMark_model.63916_t
Valid prediction for snap_scaffold_15-snap.1436-T1
Valid prediction for GlimmerHMM_glimmerT_37134-T1
Valid prediction for snap_scaffold_15-snap.1450-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g24907.t1
Valid prediction for GlimmerHMM_glimmerT_37143-T1
Valid prediction for snap_scaffold_15-snap.1440-T1
Valid prediction for HiQ_model.g24916.t1
Valid prediction for Augustus_model.g24895.t1
Valid prediction for snap_scaffold_15-snap.1433-T1
Valid prediction for GlimmerHMM_glimmerT_37157-T1
Valid prediction for HiQ_model.g24902.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 42290, rend_intergenic: 39086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54053, rend_intergenic: 51435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85049, rend_intergenic: 80363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130456, rend_intergenic: 122897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171312, rend_intergenic: 170258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175438, rend_intergenic: 171581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199305, rend_intergenic: 195589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 223393
-exon list size: 523


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 42290, rend_intergenic: 39086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54053, rend_intergenic: 51435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85049, rend_intergenic: 80363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130456, rend_intergenic: 122897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171312, rend_intergenic: 170258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175438, rend_intergenic: 171581  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199305, rend_intergenic: 195589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support