-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_7452242-7581627

-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.88355_t
Valid prediction for GlimmerHMM_glimmerT_50967-T1
Valid prediction for snap_scaffold_22-snap.1531-T1
Valid prediction for snap_scaffold_22-snap.1512-T1
Valid prediction for snap_scaffold_22-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_50971-T1
Valid prediction for snap_scaffold_22-snap.1538-T1
Valid prediction for HiQ_model.g34193.t1
Valid prediction for snap_scaffold_22-snap.1527-T1
Couldn't classify 117762, 118091
Sorry, prediction pasa_asmbl_29753.p1 fails validation.
(AGA)	 AC	117762-118091	TT	GAT
Couldn't classify 120352, 120676
Couldn't classify 121055, 121296
Sorry, prediction pasa_asmbl_29486.p1 fails validation.
(CTC)	 AG	120352-120676	GT	AGG
(CCA)	 AG	121055-121296	AG	AGA
-recovered pasa_asmbl_29486.p1, internal, 120352, 120676
Valid prediction for GlimmerHMM_glimmerT_50979-T1
Valid prediction for GlimmerHMM_glimmerT_50980-T1
Valid prediction for GeneMark_model.88332_t
Valid prediction for GeneMark_model.88340_t
Valid prediction for GeneMark_model.88351_t
Valid prediction for snap_scaffold_22-snap.1536-T1
Valid prediction for snap_scaffold_22-snap.1515-T1
Valid prediction for GeneMark_model.88341_t
Valid prediction for GlimmerHMM_glimmerT_50977-T1
Couldn't classify 40072, 41085
Sorry, prediction pasa_asmbl_29481.p1 fails validation.
(ATG)	 GA	40072-41085	CC	ACC
Valid prediction for GeneMark_model.88348_t
Valid prediction for GeneMark_model.88336_t
Couldn't classify 121396, 122099
Couldn't classify 122757, 122901
Sorry, prediction pasa_asmbl_29487.p2 fails validation.
(TTC)	 CC	121396-122099	GT	AGG
(GTA)	 AG	122757-122901	CA	GCC
Valid prediction for GlimmerHMM_glimmerT_50987-T1
Valid prediction for GeneMark_model.88330_t
Valid prediction for snap_scaffold_22-snap.1509-T1
Valid prediction for GlimmerHMM_glimmerT_50975-T1
Valid prediction for snap_scaffold_22-snap.1519-T1
Valid prediction for snap_scaffold_22-snap.1534-T1
Couldn't classify 888, 1847
Sorry, prediction pasa_asmbl_29479.p1 fails validation.
(GAT)	 CA	888-1847	GG	GAG
Valid prediction for GeneMark_model.88338_t
Valid prediction for GlimmerHMM_glimmerT_50978-T1
Valid prediction for snap_scaffold_22-snap.1528-T1
Valid prediction for GeneMark_model.88357_t
Couldn't classify 36379, 36465
Sorry, prediction pasa_asmbl_29480.p1 fails validation.
(TCC)	 CT	36379-36465	GT	AGG
(GTT)	 AG	37055-37143	GT	AGG
(CTT)	 AG	37433-37556	GT	AGG
(ATC)	 AG	38055-38243	CG	AGC
-recovered pasa_asmbl_29480.p1, terminal, 38055, 38243
-recovered pasa_asmbl_29480.p1, internal, 37055, 37143
-recovered pasa_asmbl_29480.p1, internal, 37433, 37556
Valid prediction for HiQ_model.g34192.t1
Valid prediction for GlimmerHMM_glimmerT_50989-T1
Valid prediction for GlimmerHMM_glimmerT_50985-T1
Valid prediction for snap_scaffold_22-snap.1525-T1
Valid prediction for snap_scaffold_22-snap.1541-T1
Valid prediction for GeneMark_model.88353_t
Valid prediction for GeneMark_model.88342_t
Valid prediction for Augustus_model.g34191.t1
Valid prediction for snap_scaffold_22-snap.1510-T1
Valid prediction for GeneMark_model.88359_t
Valid prediction for snap_scaffold_22-snap.1518-T1
Valid prediction for GeneMark_model.88334_t
Valid prediction for snap_scaffold_22-snap.1513-T1
Valid prediction for GlimmerHMM_glimmerT_50974-T1
Valid prediction for snap_scaffold_22-snap.1539-T1
Valid prediction for HiQ_model.g34187.t1
Valid prediction for GeneMark_model.88344_t
Valid prediction for snap_scaffold_22-snap.1523-T1
Valid prediction for GlimmerHMM_glimmerT_50969-T1
Valid prediction for HiQ_model.g34183.t1
Valid prediction for snap_scaffold_22-snap.1522-T1
Valid prediction for Augustus_model.g34186.t1
Valid prediction for GlimmerHMM_glimmerT_50988-T1
Valid prediction for snap_scaffold_22-snap.1520-T1
Valid prediction for GlimmerHMM_glimmerT_50991-T1
Valid prediction for GeneMark_model.88349_t
Valid prediction for snap_scaffold_22-snap.1524-T1
Valid prediction for GeneMark_model.88346_t
Valid prediction for HiQ_model.g34184.t1
Couldn't classify 114466, 114576
Sorry, prediction pasa_asmbl_29754.p1 fails validation.
(TCC)	 TC	114466-114576	GT	AGG
(CTG)	 AG	114898-114970	GT	AGG
(GGG)	 AG	115505-115642	GT	GGG
(ATC)	 AG	115903-116077	GT	AGG
(TTG)	 AG	116556-116616	GT	GGG
(CAT)	 AG	116750-116827	GT	AGG
(GTC)	 AG	117029-117132	GT	AGG
(GCT)	 AG	117398-117557	CC	AGC
-recovered pasa_asmbl_29754.p1, terminal, 117398, 117557
-recovered pasa_asmbl_29754.p1, internal, 114898, 114970
-recovered pasa_asmbl_29754.p1, internal, 115505, 115642
-recovered pasa_asmbl_29754.p1, internal, 115903, 116077
-recovered pasa_asmbl_29754.p1, internal, 116556, 116616
-recovered pasa_asmbl_29754.p1, internal, 116750, 116827
-recovered pasa_asmbl_29754.p1, internal, 117029, 117132

-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 CodingQuarry_transcript_34153-T1
Valid prediction for GlimmerHMM_glimmerT_50982-T1
Valid prediction for GeneMark_model.88354_t
Valid prediction for GeneMark_model.88329_t
Valid prediction for snap_scaffold_22-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_50984-T1
Valid prediction for GlimmerHMM_glimmerT_50968-T1
Valid prediction for Augustus_model.g34181.t1
Valid prediction for GlimmerHMM_glimmerT_50973-T1
Valid prediction for Augustus_model.g34179.t1
Valid prediction for GlimmerHMM_glimmerT_50972-T1
Valid prediction for snap_scaffold_22-snap.1516-T1
Valid prediction for snap_scaffold_22-snap.1537-T1
Valid prediction for snap_scaffold_22-snap.1532-T1
Valid prediction for GeneMark_model.88350_t
Couldn't classify 55881, 55900
Sorry, prediction pasa_asmbl_30175.p1 fails validation.
(ATG)	 AG	54333-54479	GT	GGG
(ACG)	 AG	54687-54801	GT	TAG
(CCT)	 AG	55224-55296	GT	AGG
(AGA)	 AG	55549-55640	GT	GGG
(AGT)	 AG	55881-55900	CC	GTC
-recovered pasa_asmbl_30175.p1, initial, 54333, 54479
-recovered pasa_asmbl_30175.p1, internal, 54333, 54479
-recovered pasa_asmbl_30175.p1, internal, 54687, 54801
-recovered pasa_asmbl_30175.p1, internal, 55224, 55296
-recovered pasa_asmbl_30175.p1, internal, 55549, 55640
Valid prediction for GeneMark_model.88339_t
Valid prediction for Augustus_model.g34185.t1
Valid prediction for snap_scaffold_22-snap.1517-T1
Valid prediction for snap_scaffold_22-snap.1530-T1
Valid prediction for Augustus_model.g34182.t1
Valid prediction for Augustus_model.g34189.t1
Valid prediction for snap_scaffold_22-snap.1540-T1
Valid prediction for snap_scaffold_22-snap.1535-T1
Valid prediction for snap_scaffold_22-snap.1521-T1
Valid prediction for GlimmerHMM_glimmerT_50981-T1
Valid prediction for GeneMark_model.88356_t
Valid prediction for GeneMark_model.88347_t
Valid prediction for GlimmerHMM_glimmerT_50970-T1
Valid prediction for GeneMark_model.88331_t
Valid prediction for GeneMark_model.88343_t
Valid prediction for Augustus_model.g34180.t1
Valid prediction for snap_scaffold_22-snap.1508-T1
Valid prediction for GeneMark_model.88335_t
Valid prediction for snap_scaffold_22-snap.1533-T1
Valid prediction for GlimmerHMM_glimmerT_50990-T1
Valid prediction for Augustus_model.g34190.t1
Valid prediction for snap_scaffold_22-snap.1514-T1
Valid prediction for Augustus_model.g34188.t1
Valid prediction for GeneMark_model.88358_t
Valid prediction for GeneMark_model.88333_t
Valid prediction for GlimmerHMM_glimmerT_50976-T1
Valid prediction for GeneMark_model.88345_t
Valid prediction for GlimmerHMM_glimmerT_50983-T1
Valid prediction for GlimmerHMM_glimmerT_50986-T1
Couldn't classify 94417, 94509
Sorry, prediction pasa_asmbl_30173.p1 fails validation.
(ATG)	 CA	93309-93400	GT	AGG
(GAT)	 AG	93632-93859	GT	AGG
(TTC)	 AG	93984-94087	GT	AGG
(GTG)	 AG	94162-94298	GT	AGG
(GTT)	 AG	94417-94509	TT	CCT
-recovered pasa_asmbl_30173.p1, initial, 93309, 93400
-recovered pasa_asmbl_30173.p1, internal, 93632, 93859
-recovered pasa_asmbl_30173.p1, internal, 93984, 94087
-recovered pasa_asmbl_30173.p1, internal, 94162, 94298
Valid prediction for snap_scaffold_22-snap.1526-T1
Valid prediction for GeneMark_model.88337_t
Couldn't classify 109593, 109754
Couldn't classify 114926, 115071
Sorry, prediction pasa_asmbl_30503.p1 fails validation.
(GGA)	 CA	109593-109754	GT	AGG
(ATT)	 AG	110696-110795	GT	AGG
(GTG)	 AG	111166-111353	GT	AGG
(GGC)	 AG	111566-111688	GT	AGG
(ATC)	 AG	111927-112133	GT	AGG
(GTC)	 AG	112309-112389	GT	AGG
(GTG)	 AG	112777-113029	GT	CGG
(GAA)	 AG	113518-113810	GT	AGG
(GTC)	 AG	114002-114188	GT	GGG
(GCG)	 AG	114926-115071	CA	CGC
-recovered pasa_asmbl_30503.p1, internal, 110696, 110795
-recovered pasa_asmbl_30503.p1, internal, 111166, 111353
-recovered pasa_asmbl_30503.p1, internal, 111566, 111688
-recovered pasa_asmbl_30503.p1, internal, 111927, 112133
-recovered pasa_asmbl_30503.p1, internal, 112309, 112389
-recovered pasa_asmbl_30503.p1, internal, 112777, 113029
-recovered pasa_asmbl_30503.p1, internal, 113518, 113810
-recovered pasa_asmbl_30503.p1, internal, 114002, 114188
Valid prediction for GeneMark_model.88352_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15959, rend_intergenic: 4882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20363, rend_intergenic: 16131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29513, rend_intergenic: 23016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45046, rend_intergenic: 43235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78005, rend_intergenic: 67578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92226, rend_intergenic: 83002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97160, rend_intergenic: 96468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98817, rend_intergenic: 98417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101732, rend_intergenic: 99219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107559, rend_intergenic: 105477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118141, rend_intergenic: 111947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 129386
-exon list size: 569


building trellis

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99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 15959, rend_intergenic: 4882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20363, rend_intergenic: 16131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29513, rend_intergenic: 23016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45046, rend_intergenic: 43235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78005, rend_intergenic: 67578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92226, rend_intergenic: 83002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97160, rend_intergenic: 96468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98817, rend_intergenic: 98417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101732, rend_intergenic: 99219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107559, rend_intergenic: 105477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118141, rend_intergenic: 111947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support