-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_4362567-4583236

-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_11-snap.1111-T1
Valid prediction for Augustus_model.g17858.t1
Couldn't classify 18881, 18955
Couldn't classify 19852, 19920
Sorry, prediction pasa_asmbl_5473.p1 fails validation.
(GCC)	 TC	18881-18955	GT	AGG
(GGT)	 AG	19104-19232	GT	AGG
(CTG)	 AG	19424-19555	GT	AGG
(GGC)	 AG	19852-19920	AT	AGA
-recovered pasa_asmbl_5473.p1, internal, 19104, 19232
-recovered pasa_asmbl_5473.p1, internal, 19424, 19555
Valid prediction for GlimmerHMM_glimmerT_27002-T1
Valid prediction for snap_scaffold_11-snap.1100-T1
Valid prediction for snap_scaffold_11-snap.1091-T1
Valid prediction for snap_scaffold_11-snap.1075-T1
Valid prediction for HiQ_model.g17846.t1
Valid prediction for snap_scaffold_11-snap.1073-T1
Valid prediction for snap_scaffold_11-snap.1080-T1
Valid prediction for snap_scaffold_11-snap.1095-T1
Valid prediction for GlimmerHMM_glimmerT_26989-T1
Couldn't classify 25547, 25662
Couldn't classify 26067, 26267
Sorry, prediction pasa_asmbl_6307.p2 fails validation.
(GTG)	 AG	25547-25662	GT	AGG
(CGA)	 AG	25787-25928	GT	AGG
(GTC)	 AG	26067-26267	GG	CCG
-recovered pasa_asmbl_6307.p2, internal, 25547, 25662
-recovered pasa_asmbl_6307.p2, internal, 25787, 25928
Valid prediction for snap_scaffold_11-snap.1085-T1
Valid prediction for Augustus_model.g17853.t1
Valid prediction for HiQ_model.g17854.t1
Valid prediction for snap_scaffold_11-snap.1106-T1
Valid prediction for Augustus_model.g17848.t1
Valid prediction for snap_scaffold_11-snap.1096-T1
Valid prediction for Augustus_model.g17850.t1
Valid prediction for snap_scaffold_11-snap.1090-T1
Valid prediction for snap_scaffold_11-snap.1069-T1
Couldn't classify 66301, 66385
Sorry, prediction pasa_asmbl_5484.p1 fails validation.
(ATG)	 TC	62241-62470	GT	AGG
(GTA)	 AG	64840-65016	GT	AGG
(GTT)	 AG	66301-66385	AG	AGA
-recovered pasa_asmbl_5484.p1, initial, 62241, 62470
-recovered pasa_asmbl_5484.p1, internal, 64840, 65016
Valid prediction for snap_scaffold_11-snap.1092-T1
Valid prediction for snap_scaffold_11-snap.1098-T1
Valid prediction for GlimmerHMM_glimmerT_27000-T1
Valid prediction for GlimmerHMM_glimmerT_26998-T1
Valid prediction for GlimmerHMM_glimmerT_26994-T1
Couldn't classify 20390, 20605
Couldn't classify 21301, 21515
Sorry, prediction pasa_asmbl_5474.p1 fails validation.
(CGG)	 GG	20390-20605	GT	AGG
(GTG)	 AG	20863-20995	GT	CGG
(TGT)	 AG	21301-21515	CA	CCC
-recovered pasa_asmbl_5474.p1, internal, 20863, 20995
Valid prediction for GlimmerHMM_glimmerT_26992-T1
Valid prediction for snap_scaffold_11-snap.1067-T1
Couldn't classify 54620, 54759
Couldn't classify 58035, 58057
Sorry, prediction pasa_asmbl_5482.p1 fails validation.
(CAC)	 CC	54620-54759	GT	AGG
(CAA)	 AG	55157-55208	GT	AGG
(ATC)	 AG	55395-55499	GT	TGG
(GAC)	 AG	55749-55913	GT	AGG
(AAA)	 AG	56009-56089	GT	AGG
(CTG)	 AG	56293-56367	GT	AGG
(GGT)	 AG	56518-56610	GT	AGG
(GTG)	 AG	56860-57000	GT	AGG
(AAG)	 AG	57215-57398	GT	AGG
(AGT)	 AG	58035-58057	GA	ACG
add_exon() Sorry, pasa_asmbl_5482.p1 57215-57398-terminal-3 is invalid.
-recovered pasa_asmbl_5482.p1, terminal, 57215, 57398
-recovered pasa_asmbl_5482.p1, internal, 55157, 55208
-recovered pasa_asmbl_5482.p1, internal, 55395, 55499
-recovered pasa_asmbl_5482.p1, internal, 55749, 55913
-recovered pasa_asmbl_5482.p1, internal, 56009, 56089
-recovered pasa_asmbl_5482.p1, internal, 56293, 56367
-recovered pasa_asmbl_5482.p1, internal, 56518, 56610
-recovered pasa_asmbl_5482.p1, internal, 56860, 57000
-recovered pasa_asmbl_5482.p1, internal, 57215, 57398
Valid prediction for snap_scaffold_11-snap.1102-T1
Couldn't classify 46388, 46435
Sorry, prediction pasa_asmbl_5480.p1 fails validation.
(CCG)	 AC	46388-46435	GT	AGG
(GTG)	 AG	46639-46743	GT	AGG
(CCT)	 AG	46959-47162	GT	AGG
(ATC)	 AG	47310-47387	GT	AGG
(GTG)	 AG	47477-47534	GT	AGG
(CCA)	 AG	47650-47915	GT	AGG
(GAG)	 AG	48175-48216	GC	GAG
-recovered pasa_asmbl_5480.p1, terminal, 48175, 48216
-recovered pasa_asmbl_5480.p1, internal, 46639, 46743
-recovered pasa_asmbl_5480.p1, internal, 46959, 47162
-recovered pasa_asmbl_5480.p1, internal, 47310, 47387
-recovered pasa_asmbl_5480.p1, internal, 47477, 47534
-recovered pasa_asmbl_5480.p1, internal, 47650, 47915
-recovered pasa_asmbl_5480.p1, internal, 48175, 48216
Valid prediction for snap_scaffold_11-snap.1108-T1
Valid prediction for Augustus_model.g17860.t1
Valid prediction for GlimmerHMM_glimmerT_26997-T1
Valid prediction for pasa_asmbl_5472.p1
Valid prediction for snap_scaffold_11-snap.1077-T1
Valid prediction for snap_scaffold_11-snap.1086-T1
Valid prediction for snap_scaffold_11-snap.1082-T1
Valid prediction for GlimmerHMM_glimmerT_27001-T1
Valid prediction for GlimmerHMM_glimmerT_26987-T1
Valid prediction for snap_scaffold_11-snap.1109-T1
Valid prediction for Augustus_model.g17855.t1
Couldn't classify 22956, 23357
Couldn't classify 24080, 24180
Sorry, prediction pasa_asmbl_5475.p1 fails validation.
(CCA)	 CT	22956-23357	GT	AGG
(CTG)	 AG	23530-23713	GT	AGG
(GCT)	 AG	24080-24180	AC	AGA
-recovered pasa_asmbl_5475.p1, internal, 23530, 23713
Valid prediction for snap_scaffold_11-snap.1076-T1
Valid prediction for GlimmerHMM_glimmerT_26996-T1
Valid prediction for GlimmerHMM_glimmerT_26985-T1
Valid prediction for GlimmerHMM_glimmerT_26983-T1
Valid prediction for GlimmerHMM_glimmerT_26999-T1
Valid prediction for snap_scaffold_11-snap.1112-T1
Valid prediction for snap_scaffold_11-snap.1083-T1
Couldn't classify 34120, 34263
Sorry, prediction pasa_asmbl_5476.p1 fails validation.
(GTC)	 AC	34120-34263	GT	AGG
(CCA)	 AG	34453-34594	GT	AGG
(GCC)	 AG	34901-35050	GT	CGG
(TGA)	 AG	35721-35872	AC	AAA
-recovered pasa_asmbl_5476.p1, terminal, 35721, 35872
-recovered pasa_asmbl_5476.p1, internal, 34453, 34594
-recovered pasa_asmbl_5476.p1, internal, 34901, 35050
Valid prediction for snap_scaffold_11-snap.1065-T1
Valid prediction for CodingQuarry_transcript_8039-T1
Valid prediction for GlimmerHMM_glimmerT_26993-T1
Valid prediction for snap_scaffold_11-snap.1104-T1
Valid prediction for Augustus_model.g17857.t1
Couldn't classify 45509, 45637
Sorry, prediction pasa_asmbl_5479.p1 fails validation.
(ATG)	 AG	44227-44383	GT	TGG
(GTG)	 AG	44486-44545	GT	TGG
(AGG)	 AG	45081-45161	GT	ACG
(TTG)	 AG	45286-45338	GT	AGG
(GCG)	 AG	45509-45637	CA	TCC
-recovered pasa_asmbl_5479.p1, initial, 44227, 44383
-recovered pasa_asmbl_5479.p1, internal, 44227, 44383
-recovered pasa_asmbl_5479.p1, internal, 44486, 44545
-recovered pasa_asmbl_5479.p1, internal, 45081, 45161
-recovered pasa_asmbl_5479.p1, internal, 45286, 45338
Valid prediction for snap_scaffold_11-snap.1070-T1
Couldn't classify 69226, 69615
Sorry, prediction pasa_asmbl_5485.p1 fails validation.
(CGC)	 TG	69226-69615	GT	AGG
(GTG)	 AG	71157-71321	GT	AGG
(GAG)	 AG	72229-72786	TC	AGT
-recovered pasa_asmbl_5485.p1, terminal, 72229, 72786
-recovered pasa_asmbl_5485.p1, internal, 71157, 71321
Valid prediction for GlimmerHMM_glimmerT_27005-T1
Valid prediction for snap_scaffold_11-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_26986-T1
Valid prediction for Augustus_model.g17849.t1
Valid prediction for snap_scaffold_11-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_26995-T1
Valid prediction for Augustus_model.g17859.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_11-snap.1071-T1
Valid prediction for snap_scaffold_11-snap.1101-T1
Valid prediction for snap_scaffold_11-snap.1094-T1
Valid prediction for pasa_asmbl_6602.p1
Valid prediction for snap_scaffold_11-snap.1107-T1
Valid prediction for snap_scaffold_11-snap.1078-T1
Valid prediction for snap_scaffold_11-snap.1103-T1
Valid prediction for Augustus_model.g17856.t1
Valid prediction for snap_scaffold_11-snap.1093-T1
Valid prediction for GlimmerHMM_glimmerT_27004-T1
Valid prediction for snap_scaffold_11-snap.1068-T1
Valid prediction for snap_scaffold_11-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_26991-T1
Valid prediction for snap_scaffold_11-snap.1097-T1
Valid prediction for snap_scaffold_11-snap.1110-T1
Valid prediction for GlimmerHMM_glimmerT_26988-T1
Valid prediction for snap_scaffold_11-snap.1081-T1
Valid prediction for GlimmerHMM_glimmerT_27003-T1
Valid prediction for snap_scaffold_11-snap.1084-T1
Valid prediction for HiQ_model.g17847.t1
Valid prediction for snap_scaffold_11-snap.1105-T1
Valid prediction for GlimmerHMM_glimmerT_26982-T1
Valid prediction for snap_scaffold_11-snap.1087-T1
Valid prediction for snap_scaffold_11-snap.1079-T1
Valid prediction for Augustus_model.g17852.t1
Valid prediction for Augustus_model.g17861.t1
Valid prediction for snap_scaffold_11-snap.1072-T1
Valid prediction for snap_scaffold_11-snap.1088-T1
Valid prediction for Augustus_model.g17845.t1
Valid prediction for GlimmerHMM_glimmerT_26984-T1
Valid prediction for GlimmerHMM_glimmerT_26990-T1
Valid prediction for Augustus_model.g17851.t1
Valid prediction for snap_scaffold_11-snap.1099-T1
Valid prediction for snap_scaffold_11-snap.1089-T1
Valid prediction for snap_scaffold_11-snap.1074-T1
Valid prediction for GlimmerHMM_glimmerT_27006-T1
Valid prediction for GlimmerHMM_glimmerT_27007-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9370, rend_intergenic: 4570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27178, rend_intergenic: 24120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38242, rend_intergenic: 30524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58597, rend_intergenic: 51707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66981, rend_intergenic: 63936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67846, rend_intergenic: 67570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87389, rend_intergenic: 78718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110926, rend_intergenic: 98592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149173, rend_intergenic: 140802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157239, rend_intergenic: 154035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160640, rend_intergenic: 157249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164312, rend_intergenic: 162469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175236, rend_intergenic: 170971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183897, rend_intergenic: 180555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187388, rend_intergenic: 185494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213780, rend_intergenic: 202648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220670
-exon list size: 476


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 9370, rend_intergenic: 4570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27178, rend_intergenic: 24120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38242, rend_intergenic: 30524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58597, rend_intergenic: 51707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66981, rend_intergenic: 63936  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67846, rend_intergenic: 67570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87389, rend_intergenic: 78718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110926, rend_intergenic: 98592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149173, rend_intergenic: 140802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157239, rend_intergenic: 154035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160640, rend_intergenic: 157249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164312, rend_intergenic: 162469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175236, rend_intergenic: 170971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183897, rend_intergenic: 180555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187388, rend_intergenic: 185494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213780, rend_intergenic: 202648  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