-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_5477802-5678525

-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 pasa_asmbl_10864.p1
Valid prediction for pasa_asmbl_10854.p1
Couldn't classify 107477, 109096
Sorry, prediction pasa_asmbl_10877.p1 fails validation.
(TCC)	 GT	107477-109096	AA	AAA
Valid prediction for GlimmerHMM_glimmerT_31685-T1
Valid prediction for CodingQuarry_transcript_13036-T1
Valid prediction for snap_scaffold_13-snap.1041-T1
Couldn't classify 116659, 117465
Sorry, prediction pasa_asmbl_10882.p1 fails validation.
(GAC)	 GA	116659-117465	AT	AAA
Valid prediction for GlimmerHMM_glimmerT_31675-T1
Valid prediction for HiQ_model.g21072.t1
Valid prediction for snap_scaffold_13-snap.1044-T1
Valid prediction for snap_scaffold_13-snap.1068-T1
Valid prediction for snap_scaffold_13-snap.1064-T1
Valid prediction for GlimmerHMM_glimmerT_31679-T1
Valid prediction for pasa_asmbl_10869.p1
Couldn't classify 109860, 110097
Sorry, prediction pasa_asmbl_10878.p1 fails validation.
(CAA)	 CT	109860-110097	GT	AGG
(GTA)	 AG	110248-111236	GG	AAG
-recovered pasa_asmbl_10878.p1, terminal, 110248, 111236
Valid prediction for CodingQuarry_transcript_13033-T1
Valid prediction for Augustus_model.g21090.t1
Valid prediction for Augustus_model.g21081.t1
Valid prediction for HiQ_model.g21080.t1
Valid prediction for GlimmerHMM_glimmerT_31690-T1
Valid prediction for snap_scaffold_13-snap.1059-T1
Valid prediction for Augustus_model.g21070.t1
Couldn't classify 68940, 69018
Sorry, prediction pasa_asmbl_10871.p1 fails validation.
(CCC)	 TT	68940-69018	GT	AAG
(GTG)	 AG	69669-69770	GT	GTG
(CAT)	 AG	69875-69998	GT	AGG
(GCC)	 AG	70134-70255	GT	AGG
(GTG)	 AG	70374-70519	GT	AGG
(TGC)	 AG	70706-70847	GT	AGG
(TGA)	 AG	71003-71115	GT	GGG
(CTG)	 AG	71406-71558	GT	GGG
(GAA)	 AG	71761-71865	GT	AGG
(GTA)	 AG	72146-72223	GC	AGG
(GTG)	 AG	72339-72508	GT	AAG
(ATA)	 AG	72618-72720	GT	AGG
(GCT)	 AG	72912-73010	GT	TGG
(GTC)	 AG	73329-73416	GT	GAG
(AAT)	 AG	73736-73905	GT	AGG
(CTC)	 AG	74062-74274	GT	AGG
(ATG)	 AG	74463-74585	TG	GAT
add_exon() Sorry, pasa_asmbl_10871.p1 73329-73416-terminal-3 is invalid.
-recovered pasa_asmbl_10871.p1, terminal, 73329, 73416
-recovered pasa_asmbl_10871.p1, terminal, 74463, 74585
-recovered pasa_asmbl_10871.p1, internal, 69669, 69770
-recovered pasa_asmbl_10871.p1, internal, 69875, 69998
-recovered pasa_asmbl_10871.p1, internal, 70134, 70255
-recovered pasa_asmbl_10871.p1, internal, 70374, 70519
-recovered pasa_asmbl_10871.p1, internal, 70706, 70847
-recovered pasa_asmbl_10871.p1, internal, 71003, 71115
-recovered pasa_asmbl_10871.p1, internal, 71406, 71558
-recovered pasa_asmbl_10871.p1, internal, 71761, 71865
-recovered pasa_asmbl_10871.p1, internal, 72146, 72223
-recovered pasa_asmbl_10871.p1, internal, 72339, 72508
-recovered pasa_asmbl_10871.p1, internal, 72618, 72720
-recovered pasa_asmbl_10871.p1, internal, 72912, 73010
-recovered pasa_asmbl_10871.p1, internal, 73329, 73416
-recovered pasa_asmbl_10871.p1, internal, 73736, 73905
-recovered pasa_asmbl_10871.p1, internal, 74062, 74274
Valid prediction for Augustus_model.g21083.t1
Valid prediction for snap_scaffold_13-snap.1048-T1
Valid prediction for snap_scaffold_13-snap.1069-T1
Valid prediction for snap_scaffold_13-snap.1065-T1
Valid prediction for snap_scaffold_13-snap.1063-T1
Valid prediction for CodingQuarry_transcript_13038-T1
Valid prediction for GlimmerHMM_glimmerT_31684-T1
Valid prediction for GlimmerHMM_glimmerT_31693-T1
Couldn't classify 35141, 35252
Couldn't classify 37579, 37761
Sorry, prediction pasa_asmbl_10859.p1 fails validation.
(CCG)	 CG	35141-35252	GT	TGG
(ACA)	 AG	36366-36526	GT	AGG
(GTG)	 AG	36776-37279	GT	AGG
(ATG)	 AG	37579-37761	AG	TCA
-recovered pasa_asmbl_10859.p1, internal, 36366, 36526
-recovered pasa_asmbl_10859.p1, internal, 36776, 37279
Couldn't classify 81042, 81060
Couldn't classify 81852, 81993
Sorry, prediction pasa_asmbl_11646.p1 fails validation.
(AAG)	 TC	81042-81060	GT	TGG
(AAA)	 AG	81371-81506	GT	AGG
(GCT)	 AG	81852-81993	GC	GGG
-recovered pasa_asmbl_11646.p1, internal, 81371, 81506
-recovered pasa_asmbl_11646.p1, internal, 81852, 81993
Valid prediction for snap_scaffold_13-snap.1058-T1
Valid prediction for GlimmerHMM_glimmerT_31674-T1
Valid prediction for GlimmerHMM_glimmerT_31682-T1
Valid prediction for Augustus_model.g21069.t1
Valid prediction for snap_scaffold_13-snap.1062-T1
Valid prediction for snap_scaffold_13-snap.1039-T1
Couldn't classify 38201, 38385
Couldn't classify 40055, 40089
Sorry, prediction pasa_asmbl_10861.p1 fails validation.
(CTC)	 CC	38201-38385	GT	AGG
(GGT)	 AG	38577-38678	GT	CTG
(TAT)	 AG	38865-39052	GT	CTG
(CTC)	 AG	39230-39370	GT	AGG
(ATG)	 AG	39504-39559	GT	AGG
(GGT)	 AG	39758-39884	GT	CAG
(TCA)	 AG	40055-40089	CC	ACC
-recovered pasa_asmbl_10861.p1, initial, 39504, 39559
-recovered pasa_asmbl_10861.p1, internal, 38577, 38678
-recovered pasa_asmbl_10861.p1, internal, 38865, 39052
-recovered pasa_asmbl_10861.p1, internal, 39230, 39370
-recovered pasa_asmbl_10861.p1, internal, 39504, 39559
-recovered pasa_asmbl_10861.p1, internal, 39758, 39884
Valid prediction for GlimmerHMM_glimmerT_31694-T1
Valid prediction for snap_scaffold_13-snap.1038-T1
Valid prediction for snap_scaffold_13-snap.1073-T1
Valid prediction for snap_scaffold_13-snap.1049-T1
Valid prediction for HiQ_model.g21075.t1
Valid prediction for GlimmerHMM_glimmerT_31700-T1
Valid prediction for GlimmerHMM_glimmerT_31686-T1
Valid prediction for GlimmerHMM_glimmerT_31683-T1
Valid prediction for Augustus_model.g21089.t1
Couldn't classify 115392, 115449
Couldn't classify 116260, 116508
Sorry, prediction pasa_asmbl_11683.p1 fails validation.
(TTG)	 AA	115392-115449	GT	TGG
(TAG)	 AG	115844-115941	GT	AGG
(CCT)	 AG	116260-116508	AG	CGA
-recovered pasa_asmbl_11683.p1, internal, 115844, 115941
Valid prediction for snap_scaffold_13-snap.1072-T1
Valid prediction for snap_scaffold_13-snap.1056-T1
Valid prediction for Augustus_model.g21087.t1
Valid prediction for GlimmerHMM_glimmerT_31698-T1
Valid prediction for Augustus_model.g21086.t1
Valid prediction for HiQ_model.g21078.t1
Valid prediction for GlimmerHMM_glimmerT_31696-T1
Valid prediction for HiQ_model.g21082.t1
Valid prediction for snap_scaffold_13-snap.1060-T1
Valid prediction for snap_scaffold_13-snap.1051-T1
Valid prediction for GlimmerHMM_glimmerT_31677-T1
Couldn't classify 113791, 114479
Sorry, prediction pasa_asmbl_10880.p1 fails validation.
(ATG)	 GA	113075-113549	GT	TGG
(GCA)	 AG	113791-114479	TC	CCT
-recovered pasa_asmbl_10880.p1, initial, 113075, 113549
Valid prediction for snap_scaffold_13-snap.1047-T1
Valid prediction for HiQ_model.g21079.t1
Valid prediction for Augustus_model.g21092.t1
Valid prediction for CodingQuarry_transcript_13039-T1
Couldn't classify 84860, 84989
Sorry, prediction pasa_asmbl_10875.p1 fails validation.
(TCA)	 GA	84860-84989	GT	TGG
(AAG)	 AG	85186-85277	GT	GGG
(ATG)	 AG	85418-85456	GT	AGG
(AAA)	 AG	85998-86030	GT	ATG
(GGA)	 AG	86174-86245	GA	GAG
-recovered pasa_asmbl_10875.p1, initial, 85418, 85456
-recovered pasa_asmbl_10875.p1, terminal, 86174, 86245
-recovered pasa_asmbl_10875.p1, internal, 85186, 85277
-recovered pasa_asmbl_10875.p1, internal, 85418, 85456
-recovered pasa_asmbl_10875.p1, internal, 85998, 86030
Valid prediction for snap_scaffold_13-snap.1052-T1
Valid prediction for GlimmerHMM_glimmerT_31687-T1
Valid prediction for GlimmerHMM_glimmerT_31691-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 CodingQuarry_transcript_13042-T1
Valid prediction for snap_scaffold_13-snap.1061-T1
Valid prediction for HiQ_model.g21088.t1
Valid prediction for CodingQuarry_transcript_13034-T1
Valid prediction for pasa_asmbl_9701.p1
Valid prediction for snap_scaffold_13-snap.1066-T1
Valid prediction for Augustus_model.g21091.t1
Valid prediction for Augustus_model.g21077.t1
Valid prediction for GlimmerHMM_glimmerT_31695-T1
Valid prediction for CodingQuarry_transcript_13041-T1
Valid prediction for snap_scaffold_13-snap.1054-T1
Valid prediction for snap_scaffold_13-snap.1055-T1
Valid prediction for HiQ_model.g21073.t1
Valid prediction for Augustus_model.g21076.t1
Valid prediction for snap_scaffold_13-snap.1057-T1
Valid prediction for snap_scaffold_13-snap.1046-T1
Valid prediction for HiQ_model.g21085.t1
Valid prediction for GlimmerHMM_glimmerT_31697-T1
Valid prediction for snap_scaffold_13-snap.1074-T1
Valid prediction for snap_scaffold_13-snap.1045-T1
Valid prediction for Augustus_model.g21093.t1
Valid prediction for pasa_asmbl_9694.p1
Valid prediction for snap_scaffold_13-snap.1040-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g21074.t1
Valid prediction for GlimmerHMM_glimmerT_31688-T1
Valid prediction for Augustus_model.g21094.t1
Valid prediction for GlimmerHMM_glimmerT_31676-T1
Valid prediction for Augustus_model.g21071.t1
Valid prediction for GlimmerHMM_glimmerT_31681-T1
Valid prediction for CodingQuarry_transcript_13040-T1
Valid prediction for snap_scaffold_13-snap.1043-T1
Valid prediction for HiQ_model.g21084.t1
Valid prediction for snap_scaffold_13-snap.1067-T1
Valid prediction for GlimmerHMM_glimmerT_31680-T1
Valid prediction for snap_scaffold_13-snap.1053-T1
Valid prediction for pasa_asmbl_10365.p1
Valid prediction for Augustus_model.g21068.t1
Valid prediction for snap_scaffold_13-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_31678-T1
Valid prediction for GlimmerHMM_glimmerT_31692-T1
Valid prediction for snap_scaffold_13-snap.1037-T1
Valid prediction for snap_scaffold_13-snap.1050-T1
Couldn't classify 181673, 181812
Couldn't classify 182182, 182316
Sorry, prediction pasa_asmbl_10428.p1 fails validation.
(GGC)	 AA	181673-181812	GT	GGG
(GCT)	 AG	181951-182014	GT	AGG
(GCG)	 AG	182182-182316	GT	AGG
-recovered pasa_asmbl_10428.p1, internal, 181951, 182014
-recovered pasa_asmbl_10428.p1, internal, 182182, 182316
Valid prediction for GlimmerHMM_glimmerT_31673-T1
Valid prediction for snap_scaffold_13-snap.1070-T1
Valid prediction for GlimmerHMM_glimmerT_31699-T1
Valid prediction for snap_scaffold_13-snap.1042-T1
Valid prediction for pasa_asmbl_9698.p1
Valid prediction for GlimmerHMM_glimmerT_31689-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17002, rend_intergenic: 16423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94781, rend_intergenic: 90605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109096, rend_intergenic: 105552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152341, rend_intergenic: 150694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175794, rend_intergenic: 154538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194869, rend_intergenic: 183874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198010, rend_intergenic: 195295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200724
-exon list size: 456


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 17002, rend_intergenic: 16423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94781, rend_intergenic: 90605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109096, rend_intergenic: 105552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152341, rend_intergenic: 150694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175794, rend_intergenic: 154538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194869, rend_intergenic: 183874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198010, rend_intergenic: 195295  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