-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_7973397-8168953

-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_23-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_51407-T1
Valid prediction for CodingQuarry_transcript_35757-T1
Valid prediction for snap_scaffold_23-snap.1527-T1
Valid prediction for Augustus_model.g34383.t1
Valid prediction for Augustus_model.g34398.t1
Valid prediction for Augustus_model.g34393.t1
Valid prediction for GlimmerHMM_glimmerT_51409-T1
Valid prediction for snap_scaffold_23-snap.1495-T1
Valid prediction for pasa_asmbl_31750.p1
Valid prediction for GlimmerHMM_glimmerT_51421-T1
Valid prediction for snap_scaffold_23-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_51394-T1
Valid prediction for Augustus_model.g34391.t1
Valid prediction for pasa_asmbl_31759.p1
Valid prediction for snap_scaffold_23-snap.1524-T1
Valid prediction for Augustus_model.g34394.t1
Valid prediction for snap_scaffold_23-snap.1516-T1
Valid prediction for snap_scaffold_23-snap.1493-T1
Valid prediction for HiQ_model.g34379.t1
Valid prediction for CodingQuarry_transcript_35758-T1
Valid prediction for snap_scaffold_23-snap.1505-T1
Valid prediction for GlimmerHMM_glimmerT_51405-T1
Valid prediction for snap_scaffold_23-snap.1502-T1
Valid prediction for snap_scaffold_23-snap.1519-T1
Valid prediction for snap_scaffold_23-snap.1490-T1
Valid prediction for GlimmerHMM_glimmerT_51392-T1
Valid prediction for snap_scaffold_23-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_51400-T1
Valid prediction for snap_scaffold_23-snap.1513-T1
Valid prediction for CodingQuarry_transcript_35751-T1
Couldn't classify 105942, 106078
Sorry, prediction pasa_asmbl_31943.p1 fails validation.
(GTG)	 CT	105942-106078	GT	AGG
(GCC)	 AG	106381-106551	GT	TGG
(TCA)	 AG	106701-106791	GT	CCG
(GTG)	 AG	106999-107240	GT	AGG
(GTG)	 AG	107528-107680	GT	AGG
(AGT)	 AG	107903-108016	GT	CGG
(AAC)	 AG	108240-108334	GT	AGG
(ACA)	 AG	108537-108610	GT	GGG
(GAC)	 AG	108740-108829	GT	AGG
(ACG)	 AG	109176-109281	GT	CAG
(TTC)	 AG	109363-109466	GT	AAG
(AAG)	 AG	109632-109715	TC	AGT
-recovered pasa_asmbl_31943.p1, terminal, 109632, 109715
-recovered pasa_asmbl_31943.p1, internal, 106381, 106551
-recovered pasa_asmbl_31943.p1, internal, 106701, 106791
-recovered pasa_asmbl_31943.p1, internal, 106999, 107240
-recovered pasa_asmbl_31943.p1, internal, 107528, 107680
-recovered pasa_asmbl_31943.p1, internal, 107903, 108016
-recovered pasa_asmbl_31943.p1, internal, 108240, 108334
-recovered pasa_asmbl_31943.p1, internal, 108537, 108610
-recovered pasa_asmbl_31943.p1, internal, 108740, 108829
-recovered pasa_asmbl_31943.p1, internal, 109176, 109281
-recovered pasa_asmbl_31943.p1, internal, 109363, 109466
Valid prediction for GlimmerHMM_glimmerT_51396-T1
Valid prediction for CodingQuarry_transcript_35752-T1
Valid prediction for GlimmerHMM_glimmerT_51395-T1
Valid prediction for GlimmerHMM_glimmerT_51420-T1
Valid prediction for pasa_asmbl_31754.p1
Valid prediction for snap_scaffold_23-snap.1507-T1
Valid prediction for snap_scaffold_23-snap.1514-T1
Valid prediction for CodingQuarry_transcript_35750-T1
Valid prediction for GlimmerHMM_glimmerT_51416-T1
Valid prediction for Augustus_model.g34384.t1
Valid prediction for snap_scaffold_23-snap.1521-T1
Valid prediction for snap_scaffold_23-snap.1506-T1
Valid prediction for Augustus_model.g34401.t1
Valid prediction for snap_scaffold_23-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_51410-T1
Valid prediction for HiQ_model.g34395.t1
Couldn't classify 85638, 85687
Couldn't classify 86190, 86306
Sorry, prediction pasa_asmbl_31920.p1 fails validation.
(CTC)	 CA	85638-85687	GT	TTG
(CTA)	 AG	85791-85941	GT	AGG
(GTG)	 AG	86190-86306	CA	AGC
-recovered pasa_asmbl_31920.p1, internal, 85791, 85941
Valid prediction for Augustus_model.g34385.t1
Valid prediction for GlimmerHMM_glimmerT_51413-T1
Valid prediction for CodingQuarry_transcript_35749-T1
Valid prediction for Augustus_model.g34389.t1
Valid prediction for pasa_asmbl_31753.p1
Valid prediction for snap_scaffold_23-snap.1523-T1
Valid prediction for snap_scaffold_23-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_51411-T1
Valid prediction for snap_scaffold_23-snap.1497-T1
Valid prediction for GlimmerHMM_glimmerT_51391-T1
Valid prediction for pasa_asmbl_31746.p1
Valid prediction for GlimmerHMM_glimmerT_51404-T1
Valid prediction for GlimmerHMM_glimmerT_51402-T1
Valid prediction for GlimmerHMM_glimmerT_51418-T1
Valid prediction for HiQ_model.g34382.t1
Valid prediction for CodingQuarry_transcript_35746-T1
Valid prediction for snap_scaffold_23-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_51403-T1
Valid prediction for snap_scaffold_23-snap.1496-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_23-snap.1491-T1
Valid prediction for Augustus_model.g34388.t1
Valid prediction for GlimmerHMM_glimmerT_51390-T1
Valid prediction for CodingQuarry_transcript_35755-T1
Valid prediction for snap_scaffold_23-snap.1522-T1
Valid prediction for CodingQuarry_transcript_35756-T1
Valid prediction for HiQ_model.g34390.t1
Valid prediction for CodingQuarry_transcript_35745-T1
Valid prediction for snap_scaffold_23-snap.1489-T1
Valid prediction for HiQ_model.g34378.t1
Valid prediction for GlimmerHMM_glimmerT_51414-T1
Valid prediction for snap_scaffold_23-snap.1526-T1
Valid prediction for GlimmerHMM_glimmerT_51399-T1
Valid prediction for snap_scaffold_23-snap.1512-T1
Valid prediction for Augustus_model.g34387.t1
Valid prediction for snap_scaffold_23-snap.1518-T1
Valid prediction for HiQ_model.g34386.t1
Valid prediction for GlimmerHMM_glimmerT_51419-T1
Valid prediction for GlimmerHMM_glimmerT_51408-T1
Valid prediction for snap_scaffold_23-snap.1492-T1
Valid prediction for snap_scaffold_23-snap.1510-T1
Valid prediction for GlimmerHMM_glimmerT_51412-T1
Valid prediction for CodingQuarry_transcript_35748-T1
Valid prediction for GlimmerHMM_glimmerT_51393-T1
Valid prediction for GlimmerHMM_glimmerT_51398-T1
Valid prediction for GlimmerHMM_glimmerT_51401-T1
Couldn't classify 35827, 35843
Couldn't classify 39947, 40012
Sorry, prediction pasa_asmbl_31081.p1 fails validation.
(TGT)	 CG	35827-35843	GT	AAG
(GAT)	 AG	37617-37729	GT	CGG
(CTC)	 AG	38022-38128	GT	GGG
(GTG)	 AG	39947-40012	AA	ACA
-recovered pasa_asmbl_31081.p1, internal, 37617, 37729
-recovered pasa_asmbl_31081.p1, internal, 38022, 38128
Valid prediction for snap_scaffold_23-snap.1530-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1508-T1
Valid prediction for snap_scaffold_23-snap.1517-T1
Valid prediction for pasa_asmbl_31072.p1
Valid prediction for pasa_asmbl_31223.p1
Couldn't classify 97015, 97199
Sorry, prediction pasa_asmbl_31075.p1 fails validation.
(ATG)	 CC	92798-92917	GT	AGG
(AAT)	 AG	93468-93628	GT	AGG
(GAA)	 AG	95083-95224	GT	TGG
(GGG)	 AG	95527-95730	GT	AGG
(TTT)	 AG	96016-96111	GT	CAG
(CTG)	 AG	96232-96347	GT	AGG
(GTC)	 AG	96537-96703	GT	TAG
(ACT)	 AG	97015-97199	GA	CTG
-recovered pasa_asmbl_31075.p1, initial, 92798, 92917
-recovered pasa_asmbl_31075.p1, internal, 93468, 93628
-recovered pasa_asmbl_31075.p1, internal, 95083, 95224
-recovered pasa_asmbl_31075.p1, internal, 95527, 95730
-recovered pasa_asmbl_31075.p1, internal, 96016, 96111
-recovered pasa_asmbl_31075.p1, internal, 96232, 96347
-recovered pasa_asmbl_31075.p1, internal, 96537, 96703
Valid prediction for Augustus_model.g34392.t1
Valid prediction for CodingQuarry_transcript_35753-T1
Valid prediction for GlimmerHMM_glimmerT_51406-T1
Valid prediction for Augustus_model.g34399.t1
Valid prediction for pasa_asmbl_31068.p1
Valid prediction for HiQ_model.g34381.t1
Valid prediction for snap_scaffold_23-snap.1500-T1
Valid prediction for CodingQuarry_transcript_35754-T1
Valid prediction for snap_scaffold_23-snap.1520-T1
Valid prediction for pasa_asmbl_31076.p1
Valid prediction for snap_scaffold_23-snap.1499-T1
Valid prediction for Augustus_model.g34396.t1
Valid prediction for HiQ_model.g34380.t1
Valid prediction for snap_scaffold_23-snap.1501-T1
Valid prediction for pasa_asmbl_31070.p1
Valid prediction for CodingQuarry_transcript_35747-T1
Valid prediction for GlimmerHMM_glimmerT_51417-T1
Valid prediction for snap_scaffold_23-snap.1494-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1515-T1
Valid prediction for GlimmerHMM_glimmerT_51397-T1
Valid prediction for snap_scaffold_23-snap.1525-T1
Valid prediction for GlimmerHMM_glimmerT_51415-T1
Valid prediction for snap_scaffold_23-snap.1509-T1
Valid prediction for Augustus_model.g34400.t1
Valid prediction for Augustus_model.g34397.t1
Valid prediction for CodingQuarry_transcript_35744-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29561, rend_intergenic: 24052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77132, rend_intergenic: 51468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88962, rend_intergenic: 84122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122443, rend_intergenic: 119706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133799, rend_intergenic: 131591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153768, rend_intergenic: 153477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155597, rend_intergenic: 153768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158205, rend_intergenic: 156964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164667, rend_intergenic: 158583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176463, rend_intergenic: 173292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194197, rend_intergenic: 185953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195557
-exon list size: 458


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 29561, rend_intergenic: 24052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77132, rend_intergenic: 51468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88962, rend_intergenic: 84122  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122443, rend_intergenic: 119706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133799, rend_intergenic: 131591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153768, rend_intergenic: 153477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155597, rend_intergenic: 153768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158205, rend_intergenic: 156964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164667, rend_intergenic: 158583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176463, rend_intergenic: 173292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194197, rend_intergenic: 185953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support