-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_817836-970184

-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.5164_t
Valid prediction for snap_scaffold_2-snap.192-T1
Valid prediction for GeneMark_model.5162_t
Valid prediction for pasa_asmbl_24138.p1
Valid prediction for GlimmerHMM_glimmerT_3178-T1
Valid prediction for HiQ_model.g2158.t1
Valid prediction for CodingQuarry_transcript_28383-T1
Valid prediction for GeneMark_model.5154_t
Valid prediction for GlimmerHMM_glimmerT_3180-T1
Valid prediction for pasa_asmbl_24142.p2
Valid prediction for snap_scaffold_2-snap.202-T1
Valid prediction for Augustus_model.g2166.t1
Valid prediction for snap_scaffold_2-snap.201-T1
Valid prediction for snap_scaffold_2-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_3198-T1
Valid prediction for pasa_asmbl_24165.p1
Valid prediction for snap_scaffold_2-snap.185-T1
Valid prediction for snap_scaffold_2-snap.206-T1
Valid prediction for GlimmerHMM_glimmerT_3183-T1
Valid prediction for GeneMark_model.5145_t
Valid prediction for Augustus_model.g2164.t1
Valid prediction for snap_scaffold_2-snap.221-T1
Valid prediction for CodingQuarry_transcript_28376-T1
Valid prediction for GeneMark_model.5142_t
Valid prediction for snap_scaffold_2-snap.217-T1
Valid prediction for GeneMark_model.5139_t
Valid prediction for Augustus_model.g2154.t1
Valid prediction for Augustus_model.g2163.t1
Valid prediction for GlimmerHMM_glimmerT_3188-T1
Valid prediction for GeneMark_model.5170_t
Valid prediction for GeneMark_model.5149_t
Valid prediction for GlimmerHMM_glimmerT_3193-T1
Valid prediction for GeneMark_model.5150_t
Valid prediction for snap_scaffold_2-snap.203-T1
Valid prediction for snap_scaffold_2-snap.184-T1
Couldn't classify 103750, 103921
Couldn't classify 104300, 104442
Sorry, prediction pasa_asmbl_25476.p1 fails validation.
(GGC)	 CA	103750-103921	GT	GGG
(GTC)	 AG	104300-104442	GG	CAG
Valid prediction for snap_scaffold_2-snap.209-T1
Valid prediction for snap_scaffold_2-snap.200-T1
Valid prediction for snap_scaffold_2-snap.205-T1
Valid prediction for GeneMark_model.5160_t
Valid prediction for CodingQuarry_transcript_28384-T1
Valid prediction for GeneMark_model.5140_t
Valid prediction for GeneMark_model.5143_t
Valid prediction for pasa_asmbl_24163.p2
Valid prediction for pasa_asmbl_24188.p2
Valid prediction for GlimmerHMM_glimmerT_3196-T1
Valid prediction for CodingQuarry_transcript_28377-T1
Valid prediction for CodingQuarry_transcript_28381-T1
Valid prediction for HiQ_model.g2160.t1
Valid prediction for GeneMark_model.5153_t
Valid prediction for GlimmerHMM_glimmerT_3184-T1
Valid prediction for GlimmerHMM_glimmerT_3177-T1
Valid prediction for GlimmerHMM_glimmerT_3174-T1
Valid prediction for Augustus_model.g2155.t1
Valid prediction for snap_scaffold_2-snap.187-T1
Valid prediction for snap_scaffold_2-snap.189-T1
Valid prediction for snap_scaffold_2-snap.213-T1
Valid prediction for snap_scaffold_2-snap.198-T1
Valid prediction for CodingQuarry_transcript_28385-T1
Valid prediction for snap_scaffold_2-snap.218-T1
Valid prediction for GlimmerHMM_glimmerT_3187-T1
Valid prediction for CodingQuarry_transcript_28378-T1
Valid prediction for GeneMark_model.5155_t
Valid prediction for GlimmerHMM_glimmerT_3189-T1
Valid prediction for GlimmerHMM_glimmerT_3199-T1
Valid prediction for GlimmerHMM_glimmerT_3194-T1
Valid prediction for GlimmerHMM_glimmerT_3186-T1
Valid prediction for snap_scaffold_2-snap.195-T1
Valid prediction for GeneMark_model.5146_t
Valid prediction for snap_scaffold_2-snap.190-T1
Valid prediction for pasa_asmbl_24135.p1
Valid prediction for GeneMark_model.5151_t
Valid prediction for Augustus_model.g2152.t1
Valid prediction for Augustus_model.g2159.t1
Valid prediction for Augustus_model.g2156.t1
Valid prediction for HiQ_model.g2161.t1
Valid prediction for GeneMark_model.5173_t
Couldn't classify 111108, 111218
Couldn't classify 115317, 115427
Sorry, prediction pasa_asmbl_24178.p1 fails validation.
(TCA)	 CC	111108-111218	GT	AGG
(AGT)	 AG	112775-112912	GC	AGG
(GAT)	 AG	113829-113927	GT	CGG
(GAC)	 AG	114744-114827	GT	AGG
(GGT)	 AG	115317-115427	GG	CAG
-recovered pasa_asmbl_24178.p1, internal, 112775, 112912
-recovered pasa_asmbl_24178.p1, internal, 113829, 113927
-recovered pasa_asmbl_24178.p1, internal, 114744, 114827
Valid prediction for GlimmerHMM_glimmerT_3182-T1
Valid prediction for GeneMark_model.5156_t
Valid prediction for CodingQuarry_transcript_28380-T1
Valid prediction for HiQ_model.g2157.t1
Couldn't classify 104786, 105079
Sorry, prediction pasa_asmbl_24174.p1 fails validation.
(GGG)	 TG	104786-105079	GT	AGG
(AGA)	 AG	105185-105315	GT	AGG
(CAC)	 AG	105409-105679	GT	AGG
(GCG)	 AG	105929-106057	GT	AGG
(ACT)	 AG	106647-106658	GT	GAG
-recovered pasa_asmbl_24174.p1, terminal, 106647, 106658
-recovered pasa_asmbl_24174.p1, internal, 105185, 105315
-recovered pasa_asmbl_24174.p1, internal, 105409, 105679
-recovered pasa_asmbl_24174.p1, internal, 105929, 106057
-recovered pasa_asmbl_24174.p1, internal, 106647, 106658
Valid prediction for snap_scaffold_2-snap.197-T1
Valid prediction for Augustus_model.g2167.t1
Valid prediction for GeneMark_model.5168_t
Valid prediction for Augustus_model.g2151.t1
Valid prediction for CodingQuarry_transcript_28379-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 Augustus_model.g2150.t1
Valid prediction for GeneMark_model.5157_t
Valid prediction for GeneMark_model.5152_t
Valid prediction for snap_scaffold_2-snap.196-T1
Valid prediction for GeneMark_model.5144_t
Valid prediction for Augustus_model.g2170.t1
Valid prediction for snap_scaffold_2-snap.211-T1
Valid prediction for Augustus_model.g2162.t1
Valid prediction for snap_scaffold_2-snap.216-T1
Valid prediction for GlimmerHMM_glimmerT_3197-T1
Valid prediction for GlimmerHMM_glimmerT_3195-T1
Valid prediction for GlimmerHMM_glimmerT_3203-T1
Valid prediction for GeneMark_model.5171_t
Valid prediction for snap_scaffold_2-snap.194-T1
Valid prediction for snap_scaffold_2-snap.183-T1
Valid prediction for GeneMark_model.5174_t
Valid prediction for Augustus_model.g2149.t1
Valid prediction for snap_scaffold_2-snap.193-T1
Valid prediction for HiQ_model.g2169.t1
Valid prediction for GlimmerHMM_glimmerT_3201-T1
Valid prediction for GeneMark_model.5169_t
Valid prediction for pasa_asmbl_22851.p1
Valid prediction for HiQ_model.g2168.t1
Valid prediction for GeneMark_model.5165_t
Valid prediction for snap_scaffold_2-snap.207-T1
Valid prediction for GlimmerHMM_glimmerT_3181-T1
Couldn't classify 32893, 33264
Sorry, prediction pasa_asmbl_24053.p2 fails validation.
(AAA)	 AT	32893-33264	GA	AAG
Valid prediction for GeneMark_model.5158_t
Valid prediction for GlimmerHMM_glimmerT_3192-T1
Valid prediction for CodingQuarry_transcript_28386-T1
Valid prediction for snap_scaffold_2-snap.215-T1
Valid prediction for GeneMark_model.5147_t
Valid prediction for GlimmerHMM_glimmerT_3200-T1
Valid prediction for pasa_asmbl_22855.p1
Valid prediction for GlimmerHMM_glimmerT_3176-T1
Valid prediction for GlimmerHMM_glimmerT_3179-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.220-T1
Valid prediction for GeneMark_model.5172_t
Valid prediction for GeneMark_model.5161_t
Valid prediction for CodingQuarry_transcript_28387-T1
Valid prediction for snap_scaffold_2-snap.212-T1
Valid prediction for GlimmerHMM_glimmerT_3204-T1
Valid prediction for GlimmerHMM_glimmerT_3175-T1
Valid prediction for GeneMark_model.5167_t
Valid prediction for Augustus_model.g2165.t1
Valid prediction for snap_scaffold_2-snap.214-T1
Valid prediction for CodingQuarry_transcript_28389-T1
Valid prediction for GlimmerHMM_glimmerT_3173-T1
Valid prediction for GeneMark_model.5141_t
Valid prediction for Augustus_model.g2153.t1
Valid prediction for GlimmerHMM_glimmerT_3191-T1
Valid prediction for GlimmerHMM_glimmerT_3190-T1
Valid prediction for snap_scaffold_2-snap.204-T1
Valid prediction for snap_scaffold_2-snap.186-T1
Valid prediction for snap_scaffold_2-snap.191-T1
Couldn't classify 113999, 114205
Sorry, prediction pasa_asmbl_22849.p1 fails validation.
(ATG)	 CA	112670-112705	GT	AGG
(AGA)	 AG	112801-112920	GT	AGG
(GCA)	 AG	113153-113282	GT	CGG
(GTC)	 AG	113454-113576	GT	AGG
(GTG)	 AG	113690-113859	GT	AGG
(GAC)	 AG	113999-114205	CT	TCC
-recovered pasa_asmbl_22849.p1, initial, 112670, 112705
-recovered pasa_asmbl_22849.p1, internal, 112801, 112920
-recovered pasa_asmbl_22849.p1, internal, 113153, 113282
-recovered pasa_asmbl_22849.p1, internal, 113454, 113576
-recovered pasa_asmbl_22849.p1, internal, 113690, 113859
Valid prediction for snap_scaffold_2-snap.219-T1
Valid prediction for GeneMark_model.5159_t
Valid prediction for snap_scaffold_2-snap.188-T1
Valid prediction for GlimmerHMM_glimmerT_3202-T1
Valid prediction for GeneMark_model.5148_t
Valid prediction for snap_scaffold_2-snap.210-T1
Valid prediction for GlimmerHMM_glimmerT_3185-T1
Valid prediction for snap_scaffold_2-snap.208-T1
Valid prediction for CodingQuarry_transcript_28390-T1
Valid prediction for GeneMark_model.5163_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7278, rend_intergenic: 3295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19963, rend_intergenic: 15966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21688, rend_intergenic: 20605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45606, rend_intergenic: 42324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51584, rend_intergenic: 49805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99576, rend_intergenic: 89278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108272, rend_intergenic: 103484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111376, rend_intergenic: 110797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114860, rend_intergenic: 112295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134169, rend_intergenic: 127456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147998, rend_intergenic: 145736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151088, rend_intergenic: 148408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 16414, rend_intergenic: 16411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 152349
-exon list size: 584


building trellis

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99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 7278, rend_intergenic: 3295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19963, rend_intergenic: 15966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21688, rend_intergenic: 20605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45606, rend_intergenic: 42324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51584, rend_intergenic: 49805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99576, rend_intergenic: 89278  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108272, rend_intergenic: 103484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111376, rend_intergenic: 110797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114860, rend_intergenic: 112295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134169, rend_intergenic: 127456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147998, rend_intergenic: 145736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151088, rend_intergenic: 148408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 16414, rend_intergenic: 16411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support