-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_7018449-7228427

-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_25-snap.1532-T1
Valid prediction for GlimmerHMM_glimmerT_54420-T1
Valid prediction for GlimmerHMM_glimmerT_54424-T1
Valid prediction for snap_scaffold_25-snap.1509-T1
Valid prediction for snap_scaffold_25-snap.1492-T1
Valid prediction for snap_scaffold_25-snap.1518-T1
Valid prediction for snap_scaffold_25-snap.1521-T1
Valid prediction for snap_scaffold_25-snap.1493-T1
Valid prediction for snap_scaffold_25-snap.1497-T1
Valid prediction for GlimmerHMM_glimmerT_54418-T1
Valid prediction for snap_scaffold_25-snap.1523-T1
Valid prediction for GlimmerHMM_glimmerT_54422-T1
Valid prediction for snap_scaffold_25-snap.1535-T1
Valid prediction for snap_scaffold_25-snap.1512-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54438-T1
Valid prediction for snap_scaffold_25-snap.1502-T1
Valid prediction for snap_scaffold_25-snap.1508-T1
Valid prediction for snap_scaffold_25-snap.1528-T1
Valid prediction for snap_scaffold_25-snap.1524-T1
Valid prediction for Augustus_model.g36116.t1
Valid prediction for snap_scaffold_25-snap.1499-T1
Valid prediction for GlimmerHMM_glimmerT_54419-T1
Valid prediction for GlimmerHMM_glimmerT_54445-T1
Couldn't classify 9034, 9342
Sorry, prediction pasa_asmbl_33654.p1 fails validation.
(CGT)	 AA	9034-9342	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_54423-T1
Valid prediction for Augustus_model.g36123.t1
Valid prediction for snap_scaffold_25-snap.1496-T1
Valid prediction for GlimmerHMM_glimmerT_54421-T1
Valid prediction for snap_scaffold_25-snap.1505-T1
Valid prediction for snap_scaffold_25-snap.1498-T1
Valid prediction for snap_scaffold_25-snap.1495-T1
Valid prediction for snap_scaffold_25-snap.1515-T1
Couldn't classify 4939, 5034
Sorry, prediction pasa_asmbl_33652.p1 fails validation.
(ATG)	 CC	4494-4550	GT	CGG
(TAC)	 AG	4634-4819	GT	AGG
(CCT)	 AG	4939-5034	GG	CTG
-recovered pasa_asmbl_33652.p1, initial, 4494, 4550
-recovered pasa_asmbl_33652.p1, internal, 4634, 4819
Valid prediction for HiQ_model.g36117.t1
Valid prediction for snap_scaffold_25-snap.1491-T1
Couldn't classify 105456, 105469
Sorry, prediction pasa_asmbl_33657.p1 fails validation.
(AGA)	 GA	105456-105469	GT	AGG
(TCT)	 AG	105593-105701	GT	TGG
(GTC)	 AG	105833-105940	GT	CGG
(AAC)	 AG	106325-106393	GA	AGG
-recovered pasa_asmbl_33657.p1, terminal, 106325, 106393
-recovered pasa_asmbl_33657.p1, internal, 105593, 105701
-recovered pasa_asmbl_33657.p1, internal, 105833, 105940
Valid prediction for GlimmerHMM_glimmerT_54430-T1
Valid prediction for pasa_asmbl_33656.p1
Valid prediction for GlimmerHMM_glimmerT_54450-T1
Valid prediction for GlimmerHMM_glimmerT_54417-T1
Valid prediction for snap_scaffold_25-snap.1522-T1
Valid prediction for snap_scaffold_25-snap.1516-T1
Valid prediction for GlimmerHMM_glimmerT_54428-T1
Valid prediction for GlimmerHMM_glimmerT_54425-T1
Valid prediction for CodingQuarry_transcript_38773-T1
Valid prediction for GlimmerHMM_glimmerT_54448-T1
Valid prediction for Augustus_model.g36122.t1
Valid prediction for GlimmerHMM_glimmerT_54434-T1
Valid prediction for Augustus_model.g36134.t1
Valid prediction for CodingQuarry_transcript_38771-T1
Valid prediction for Augustus_model.g36115.t1
Valid prediction for snap_scaffold_25-snap.1494-T1
Valid prediction for snap_scaffold_25-snap.1514-T1
Valid prediction for Augustus_model.g36130.t1
Valid prediction for Augustus_model.g36131.t1
Valid prediction for GlimmerHMM_glimmerT_54435-T1
Valid prediction for GlimmerHMM_glimmerT_54439-T1
Valid prediction for GlimmerHMM_glimmerT_54443-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 GlimmerHMM_glimmerT_54442-T1
Valid prediction for Augustus_model.g36118.t1
Valid prediction for snap_scaffold_25-snap.1534-T1
Couldn't classify 133445, 133651
Sorry, prediction pasa_asmbl_34383.p1 fails validation.
(ATC)	 AG	133445-133651	GT	AGG
(GCT)	 AG	133757-133858	GT	AGG
(GAA)	 AG	136724-136866	GT	AGG
(TCT)	 AG	138771-138860	GT	AGG
(TTC)	 AG	139173-139407	GC	AGG
-recovered pasa_asmbl_34383.p1, terminal, 139173, 139407
-recovered pasa_asmbl_34383.p1, internal, 133445, 133651
-recovered pasa_asmbl_34383.p1, internal, 133757, 133858
-recovered pasa_asmbl_34383.p1, internal, 136724, 136866
-recovered pasa_asmbl_34383.p1, internal, 138771, 138860
-recovered pasa_asmbl_34383.p1, internal, 139173, 139407
Valid prediction for snap_scaffold_25-snap.1527-T1
Valid prediction for snap_scaffold_25-snap.1501-T1
Valid prediction for Augustus_model.g36127.t1
Valid prediction for GlimmerHMM_glimmerT_54447-T1
Valid prediction for Augustus_model.g36128.t1
Valid prediction for Augustus_model.g36133.t1
Valid prediction for snap_scaffold_25-snap.1511-T1
Valid prediction for snap_scaffold_25-snap.1529-T1
Valid prediction for snap_scaffold_25-snap.1519-T1
Valid prediction for GlimmerHMM_glimmerT_54427-T1
Valid prediction for CodingQuarry_transcript_38775-T1
Valid prediction for snap_scaffold_25-snap.1531-T1
Valid prediction for Augustus_model.g36121.t1
Valid prediction for snap_scaffold_25-snap.1517-T1
Valid prediction for Augustus_model.g36129.t1
Valid prediction for GlimmerHMM_glimmerT_54432-T1
Valid prediction for GlimmerHMM_glimmerT_54446-T1
Valid prediction for CodingQuarry_transcript_38774-T1
Valid prediction for GlimmerHMM_glimmerT_54440-T1
Valid prediction for HiQ_model.g36135.t1
Valid prediction for snap_scaffold_25-snap.1513-T1
Valid prediction for snap_scaffold_25-snap.1526-T1
Valid prediction for snap_scaffold_25-snap.1507-T1
Valid prediction for snap_scaffold_25-snap.1510-T1
Valid prediction for snap_scaffold_25-snap.1533-T1
Valid prediction for Augustus_model.g36132.t1
Valid prediction for snap_scaffold_25-snap.1500-T1
Valid prediction for GlimmerHMM_glimmerT_54437-T1
Valid prediction for GlimmerHMM_glimmerT_54426-T1
Valid prediction for pasa_asmbl_34389.p1
Valid prediction for Augustus_model.g36124.t1
Couldn't classify 21601, 21657
Sorry, prediction pasa_asmbl_34386.p1 fails validation.
(CTT)	 AA	21601-21657	GT	TTG
(AGC)	 AG	22228-22312	GT	AGG
(TGG)	 AG	22450-22559	GT	ACG
(GGT)	 AG	22694-22900	GT	CTG
(TGG)	 AG	23122-23316	GT	ACG
(GTC)	 AG	23473-23511	GT	GAG
-recovered pasa_asmbl_34386.p1, terminal, 23473, 23511
-recovered pasa_asmbl_34386.p1, internal, 22228, 22312
-recovered pasa_asmbl_34386.p1, internal, 22450, 22559
-recovered pasa_asmbl_34386.p1, internal, 22694, 22900
-recovered pasa_asmbl_34386.p1, internal, 23122, 23316
-recovered pasa_asmbl_34386.p1, internal, 23473, 23511
Valid prediction for GlimmerHMM_glimmerT_54449-T1
Valid prediction for GlimmerHMM_glimmerT_54441-T1
Valid prediction for CodingQuarry_transcript_38772-T1
Couldn't classify 124319, 124427
Couldn't classify 125739, 125807
Sorry, prediction pasa_asmbl_34384.p1 fails validation.
(GTG)	 AG	124319-124427	GT	GGG
(AGC)	 AG	124553-124716	GT	GGG
(ATG)	 AG	124833-124907	GT	TGG
(GCT)	 AG	125014-125137	GT	AGG
(GCG)	 AG	125243-125388	GT	AGG
(GTG)	 AG	125739-125807	AA	GCA
-recovered pasa_asmbl_34384.p1, initial, 124833, 124907
-recovered pasa_asmbl_34384.p1, internal, 124319, 124427
-recovered pasa_asmbl_34384.p1, internal, 124553, 124716
-recovered pasa_asmbl_34384.p1, internal, 124833, 124907
-recovered pasa_asmbl_34384.p1, internal, 125014, 125137
-recovered pasa_asmbl_34384.p1, internal, 125243, 125388
Couldn't classify 119854, 119958
Couldn't classify 121094, 121255
Sorry, prediction pasa_asmbl_34608.p1 fails validation.
(AAC)	 GA	119854-119958	GT	AGG
(GAC)	 AG	120287-120418	GT	AGG
(AAG)	 AG	121094-121255	GA	ACG
-recovered pasa_asmbl_34608.p1, internal, 120287, 120418
Valid prediction for pasa_asmbl_34387.p1
Valid prediction for snap_scaffold_25-snap.1536-T1
Valid prediction for GlimmerHMM_glimmerT_54436-T1
Valid prediction for Augustus_model.g36120.t1
Valid prediction for snap_scaffold_25-snap.1530-T1
Valid prediction for snap_scaffold_25-snap.1503-T1
Valid prediction for Augustus_model.g36125.t1
Valid prediction for Augustus_model.g36126.t1
Valid prediction for snap_scaffold_25-snap.1537-T1
Valid prediction for GlimmerHMM_glimmerT_54444-T1
Valid prediction for snap_scaffold_25-snap.1504-T1
Valid prediction for snap_scaffold_25-snap.1506-T1
Valid prediction for GlimmerHMM_glimmerT_54431-T1
Valid prediction for snap_scaffold_25-snap.1525-T1
Valid prediction for snap_scaffold_25-snap.1520-T1
Valid prediction for GlimmerHMM_glimmerT_54433-T1
Valid prediction for GlimmerHMM_glimmerT_54429-T1
Valid prediction for Augustus_model.g36119.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52263, rend_intergenic: 47764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64019, rend_intergenic: 60300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77059, rend_intergenic: 70832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87878, rend_intergenic: 85125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94967, rend_intergenic: 88638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101098, rend_intergenic: 97708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128372, rend_intergenic: 118014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157331, rend_intergenic: 130680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169116, rend_intergenic: 158517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177057, rend_intergenic: 170063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187074, rend_intergenic: 186469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209979
-exon list size: 543


building trellis

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98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 52263, rend_intergenic: 47764  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64019, rend_intergenic: 60300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77059, rend_intergenic: 70832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87878, rend_intergenic: 85125  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94967, rend_intergenic: 88638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101098, rend_intergenic: 97708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128372, rend_intergenic: 118014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157331, rend_intergenic: 130680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169116, rend_intergenic: 158517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177057, rend_intergenic: 170063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187074, rend_intergenic: 186469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support