-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_6871048-7073856

-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 GlimmerHMM_glimmerT_46231-T1
Valid prediction for snap_scaffold_20-snap.1516-T1
Valid prediction for snap_scaffold_20-snap.1530-T1
Valid prediction for snap_scaffold_20-snap.1523-T1
Valid prediction for Augustus_model.g30686.t1
Valid prediction for snap_scaffold_20-snap.1503-T1
Valid prediction for GlimmerHMM_glimmerT_46215-T1
Valid prediction for GlimmerHMM_glimmerT_46236-T1
Valid prediction for GlimmerHMM_glimmerT_46220-T1
Couldn't classify 105291, 105446
Sorry, prediction pasa_asmbl_26692.p1 fails validation.
(CCT)	 CC	105291-105446	GT	GCG
(ATG)	 AG	106136-106186	GT	TGG
(AGT)	 AG	106534-106677	AC	AGA
-recovered pasa_asmbl_26692.p1, initial, 106136, 106186
-recovered pasa_asmbl_26692.p1, terminal, 106534, 106677
-recovered pasa_asmbl_26692.p1, internal, 106136, 106186
Valid prediction for Augustus_model.g30691.t1
Valid prediction for GlimmerHMM_glimmerT_46212-T1
Valid prediction for Augustus_model.g30690.t1
Valid prediction for snap_scaffold_20-snap.1491-T1
Valid prediction for Augustus_model.g30679.t1
Valid prediction for CodingQuarry_transcript_30538-T1
Valid prediction for HiQ_model.g30677.t1
Valid prediction for GlimmerHMM_glimmerT_46233-T1
Valid prediction for snap_scaffold_20-snap.1495-T1
Valid prediction for snap_scaffold_20-snap.1486-T1
Valid prediction for snap_scaffold_20-snap.1489-T1
Valid prediction for snap_scaffold_20-snap.1526-T1
Valid prediction for snap_scaffold_20-snap.1497-T1
Valid prediction for GlimmerHMM_glimmerT_46222-T1
Valid prediction for Augustus_model.g30684.t1
Valid prediction for Augustus_model.g30685.t1
Valid prediction for GlimmerHMM_glimmerT_46224-T1
Valid prediction for Augustus_model.g30674.t1
Valid prediction for GlimmerHMM_glimmerT_46213-T1
Valid prediction for GlimmerHMM_glimmerT_46240-T1
Valid prediction for GlimmerHMM_glimmerT_46219-T1
Valid prediction for GlimmerHMM_glimmerT_46217-T1
Valid prediction for snap_scaffold_20-snap.1484-T1
Valid prediction for snap_scaffold_20-snap.1482-T1
Valid prediction for snap_scaffold_20-snap.1511-T1
Valid prediction for snap_scaffold_20-snap.1506-T1
Valid prediction for snap_scaffold_20-snap.1513-T1
Valid prediction for GlimmerHMM_glimmerT_46234-T1
Valid prediction for GlimmerHMM_glimmerT_46228-T1
Valid prediction for snap_scaffold_20-snap.1493-T1
Valid prediction for pasa_asmbl_26685.p1
Valid prediction for snap_scaffold_20-snap.1521-T1
Valid prediction for Augustus_model.g30673.t1
Valid prediction for GlimmerHMM_glimmerT_46211-T1
Valid prediction for GlimmerHMM_glimmerT_46216-T1
Valid prediction for snap_scaffold_20-snap.1505-T1
Valid prediction for snap_scaffold_20-snap.1519-T1
Valid prediction for GlimmerHMM_glimmerT_46229-T1
Valid prediction for CodingQuarry_transcript_30541-T1
Valid prediction for snap_scaffold_20-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_46227-T1
Valid prediction for snap_scaffold_20-snap.1499-T1
Valid prediction for Augustus_model.g30683.t1
Valid prediction for Augustus_model.g30678.t1
Valid prediction for Augustus_model.g30682.t1
Valid prediction for snap_scaffold_20-snap.1512-T1
Valid prediction for snap_scaffold_20-snap.1488-T1
Valid prediction for GlimmerHMM_glimmerT_46214-T1
Valid prediction for snap_scaffold_20-snap.1507-T1
Valid prediction for Augustus_model.g30695.t1
Valid prediction for snap_scaffold_20-snap.1514-T1
Valid prediction for Augustus_model.g30693.t1
Valid prediction for GlimmerHMM_glimmerT_46235-T1
Couldn't classify 169490, 169504
Sorry, prediction pasa_asmbl_26696.p2 fails validation.
(GAC)	 AG	169490-169504	GT	TGG
(GAT)	 AG	169810-170118	GC	GAG
-recovered pasa_asmbl_26696.p2, terminal, 169810, 170118
-recovered pasa_asmbl_26696.p2, internal, 169490, 169504
-recovered pasa_asmbl_26696.p2, internal, 169810, 170118

-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.g30688.t1
Couldn't classify 81253, 81458
Sorry, prediction pasa_asmbl_26240.p1 fails validation.
(ATG)	 TC	80796-80889	GT	GGG
(GAG)	 AG	81253-81458	TT	CCT
-recovered pasa_asmbl_26240.p1, initial, 80796, 80889
Valid prediction for Augustus_model.g30689.t1
Valid prediction for HiQ_model.g30680.t1
Valid prediction for snap_scaffold_20-snap.1518-T1
Valid prediction for snap_scaffold_20-snap.1525-T1
Valid prediction for GlimmerHMM_glimmerT_46237-T1
Valid prediction for GlimmerHMM_glimmerT_46242-T1
Valid prediction for pasa_asmbl_25854.p1
Valid prediction for snap_scaffold_20-snap.1529-T1
Valid prediction for CodingQuarry_transcript_30542-T1
Valid prediction for GlimmerHMM_glimmerT_46241-T1
Valid prediction for GlimmerHMM_glimmerT_46238-T1
Valid prediction for snap_scaffold_20-snap.1515-T1
Valid prediction for CodingQuarry_transcript_30540-T1
Valid prediction for snap_scaffold_20-snap.1509-T1
Valid prediction for snap_scaffold_20-snap.1492-T1
Valid prediction for Augustus_model.g30675.t1
Valid prediction for snap_scaffold_20-snap.1524-T1
Valid prediction for snap_scaffold_20-snap.1496-T1
Valid prediction for Augustus_model.g30697.t1
Valid prediction for snap_scaffold_20-snap.1532-T1
Valid prediction for GlimmerHMM_glimmerT_46218-T1
Valid prediction for snap_scaffold_20-snap.1502-T1
Valid prediction for GlimmerHMM_glimmerT_46232-T1
Valid prediction for snap_scaffold_20-snap.1483-T1
Valid prediction for snap_scaffold_20-snap.1504-T1
Valid prediction for GlimmerHMM_glimmerT_46230-T1
Couldn't classify 5851, 6013
Sorry, prediction pasa_asmbl_25867.p2 fails validation.
(ATG)	 CC	219-327	GT	TGG
(AGT)	 AG	1024-1183	GT	AGG
(CAT)	 AG	1897-2057	GT	CGG
(GCA)	 AG	4598-4705	GT	ATG
(TGG)	 AG	4895-5014	GT	AGG
(GTG)	 AG	5183-5298	GT	AGG
(GTG)	 AG	5458-5627	GT	GGG
(AGA)	 AG	5851-6013	GT	AGG
-recovered pasa_asmbl_25867.p2, initial, 219, 327
-recovered pasa_asmbl_25867.p2, internal, 1024, 1183
-recovered pasa_asmbl_25867.p2, internal, 1897, 2057
-recovered pasa_asmbl_25867.p2, internal, 4598, 4705
-recovered pasa_asmbl_25867.p2, internal, 4895, 5014
-recovered pasa_asmbl_25867.p2, internal, 5183, 5298
-recovered pasa_asmbl_25867.p2, internal, 5458, 5627
-recovered pasa_asmbl_25867.p2, internal, 5851, 6013
Valid prediction for snap_scaffold_20-snap.1485-T1
Valid prediction for snap_scaffold_20-snap.1510-T1
Valid prediction for snap_scaffold_20-snap.1520-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_46226-T1
Valid prediction for snap_scaffold_20-snap.1498-T1
Valid prediction for snap_scaffold_20-snap.1517-T1
Valid prediction for snap_scaffold_20-snap.1522-T1
Valid prediction for snap_scaffold_20-snap.1481-T1
Valid prediction for pasa_asmbl_25853.p2
Couldn't classify 81348, 81561
Couldn't classify 81660, 81907
Sorry, prediction pasa_asmbl_26272.p1 fails validation.
(TTG)	 TC	81348-81561	GT	AGG
(GTG)	 AG	81660-81907	CA	GCC
Valid prediction for snap_scaffold_20-snap.1490-T1
Valid prediction for Augustus_model.g30681.t1
Valid prediction for pasa_asmbl_25866.p2
Valid prediction for GlimmerHMM_glimmerT_46221-T1
Valid prediction for snap_scaffold_20-snap.1531-T1
Couldn't classify 6211, 6389
Sorry, prediction pasa_asmbl_26311.p1 fails validation.
(TCC)	 CT	6211-6389	GT	AGG
(GTA)	 AG	7013-7189	GT	AAG
(GTT)	 AG	7827-7932	GT	ATG
(GCC)	 AG	8410-8553	GT	AGG
(GCG)	 AG	8662-8868	GT	AGG
(GTT)	 AG	9146-9196	GC	GAG
-recovered pasa_asmbl_26311.p1, terminal, 9146, 9196
-recovered pasa_asmbl_26311.p1, internal, 7013, 7189
-recovered pasa_asmbl_26311.p1, internal, 7827, 7932
-recovered pasa_asmbl_26311.p1, internal, 8410, 8553
-recovered pasa_asmbl_26311.p1, internal, 8662, 8868
-recovered pasa_asmbl_26311.p1, internal, 9146, 9196
Couldn't classify 85269, 85709
Sorry, prediction pasa_asmbl_25863.p1 fails validation.
(TTT)	 CA	85269-85709	AA	CTA
Valid prediction for GlimmerHMM_glimmerT_46223-T1
Valid prediction for Augustus_model.g30676.t1
Valid prediction for snap_scaffold_20-snap.1501-T1
Valid prediction for snap_scaffold_20-snap.1494-T1
Valid prediction for snap_scaffold_20-snap.1500-T1
Valid prediction for snap_scaffold_20-snap.1487-T1
Valid prediction for Augustus_model.g30694.t1
Valid prediction for Augustus_model.g30692.t1
Valid prediction for Augustus_model.g30687.t1
Valid prediction for snap_scaffold_20-snap.1508-T1
Valid prediction for GlimmerHMM_glimmerT_46225-T1
Valid prediction for GlimmerHMM_glimmerT_46239-T1
Valid prediction for CodingQuarry_transcript_30539-T1
Valid prediction for snap_scaffold_20-snap.1527-T1
Valid prediction for Augustus_model.g30696.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6160, rend_intergenic: 2101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8132, rend_intergenic: 7624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13867, rend_intergenic: 9331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17381, rend_intergenic: 16513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33696, rend_intergenic: 26445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59638, rend_intergenic: 57562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62689, rend_intergenic: 60082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67929, rend_intergenic: 63918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91486, rend_intergenic: 88479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133922, rend_intergenic: 132680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138574, rend_intergenic: 134546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159087, rend_intergenic: 151785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164631, rend_intergenic: 159668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178691, rend_intergenic: 175770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180589, rend_intergenic: 178879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198610, rend_intergenic: 194687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202809
-exon list size: 403


building trellis

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42.0    
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97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 6160, rend_intergenic: 2101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8132, rend_intergenic: 7624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13867, rend_intergenic: 9331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17381, rend_intergenic: 16513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33696, rend_intergenic: 26445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59638, rend_intergenic: 57562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62689, rend_intergenic: 60082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67929, rend_intergenic: 63918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91486, rend_intergenic: 88479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133922, rend_intergenic: 132680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138574, rend_intergenic: 134546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159087, rend_intergenic: 151785  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164631, rend_intergenic: 159668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178691, rend_intergenic: 175770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180589, rend_intergenic: 178879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198610, rend_intergenic: 194687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12462
-exon list size: 18


building trellis

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30.0    
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40.0    
45.0    
50.0    
55.0    
60.0    
65.0    
70.0    
75.0    
80.0    
85.0    
90.0    
95.0    
-found 3 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support