-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_6186049-6391653

-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_20-snap.1344-T1
Valid prediction for snap_scaffold_20-snap.1370-T1
Valid prediction for snap_scaffold_20-snap.1377-T1
Valid prediction for Augustus_model.g30609.t1
Valid prediction for GlimmerHMM_glimmerT_46131-T1
Valid prediction for GlimmerHMM_glimmerT_46118-T1
Valid prediction for Augustus_model.g30619.t1
Valid prediction for GlimmerHMM_glimmerT_46129-T1
Valid prediction for snap_scaffold_20-snap.1338-T1
Valid prediction for GlimmerHMM_glimmerT_46120-T1
Valid prediction for snap_scaffold_20-snap.1351-T1
Valid prediction for snap_scaffold_20-snap.1357-T1
Valid prediction for GlimmerHMM_glimmerT_46128-T1
Valid prediction for snap_scaffold_20-snap.1366-T1
Valid prediction for snap_scaffold_20-snap.1345-T1
Valid prediction for snap_scaffold_20-snap.1343-T1
Valid prediction for snap_scaffold_20-snap.1362-T1
Valid prediction for snap_scaffold_20-snap.1363-T1
Valid prediction for snap_scaffold_20-snap.1349-T1
Valid prediction for GlimmerHMM_glimmerT_46115-T1
Valid prediction for snap_scaffold_20-snap.1354-T1
Valid prediction for snap_scaffold_20-snap.1352-T1
Valid prediction for snap_scaffold_20-snap.1359-T1
Valid prediction for snap_scaffold_20-snap.1375-T1
Valid prediction for GlimmerHMM_glimmerT_46119-T1
Valid prediction for snap_scaffold_20-snap.1347-T1
Valid prediction for GlimmerHMM_glimmerT_46121-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_46124-T1
Valid prediction for Augustus_model.g30618.t1
Valid prediction for snap_scaffold_20-snap.1373-T1
Valid prediction for snap_scaffold_20-snap.1368-T1
Valid prediction for snap_scaffold_20-snap.1348-T1
Valid prediction for snap_scaffold_20-snap.1350-T1
Valid prediction for GlimmerHMM_glimmerT_46138-T1
Valid prediction for GlimmerHMM_glimmerT_46134-T1
Valid prediction for GlimmerHMM_glimmerT_46137-T1
Couldn't classify 201107, 201121
Couldn't classify 202094, 202123
Sorry, prediction pasa_asmbl_25825.p1 fails validation.
(CTC)	 TC	201107-201121	GT	AGG
(GTG)	 AG	201350-201493	GT	AGG
(GGC)	 AG	201660-201817	GT	AGG
(GTG)	 AG	201941-201989	GT	AGG
(GTT)	 AG	202094-202123	GG	TGG
-recovered pasa_asmbl_25825.p1, internal, 201350, 201493
-recovered pasa_asmbl_25825.p1, internal, 201660, 201817
-recovered pasa_asmbl_25825.p1, internal, 201941, 201989
Valid prediction for GlimmerHMM_glimmerT_46132-T1
Valid prediction for HiQ_model.g30610.t1
Valid prediction for Augustus_model.g30608.t1
Valid prediction for CodingQuarry_transcript_30530-T1
Valid prediction for Augustus_model.g30611.t1
Valid prediction for snap_scaffold_20-snap.1353-T1
Valid prediction for CodingQuarry_transcript_30531-T1
Valid prediction for Augustus_model.g30614.t1
Valid prediction for snap_scaffold_20-snap.1374-T1
Valid prediction for snap_scaffold_20-snap.1340-T1
Valid prediction for GlimmerHMM_glimmerT_46136-T1
Valid prediction for GlimmerHMM_glimmerT_46122-T1
Valid prediction for snap_scaffold_20-snap.1339-T1
Valid prediction for snap_scaffold_20-snap.1358-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g30616.t1
Valid prediction for Augustus_model.g30621.t1
Valid prediction for snap_scaffold_20-snap.1360-T1
Valid prediction for snap_scaffold_20-snap.1376-T1
Valid prediction for snap_scaffold_20-snap.1365-T1
Couldn't classify 105641, 105982
Sorry, prediction pasa_asmbl_26317.p1 fails validation.
(TCT)	 CC	105641-105982	CC	CGC
Valid prediction for GlimmerHMM_glimmerT_46133-T1
Valid prediction for GlimmerHMM_glimmerT_46117-T1
Valid prediction for snap_scaffold_20-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_46125-T1
Couldn't classify 182800, 183051
Sorry, prediction pasa_asmbl_25830.p1 fails validation.
(ATG)	 TG	181624-181671	GT	AGG
(CTC)	 AG	182800-183051	AT	AGA
-recovered pasa_asmbl_25830.p1, initial, 181624, 181671
Valid prediction for GlimmerHMM_glimmerT_46135-T1
Valid prediction for snap_scaffold_20-snap.1342-T1
Valid prediction for GlimmerHMM_glimmerT_46114-T1
Valid prediction for GlimmerHMM_glimmerT_46123-T1
Valid prediction for Augustus_model.g30612.t1
Valid prediction for snap_scaffold_20-snap.1364-T1
Valid prediction for Augustus_model.g30617.t1
Valid prediction for GlimmerHMM_glimmerT_46126-T1
Valid prediction for GlimmerHMM_glimmerT_46127-T1
Valid prediction for snap_scaffold_20-snap.1355-T1
Valid prediction for snap_scaffold_20-snap.1369-T1
Valid prediction for snap_scaffold_20-snap.1367-T1
Valid prediction for snap_scaffold_20-snap.1361-T1
Valid prediction for snap_scaffold_20-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_46139-T1
Valid prediction for snap_scaffold_20-snap.1372-T1
Valid prediction for pasa_asmbl_25826.p1
Couldn't classify 96809, 98446
Couldn't classify 102816, 102917
Sorry, prediction pasa_asmbl_25833.p1 fails validation.
(AGA)	 CT	96809-98446	GT	AGG
(GGC)	 AG	100300-100500	GT	AGG
(ATC)	 AG	100712-101081	GT	CGG
(CCC)	 AG	101307-101557	GT	AGG
(TTA)	 AG	102032-102184	GT	GGG
(CTC)	 AG	102816-102917	AG	GTA
-recovered pasa_asmbl_25833.p1, internal, 100300, 100500
-recovered pasa_asmbl_25833.p1, internal, 100712, 101081
-recovered pasa_asmbl_25833.p1, internal, 101307, 101557
-recovered pasa_asmbl_25833.p1, internal, 102032, 102184
Valid prediction for Augustus_model.g30615.t1
Valid prediction for Augustus_model.g30613.t1
Couldn't classify 202450, 202500
Couldn't classify 203343, 203426
Sorry, prediction pasa_asmbl_25823.p1 fails validation.
(ACC)	 GC	202450-202500	GT	AGG
(CTG)	 AG	202688-202815	GT	CGG
(GCT)	 AG	203017-203128	GT	GGG
(CTG)	 AG	203343-203426	AA	ATA
-recovered pasa_asmbl_25823.p1, internal, 202688, 202815
-recovered pasa_asmbl_25823.p1, internal, 203017, 203128
Valid prediction for snap_scaffold_20-snap.1371-T1
Valid prediction for pasa_asmbl_25831.p1
Valid prediction for snap_scaffold_20-snap.1346-T1
Valid prediction for GlimmerHMM_glimmerT_46130-T1
Valid prediction for snap_scaffold_20-snap.1341-T1
Valid prediction for Augustus_model.g30620.t1
Valid prediction for GlimmerHMM_glimmerT_46116-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 45820, rend_intergenic: 31231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61437, rend_intergenic: 52912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62943, rend_intergenic: 61665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71046, rend_intergenic: 63086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81731, rend_intergenic: 73189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86552, rend_intergenic: 83802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86954, rend_intergenic: 86657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110137, rend_intergenic: 98297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118981, rend_intergenic: 116548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142657, rend_intergenic: 137989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149261, rend_intergenic: 143960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171154, rend_intergenic: 167261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205605
-exon list size: 323


building trellis

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31.4    
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32.3    
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32.9    
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33.5    
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37.8    
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40.9    
41.2    
41.5    
41.8    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
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50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
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55.1    
55.4    
55.7    
56.0    
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56.9    
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58.2    
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60.0    
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60.9    
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64.3    
64.6    
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67.1    
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68.0    
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68.6    
68.9    
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69.8    
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71.1    
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75.1    
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76.0    
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83.4    
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86.2    
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86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
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93.5    
93.8    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 45820, rend_intergenic: 31231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61437, rend_intergenic: 52912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62943, rend_intergenic: 61665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71046, rend_intergenic: 63086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81731, rend_intergenic: 73189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86552, rend_intergenic: 83802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86954, rend_intergenic: 86657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110137, rend_intergenic: 98297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118981, rend_intergenic: 116548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142657, rend_intergenic: 137989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149261, rend_intergenic: 143960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171154, rend_intergenic: 167261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 194665 - 205605
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal

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

-building DP trellis

-building trellis in range 195448 - 205605
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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