-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_7881767-8088701

-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_40620-T1
Valid prediction for GlimmerHMM_glimmerT_40615-T1
Valid prediction for GlimmerHMM_glimmerT_40619-T1
Valid prediction for snap_scaffold_17-snap.1592-T1
Valid prediction for Augustus_model.g27092.t1
Valid prediction for GlimmerHMM_glimmerT_40628-T1
Valid prediction for Augustus_model.g27096.t1
Valid prediction for GlimmerHMM_glimmerT_40640-T1
Valid prediction for Augustus_model.g27091.t1
Valid prediction for Augustus_model.g27099.t1
Valid prediction for snap_scaffold_17-snap.1581-T1
Valid prediction for snap_scaffold_17-snap.1590-T1
Valid prediction for Augustus_model.g27074.t1
Valid prediction for snap_scaffold_17-snap.1558-T1
Valid prediction for GlimmerHMM_glimmerT_40633-T1
Valid prediction for pasa_asmbl_18935.p1
Valid prediction for snap_scaffold_17-snap.1578-T1
Valid prediction for snap_scaffold_17-snap.1573-T1
Valid prediction for GlimmerHMM_glimmerT_40634-T1
Valid prediction for snap_scaffold_17-snap.1580-T1
Valid prediction for Augustus_model.g27100.t1
Couldn't classify 118439, 118596
Couldn't classify 122009, 122057
Sorry, prediction pasa_asmbl_18928.p1 fails validation.
(CAG)	 CA	118439-118596	GT	AGG
(AAG)	 AG	120023-120220	GT	AGG
(GAT)	 AG	122009-122057	AG	GCA
-recovered pasa_asmbl_18928.p1, internal, 120023, 120220
Valid prediction for snap_scaffold_17-snap.1588-T1
Valid prediction for snap_scaffold_17-snap.1557-T1
Valid prediction for GlimmerHMM_glimmerT_40622-T1
Valid prediction for HiQ_model.g27097.t1
Valid prediction for snap_scaffold_17-snap.1577-T1
Valid prediction for snap_scaffold_17-snap.1565-T1
Valid prediction for GlimmerHMM_glimmerT_40644-T1
Valid prediction for snap_scaffold_17-snap.1594-T1
Valid prediction for pasa_asmbl_18933.p1
Valid prediction for Augustus_model.g27087.t1
Valid prediction for snap_scaffold_17-snap.1559-T1
Valid prediction for snap_scaffold_17-snap.1562-T1
Valid prediction for snap_scaffold_17-snap.1555-T1
Valid prediction for GlimmerHMM_glimmerT_40630-T1
Valid prediction for snap_scaffold_17-snap.1552-T1
Valid prediction for GlimmerHMM_glimmerT_40611-T1
Valid prediction for Augustus_model.g27078.t1
Valid prediction for snap_scaffold_17-snap.1596-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_40638-T1
Valid prediction for CodingQuarry_transcript_22042-T1
Valid prediction for snap_scaffold_17-snap.1553-T1
Couldn't classify 148007, 148105
Couldn't classify 149769, 149817
Sorry, prediction pasa_asmbl_18931.p1 fails validation.
(CCT)	 GC	148007-148105	GT	AGG
(ATC)	 AG	148961-149118	GT	AGG
(AAT)	 AG	149769-149817	AG	GCA
-recovered pasa_asmbl_18931.p1, internal, 148961, 149118
Couldn't classify 140510, 140647
Sorry, prediction pasa_asmbl_18930.p1 fails validation.
(TGC)	 CT	140510-140647	GT	AGG
(GTG)	 AG	143074-143221	GT	TGG
(CTG)	 AG	145269-145366	AC	AGA
-recovered pasa_asmbl_18930.p1, terminal, 145269, 145366
-recovered pasa_asmbl_18930.p1, internal, 143074, 143221
Valid prediction for snap_scaffold_17-snap.1582-T1
Valid prediction for snap_scaffold_17-snap.1567-T1
Couldn't classify 154592, 154729
Sorry, prediction pasa_asmbl_18932.p1 fails validation.
(TGC)	 CT	154592-154729	GT	AGG
(GTG)	 AG	155319-155466	GT	TGG
(CGG)	 AG	155954-156051	TC	AAT
-recovered pasa_asmbl_18932.p1, terminal, 155954, 156051
-recovered pasa_asmbl_18932.p1, internal, 155319, 155466
Valid prediction for snap_scaffold_17-snap.1585-T1
Valid prediction for GlimmerHMM_glimmerT_40639-T1
Valid prediction for snap_scaffold_17-snap.1575-T1
Valid prediction for CodingQuarry_transcript_22041-T1
Valid prediction for GlimmerHMM_glimmerT_40623-T1
Valid prediction for snap_scaffold_17-snap.1550-T1
Valid prediction for Augustus_model.g27085.t1
Valid prediction for snap_scaffold_17-snap.1564-T1
Valid prediction for GlimmerHMM_glimmerT_40635-T1
Valid prediction for snap_scaffold_17-snap.1563-T1
Valid prediction for Augustus_model.g27072.t1
Valid prediction for GlimmerHMM_glimmerT_40613-T1
Valid prediction for snap_scaffold_17-snap.1570-T1
Valid prediction for GlimmerHMM_glimmerT_40643-T1
Valid prediction for snap_scaffold_17-snap.1591-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: -)Couldn't classify 48268, 48402
Sorry, prediction pasa_asmbl_18069.p1 fails validation.
(CTT)	 GT	48268-48402	GT	TGG
(GTG)	 AG	48698-48806	GT	TGG
(GCT)	 AG	49089-49330	GT	AGG
(GTT)	 AG	49500-49739	AC	GAA
-recovered pasa_asmbl_18069.p1, terminal, 49500, 49739
-recovered pasa_asmbl_18069.p1, internal, 48698, 48806
-recovered pasa_asmbl_18069.p1, internal, 49089, 49330
Valid prediction for snap_scaffold_17-snap.1597-T1
Valid prediction for HiQ_model.g27086.t1
Valid prediction for Augustus_model.g27077.t1
Valid prediction for Augustus_model.g27098.t1
Valid prediction for Augustus_model.g27084.t1
Valid prediction for CodingQuarry_transcript_22040-T1
Valid prediction for Augustus_model.g27076.t1
Valid prediction for GlimmerHMM_glimmerT_40617-T1
Valid prediction for GlimmerHMM_glimmerT_40618-T1
Valid prediction for snap_scaffold_17-snap.1554-T1
Valid prediction for Augustus_model.g27073.t1
Valid prediction for snap_scaffold_17-snap.1568-T1
Valid prediction for Augustus_model.g27075.t1
Valid prediction for pasa_asmbl_18525.p1
Valid prediction for Augustus_model.g27082.t1
Valid prediction for GlimmerHMM_glimmerT_40625-T1
Valid prediction for snap_scaffold_17-snap.1587-T1
Valid prediction for CodingQuarry_transcript_22039-T1
Valid prediction for snap_scaffold_17-snap.1574-T1
Valid prediction for Augustus_model.g27079.t1
Valid prediction for GlimmerHMM_glimmerT_40627-T1
Valid prediction for GlimmerHMM_glimmerT_40612-T1
Valid prediction for pasa_asmbl_18065.p1
Valid prediction for GlimmerHMM_glimmerT_40624-T1
Valid prediction for Augustus_model.g27080.t1
Valid prediction for GlimmerHMM_glimmerT_40641-T1
Valid prediction for snap_scaffold_17-snap.1584-T1
Valid prediction for snap_scaffold_17-snap.1579-T1
Valid prediction for snap_scaffold_17-snap.1560-T1
Valid prediction for GlimmerHMM_glimmerT_40616-T1
Valid prediction for snap_scaffold_17-snap.1571-T1
Valid prediction for snap_scaffold_17-snap.1556-T1
Valid prediction for CodingQuarry_transcript_22038-T1
Valid prediction for snap_scaffold_17-snap.1583-T1
Valid prediction for HiQ_model.g27094.t1
Valid prediction for snap_scaffold_17-snap.1595-T1
Valid prediction for CodingQuarry_transcript_22037-T1
Valid prediction for GlimmerHMM_glimmerT_40636-T1
Valid prediction for GlimmerHMM_glimmerT_40621-T1
Valid prediction for GlimmerHMM_glimmerT_40614-T1
Valid prediction for GlimmerHMM_glimmerT_40632-T1
Valid prediction for Augustus_model.g27090.t1
Valid prediction for snap_scaffold_17-snap.1566-T1
Valid prediction for pasa_asmbl_18066.p1
Valid prediction for HiQ_model.g27095.t1
Valid prediction for snap_scaffold_17-snap.1572-T1
Valid prediction for GlimmerHMM_glimmerT_40631-T1
Valid prediction for snap_scaffold_17-snap.1551-T1
Valid prediction for HiQ_model.g27081.t1
Valid prediction for HiQ_model.g27093.t1
Valid prediction for GlimmerHMM_glimmerT_40626-T1
Valid prediction for snap_scaffold_17-snap.1593-T1
Valid prediction for HiQ_model.g27083.t1
Valid prediction for GlimmerHMM_glimmerT_40629-T1
Valid prediction for GlimmerHMM_glimmerT_40637-T1
Valid prediction for CodingQuarry_transcript_22035-T1
Valid prediction for GlimmerHMM_glimmerT_40642-T1
Valid prediction for snap_scaffold_17-snap.1586-T1
Valid prediction for Augustus_model.g27089.t1
Valid prediction for pasa_asmbl_18071.p1
Valid prediction for snap_scaffold_17-snap.1569-T1
Valid prediction for snap_scaffold_17-snap.1576-T1
Valid prediction for snap_scaffold_17-snap.1589-T1
Valid prediction for CodingQuarry_transcript_22036-T1
Valid prediction for Augustus_model.g27088.t1
Valid prediction for snap_scaffold_17-snap.1561-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15138, rend_intergenic: 10670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25861, rend_intergenic: 16294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31731, rend_intergenic: 26074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45552, rend_intergenic: 34441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47951, rend_intergenic: 46233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60928, rend_intergenic: 53864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127772, rend_intergenic: 120968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138576, rend_intergenic: 135544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145564, rend_intergenic: 139424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156051, rend_intergenic: 150051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163331, rend_intergenic: 160682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176119, rend_intergenic: 170185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189578, rend_intergenic: 184661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198336, rend_intergenic: 192392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203757, rend_intergenic: 198365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 37580, rend_intergenic: 37577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206935
-exon list size: 435


building trellis

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22.9    
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23.6    
23.8    
24.0    
24.3    
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24.9    
25.2    
25.4    
25.6    
25.9    
26.1    
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26.8    
27.0    
27.2    
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27.9    
28.1    
28.4    
28.6    
28.8    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.7    
30.9    
31.1    
31.4    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
33.0    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.6    
42.8    
43.0    
43.2    
43.5    
43.7    
43.9    
44.2    
44.4    
44.6    
44.9    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
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46.9    
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47.4    
47.6    
47.8    
48.1    
48.3    
48.5    
48.7    
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50.1    
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50.6    
50.8    
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51.9    
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58.6    
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61.6    
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64.1    
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80.3    
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83.3    
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84.0    
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84.4    
84.7    
84.9    
85.1    
85.4    
85.6    
85.8    
86.0    
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87.0    
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87.4    
87.6    
87.9    
88.1    
88.3    
88.6    
88.8    
89.0    
89.2    
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89.9    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
92.4    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
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95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 15138, rend_intergenic: 10670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25861, rend_intergenic: 16294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31731, rend_intergenic: 26074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45552, rend_intergenic: 34441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47951, rend_intergenic: 46233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60928, rend_intergenic: 53864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127772, rend_intergenic: 120968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138576, rend_intergenic: 135544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145564, rend_intergenic: 139424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156051, rend_intergenic: 150051  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163331, rend_intergenic: 160682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176119, rend_intergenic: 170185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189578, rend_intergenic: 184661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198336, rend_intergenic: 192392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203757, rend_intergenic: 198365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 37580, rend_intergenic: 37577  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