-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_6492008-7019562

-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: +)Couldn't classify 82668, 83690
Sorry, prediction pasa_asmbl_8198.p1 fails validation.
(CCA)	 TG	82668-83690	GG	AGG
Couldn't classify 8345, 8408
Sorry, prediction pasa_asmbl_7689.p1 fails validation.
(GTG)	 GG	8345-8408	GT	AGG
(CCT)	 AG	8605-8762	GT	CTG
(GAA)	 AG	8940-9104	GT	GAG
(ATT)	 AG	9309-9455	GT	GTG
(ACT)	 AG	9651-9792	GT	AGG
(ACT)	 AG	9986-10198	GT	AGG
(CCA)	 AG	10329-10466	GT	AGG
(GTA)	 AG	10603-10745	GT	ACG
(AAT)	 AG	11583-11719	GT	AGG
(TCT)	 AG	12378-12508	GT	GGG
(GAA)	 AG	13419-13543	GT	TGG
(CGT)	 AG	13860-13962	GT	GCG
(CAC)	 AG	14180-14247	GT	GAG
(CTC)	 AG	14430-14454	GT	TGG
(ATG)	 AG	14815-14876	AG	AAA
-recovered pasa_asmbl_7689.p1, terminal, 14815, 14876
-recovered pasa_asmbl_7689.p1, internal, 8605, 8762
-recovered pasa_asmbl_7689.p1, internal, 8940, 9104
-recovered pasa_asmbl_7689.p1, internal, 9309, 9455
-recovered pasa_asmbl_7689.p1, internal, 9651, 9792
-recovered pasa_asmbl_7689.p1, internal, 9986, 10198
-recovered pasa_asmbl_7689.p1, internal, 10329, 10466
-recovered pasa_asmbl_7689.p1, internal, 10603, 10745
-recovered pasa_asmbl_7689.p1, internal, 11583, 11719
-recovered pasa_asmbl_7689.p1, internal, 12378, 12508
-recovered pasa_asmbl_7689.p1, internal, 13419, 13543
-recovered pasa_asmbl_7689.p1, internal, 13860, 13962
-recovered pasa_asmbl_7689.p1, internal, 14180, 14247
-recovered pasa_asmbl_7689.p1, internal, 14430, 14454
Valid prediction for snap_scaffold_12-snap.1257-T1
Valid prediction for snap_scaffold_12-snap.1247-T1
Valid prediction for snap_scaffold_12-snap.1235-T1
Valid prediction for HiQ_model.g19432.t1
Valid prediction for pasa_asmbl_7692.p1
Couldn't classify 39690, 39704
Sorry, prediction pasa_asmbl_7696.p1 fails validation.
(TCC)	 CA	39690-39704	GT	AGG
(ACG)	 AG	39855-40042	GT	CGG
(TGT)	 AG	40257-40440	GT	AGG
(GGT)	 AG	40543-40657	GT	AGG
(GTG)	 AG	40915-41042	GT	AGG
(GTG)	 AG	41240-41443	GT	CTG
(AGC)	 AG	41592-41731	GT	AGG
(GTT)	 AG	41990-42155	GT	TGG
(AAA)	 AG	42483-42582	GT	AGG
(GGA)	 AG	42706-42902	AT	GAA
add_exon() Sorry, pasa_asmbl_7696.p1 42483-42582-terminal-3 is invalid.
-recovered pasa_asmbl_7696.p1, terminal, 42483, 42582
-recovered pasa_asmbl_7696.p1, terminal, 42706, 42902
-recovered pasa_asmbl_7696.p1, internal, 39855, 40042
-recovered pasa_asmbl_7696.p1, internal, 40257, 40440
-recovered pasa_asmbl_7696.p1, internal, 40543, 40657
-recovered pasa_asmbl_7696.p1, internal, 40915, 41042
-recovered pasa_asmbl_7696.p1, internal, 41240, 41443
-recovered pasa_asmbl_7696.p1, internal, 41592, 41731
-recovered pasa_asmbl_7696.p1, internal, 41990, 42155
-recovered pasa_asmbl_7696.p1, internal, 42483, 42582
Valid prediction for CodingQuarry_transcript_10251-T1
Couldn't classify 38790, 39662
Sorry, prediction pasa_asmbl_7695.p1 fails validation.
(ATG)	 AA	38259-38261	GT	TGG
(GAT)	 AG	38483-38590	GT	CGG
(GGT)	 AG	38790-39662	GG	CAG
-recovered pasa_asmbl_7695.p1, initial, 38259, 38261
-recovered pasa_asmbl_7695.p1, internal, 38483, 38590
Valid prediction for GlimmerHMM_glimmerT_29480-T1
Valid prediction for snap_scaffold_12-snap.1232-T1
Valid prediction for snap_scaffold_12-snap.1230-T1
Valid prediction for HiQ_model.g19438.t1
Valid prediction for snap_scaffold_12-snap.1231-T1
Valid prediction for GlimmerHMM_glimmerT_29482-T1
Couldn't classify 74931, 75803
Sorry, prediction pasa_asmbl_7703.p1 fails validation.
(GTT)	 AT	74931-75803	CT	ACC
Valid prediction for GlimmerHMM_glimmerT_29473-T1
Valid prediction for snap_scaffold_12-snap.1236-T1
Valid prediction for snap_scaffold_12-snap.1237-T1
Valid prediction for snap_scaffold_12-snap.1234-T1
Valid prediction for Augustus_model.g19436.t1
Valid prediction for GlimmerHMM_glimmerT_29465-T1
Valid prediction for GlimmerHMM_glimmerT_29469-T1
Valid prediction for GlimmerHMM_glimmerT_29477-T1
Valid prediction for snap_scaffold_12-snap.1239-T1
Valid prediction for snap_scaffold_12-snap.1259-T1
Valid prediction for snap_scaffold_12-snap.1225-T1
Valid prediction for Augustus_model.g19439.t1
Valid prediction for GlimmerHMM_glimmerT_29463-T1
Couldn't classify 46568, 46591
Sorry, prediction pasa_asmbl_7699.p1 fails validation.
(CTC)	 CT	46568-46591	GT	GGG
(ACT)	 AG	47443-47601	GT	AGG
(GTT)	 AG	47893-47956	GT	CTG
(TGA)	 AG	48129-48271	GT	AGG
(GCT)	 AG	49035-49178	GT	AGG
(GTC)	 AG	49294-49423	GT	TGG
(CCA)	 AG	49604-49808	GT	AGG
(CAC)	 AG	49968-50140	GT	AGG
(GAA)	 AG	50454-50578	GT	CTG
(CTG)	 AG	51057-51215	GC	GAG
-recovered pasa_asmbl_7699.p1, terminal, 51057, 51215
-recovered pasa_asmbl_7699.p1, internal, 47443, 47601
-recovered pasa_asmbl_7699.p1, internal, 47893, 47956
-recovered pasa_asmbl_7699.p1, internal, 48129, 48271
-recovered pasa_asmbl_7699.p1, internal, 49035, 49178
-recovered pasa_asmbl_7699.p1, internal, 49294, 49423
-recovered pasa_asmbl_7699.p1, internal, 49604, 49808
-recovered pasa_asmbl_7699.p1, internal, 49968, 50140
-recovered pasa_asmbl_7699.p1, internal, 50454, 50578
-recovered pasa_asmbl_7699.p1, internal, 51057, 51215
Valid prediction for HiQ_model.g19431.t1
Couldn't classify 73545, 74771
Sorry, prediction pasa_asmbl_7702.p1 fails validation.
(ATG)	 AG	72890-73046	GT	AGG
(GGG)	 AG	73251-73450	GT	TAG
(AGT)	 AG	73545-74771	GG	CTG
-recovered pasa_asmbl_7702.p1, initial, 72890, 73046
-recovered pasa_asmbl_7702.p1, internal, 72890, 73046
-recovered pasa_asmbl_7702.p1, internal, 73251, 73450
Valid prediction for pasa_asmbl_7690.p1
Valid prediction for snap_scaffold_12-snap.1233-T1
Valid prediction for GlimmerHMM_glimmerT_29468-T1
Valid prediction for GlimmerHMM_glimmerT_29470-T1
Valid prediction for GlimmerHMM_glimmerT_29472-T1
Valid prediction for snap_scaffold_12-snap.1260-T1
Valid prediction for snap_scaffold_12-snap.1251-T1
Valid prediction for snap_scaffold_12-snap.1227-T1
Valid prediction for Augustus_model.g19434.t1
Valid prediction for snap_scaffold_12-snap.1228-T1
Valid prediction for snap_scaffold_12-snap.1248-T1
Valid prediction for GlimmerHMM_glimmerT_29489-T1
Valid prediction for CodingQuarry_transcript_10252-T1
Valid prediction for Augustus_model.g19433.t1
Valid prediction for snap_scaffold_12-snap.1229-T1
Valid prediction for snap_scaffold_12-snap.1222-T1
Valid prediction for HiQ_model.g19441.t1
Valid prediction for CodingQuarry_transcript_10255-T1
Valid prediction for GlimmerHMM_glimmerT_29474-T1
Valid prediction for GlimmerHMM_glimmerT_29485-T1
Valid prediction for snap_scaffold_12-snap.1224-T1
Valid prediction for snap_scaffold_12-snap.1249-T1
Valid prediction for CodingQuarry_transcript_10256-T1
Valid prediction for HiQ_model.g19437.t1
Valid prediction for Augustus_model.g19440.t1
Valid prediction for Augustus_model.g19442.t1
Valid prediction for snap_scaffold_12-snap.1223-T1
Valid prediction for pasa_asmbl_7705.p1
Valid prediction for GlimmerHMM_glimmerT_29467-T1
Valid prediction for GlimmerHMM_glimmerT_29492-T1
Valid prediction for pasa_asmbl_7697.p1

-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_29475-T1
Valid prediction for GlimmerHMM_glimmerT_29484-T1
Valid prediction for GlimmerHMM_glimmerT_29481-T1
Valid prediction for snap_scaffold_12-snap.1242-T1
Valid prediction for GlimmerHMM_glimmerT_29478-T1
Valid prediction for GlimmerHMM_glimmerT_29487-T1
Valid prediction for snap_scaffold_12-snap.1258-T1
Valid prediction for Augustus_model.g19446.t1
Valid prediction for HiQ_model.g19435.t1
Valid prediction for snap_scaffold_12-snap.1245-T1
Valid prediction for Augustus_model.g19444.t1
Valid prediction for snap_scaffold_12-snap.1253-T1
Valid prediction for GlimmerHMM_glimmerT_29493-T1
Valid prediction for snap_scaffold_12-snap.1254-T1
Valid prediction for GlimmerHMM_glimmerT_29464-T1
Valid prediction for snap_scaffold_12-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_29471-T1
Valid prediction for CodingQuarry_transcript_10259-T1
Valid prediction for snap_scaffold_12-snap.1240-T1
Couldn't classify 491168, 491188
Sorry, prediction pasa_asmbl_8540.p1 fails validation.
(ATT)	 TC	491168-491188	GT	AGG
(GTG)	 AG	491330-491379	GT	CTG
(GTG)	 AG	491580-491811	GT	AGG
(GGC)	 AG	492044-492193	GT	AGG
(GCC)	 AG	492303-492431	GT	CGG
(GTT)	 AG	492698-492813	GT	GGG
(TTG)	 AG	492918-493014	TT	GAT
-recovered pasa_asmbl_8540.p1, terminal, 492918, 493014
-recovered pasa_asmbl_8540.p1, internal, 491330, 491379
-recovered pasa_asmbl_8540.p1, internal, 491580, 491811
-recovered pasa_asmbl_8540.p1, internal, 492044, 492193
-recovered pasa_asmbl_8540.p1, internal, 492303, 492431
-recovered pasa_asmbl_8540.p1, internal, 492698, 492813
Valid prediction for CodingQuarry_transcript_10260-T1
Valid prediction for snap_scaffold_12-snap.1241-T1
Valid prediction for snap_scaffold_12-snap.1246-T1
Valid prediction for GlimmerHMM_glimmerT_29479-T1
Valid prediction for GlimmerHMM_glimmerT_29476-T1
Valid prediction for HiQ_model.g19449.t1
Valid prediction for GlimmerHMM_glimmerT_29491-T1
Valid prediction for HiQ_model.g19448.t1
Valid prediction for snap_scaffold_12-snap.1261-T1
Valid prediction for CodingQuarry_transcript_10258-T1
Valid prediction for Augustus_model.g19450.t1
Valid prediction for snap_scaffold_12-snap.1226-T1
Valid prediction for snap_scaffold_12-snap.1244-T1
Valid prediction for Augustus_model.g19445.t1
Valid prediction for GlimmerHMM_glimmerT_29488-T1
Valid prediction for snap_scaffold_12-snap.1250-T1
Valid prediction for Augustus_model.g19447.t1
Valid prediction for snap_scaffold_12-snap.1238-T1
Valid prediction for snap_scaffold_12-snap.1255-T1
Valid prediction for GlimmerHMM_glimmerT_29483-T1
Valid prediction for Augustus_model.g19451.t1
Valid prediction for CodingQuarry_transcript_10253-T1
Valid prediction for pasa_asmbl_8547.p1
Valid prediction for snap_scaffold_12-snap.1252-T1
Valid prediction for Augustus_model.g19443.t1
Valid prediction for GlimmerHMM_glimmerT_29486-T1
Valid prediction for CodingQuarry_transcript_10254-T1
Valid prediction for GlimmerHMM_glimmerT_29490-T1
Valid prediction for snap_scaffold_12-snap.1256-T1
Valid prediction for pasa_asmbl_8549.p1
Valid prediction for pasa_asmbl_8553.p1
Valid prediction for GlimmerHMM_glimmerT_29466-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 151783, rend_intergenic: 149706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 433909, rend_intergenic: 430365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 482431, rend_intergenic: 479953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 394532, rend_intergenic: 394529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 527555
-exon list size: 371


building trellis

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29.8    
30.0    
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30.6    
30.8    
31.1    
31.4    
31.6    
31.9    
32.2    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
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34.3    
34.6    
34.9    
35.1    
35.4    
35.7    
35.9    
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37.0    
37.3    
37.5    
37.8    
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38.3    
38.6    
38.9    
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39.4    
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39.9    
40.2    
40.5    
40.8    
41.0    
41.3    
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41.8    
42.1    
42.4    
42.6    
42.9    
43.2    
43.4    
43.7    
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44.8    
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45.3    
45.6    
45.8    
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48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
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50.7    
50.9    
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53.4    
53.6    
53.9    
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55.5    
55.8    
56.0    
56.3    
56.6    
56.8    
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57.4    
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60.9    
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64.3    
64.6    
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67.0    
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67.6    
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79.9    
80.2    
80.4    
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88.2    
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88.7    
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90.1    
90.3    
90.6    
90.9    
91.2    
91.4    
91.7    
92.0    
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92.5    
92.8    
93.0    
93.3    
93.6    
93.8    
94.1    
94.4    
94.6    
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95.4    
95.7    
96.0    
96.2    
96.5    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 151783, rend_intergenic: 149706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 433909, rend_intergenic: 430365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 482431, rend_intergenic: 479953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 394532, rend_intergenic: 394529  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 517415 - 527555
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

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