-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_8179458-8412693

-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.1816-T1
Valid prediction for GlimmerHMM_glimmerT_46446-T1
Valid prediction for Augustus_model.g30831.t1
Valid prediction for snap_scaffold_20-snap.1788-T1
Valid prediction for snap_scaffold_20-snap.1807-T1
Valid prediction for snap_scaffold_20-snap.1784-T1
Valid prediction for GlimmerHMM_glimmerT_46427-T1
Valid prediction for Augustus_model.g30846.t1
Couldn't classify 76939, 76991
Sorry, prediction pasa_asmbl_26753.p1 fails validation.
(GAA)	 AG	76939-76991	GT	AAG
(CCT)	 AG	77970-78402	GA	GAG
-recovered pasa_asmbl_26753.p1, terminal, 77970, 78402
-recovered pasa_asmbl_26753.p1, internal, 76939, 76991
Valid prediction for Augustus_model.g30830.t1
Couldn't classify 85233, 85400
Sorry, prediction pasa_asmbl_26754.p1 fails validation.
(TCT)	 CC	85233-85400	GT	AGG
(GAG)	 AG	85683-85844	GT	AGG
(GTG)	 AG	86097-86222	GT	AGG
(AAA)	 AG	86492-86778	GT	AGG
(CAG)	 AG	86961-87094	GT	AGG
(AGC)	 AG	87437-87540	AA	AGA
-recovered pasa_asmbl_26754.p1, terminal, 87437, 87540
-recovered pasa_asmbl_26754.p1, internal, 85683, 85844
-recovered pasa_asmbl_26754.p1, internal, 86097, 86222
-recovered pasa_asmbl_26754.p1, internal, 86492, 86778
-recovered pasa_asmbl_26754.p1, internal, 86961, 87094
Valid prediction for snap_scaffold_20-snap.1814-T1
Valid prediction for Augustus_model.g30829.t1
Valid prediction for snap_scaffold_20-snap.1796-T1
Valid prediction for HiQ_model.g30834.t1
Valid prediction for Augustus_model.g30850.t1
Valid prediction for GlimmerHMM_glimmerT_46421-T1
Valid prediction for snap_scaffold_20-snap.1782-T1
Couldn't classify 93809, 94366
Sorry, prediction pasa_asmbl_26755.p1 fails validation.
(TCC)	 TC	93809-94366	GT	AGG
(ATC)	 AG	94779-94861	GT	AAG
(GTA)	 AG	95061-95217	GT	AGG
(GAG)	 AG	95508-95669	GT	AGG
(ACA)	 AG	95790-95915	GT	TGG
(AAA)	 AG	96017-96237	GT	GGG
(CAT)	 AG	96545-96656	TG	AGT
-recovered pasa_asmbl_26755.p1, terminal, 96545, 96656
-recovered pasa_asmbl_26755.p1, internal, 94779, 94861
-recovered pasa_asmbl_26755.p1, internal, 95061, 95217
-recovered pasa_asmbl_26755.p1, internal, 95508, 95669
-recovered pasa_asmbl_26755.p1, internal, 95790, 95915
-recovered pasa_asmbl_26755.p1, internal, 96017, 96237
Valid prediction for snap_scaffold_20-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_46434-T1
Valid prediction for snap_scaffold_20-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_46423-T1
Valid prediction for snap_scaffold_20-snap.1791-T1
Valid prediction for Augustus_model.g30847.t1
Valid prediction for CodingQuarry_transcript_30576-T1
Valid prediction for snap_scaffold_20-snap.1820-T1
Valid prediction for Augustus_model.g30833.t1
Valid prediction for snap_scaffold_20-snap.1805-T1
Valid prediction for snap_scaffold_20-snap.1781-T1
Valid prediction for pasa_asmbl_26759.p1
Valid prediction for Augustus_model.g30825.t1
Valid prediction for pasa_asmbl_26773.p1
Valid prediction for GlimmerHMM_glimmerT_46430-T1
Valid prediction for snap_scaffold_20-snap.1795-T1
Valid prediction for Augustus_model.g30849.t1
Valid prediction for Augustus_model.g30832.t1
Valid prediction for GlimmerHMM_glimmerT_46420-T1
Valid prediction for snap_scaffold_20-snap.1801-T1
Couldn't classify 136690, 136854
Sorry, prediction pasa_asmbl_26764.p1 fails validation.
(AGG)	 TA	136690-136854	GT	AGG
(ACA)	 AG	137813-138094	GT	AGG
(GAG)	 AG	139731-139856	GT	TAG
(GAG)	 AG	140265-140485	GT	AGG
(GCA)	 AG	142296-142525	GT	AGG
(AAC)	 AG	142646-142748	GT	GAG
(GAC)	 AG	143898-144111	CC	GAC
-recovered pasa_asmbl_26764.p1, terminal, 143898, 144111
-recovered pasa_asmbl_26764.p1, internal, 137813, 138094
-recovered pasa_asmbl_26764.p1, internal, 139731, 139856
-recovered pasa_asmbl_26764.p1, internal, 140265, 140485
-recovered pasa_asmbl_26764.p1, internal, 142296, 142525
-recovered pasa_asmbl_26764.p1, internal, 142646, 142748
Valid prediction for GlimmerHMM_glimmerT_46433-T1
Valid prediction for GlimmerHMM_glimmerT_46435-T1
Valid prediction for snap_scaffold_20-snap.1780-T1
Valid prediction for GlimmerHMM_glimmerT_46426-T1
Valid prediction for GlimmerHMM_glimmerT_46445-T1
Valid prediction for snap_scaffold_20-snap.1798-T1
Couldn't classify 72212, 72247
Couldn't classify 75009, 75162
Sorry, prediction pasa_asmbl_27214.p1 fails validation.
(CAT)	 AT	72212-72247	GT	AGG
(AAA)	 AG	72572-72688	GT	AGG
(ATA)	 AG	72811-72908	GT	CCG
(AAT)	 AG	73005-73113	GT	AGG
(GCC)	 AG	73227-73305	GT	CTG
(CCT)	 AG	73502-73632	GT	GGG
(CTC)	 AG	74053-74127	GT	AGG
(CTG)	 AG	74562-74773	GT	AAG
(GAA)	 AG	75009-75162	AG	CCA
-recovered pasa_asmbl_27214.p1, internal, 72572, 72688
-recovered pasa_asmbl_27214.p1, internal, 72811, 72908
-recovered pasa_asmbl_27214.p1, internal, 73005, 73113
-recovered pasa_asmbl_27214.p1, internal, 73227, 73305
-recovered pasa_asmbl_27214.p1, internal, 73502, 73632
-recovered pasa_asmbl_27214.p1, internal, 74053, 74127
-recovered pasa_asmbl_27214.p1, internal, 74562, 74773
Valid prediction for snap_scaffold_20-snap.1794-T1
Valid prediction for snap_scaffold_20-snap.1817-T1
Valid prediction for CodingQuarry_transcript_30577-T1
Valid prediction for snap_scaffold_20-snap.1792-T1
Valid prediction for snap_scaffold_20-snap.1783-T1
Valid prediction for GlimmerHMM_glimmerT_46422-T1
Valid prediction for CodingQuarry_transcript_30575-T1
Couldn't classify 195198, 195752
Sorry, prediction pasa_asmbl_26770.p1 fails validation.
(CGC)	 AT	195198-195752	TG	AGT
Valid prediction for GlimmerHMM_glimmerT_46441-T1
Valid prediction for HiQ_model.g30839.t1
Valid prediction for GlimmerHMM_glimmerT_46431-T1
Couldn't classify 200595, 200627
Couldn't classify 201443, 201646
Sorry, prediction pasa_asmbl_27160.p2 fails validation.
(TGG)	 TA	200595-200627	GT	CAG
(TTC)	 AG	200833-200919	GT	AGG
(CGC)	 AG	201443-201646	GG	GGG
-recovered pasa_asmbl_27160.p2, internal, 200833, 200919
Couldn't classify 22465, 22675
Sorry, prediction pasa_asmbl_26750.p1 fails validation.
(ATG)	 AA	21734-22170	GT	CGG
(GCT)	 AG	22465-22675	CA	GCC
-recovered pasa_asmbl_26750.p1, initial, 21734, 22170
Valid prediction for Augustus_model.g30826.t1
Valid prediction for Augustus_model.g30838.t1
Valid prediction for HiQ_model.g30836.t1
Valid prediction for GlimmerHMM_glimmerT_46416-T1
Valid prediction for GlimmerHMM_glimmerT_46442-T1
Valid prediction for GlimmerHMM_glimmerT_46418-T1
Valid prediction for GlimmerHMM_glimmerT_46425-T1
Valid prediction for Augustus_model.g30827.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_46443-T1
Valid prediction for snap_scaffold_20-snap.1803-T1
Valid prediction for GlimmerHMM_glimmerT_46444-T1
Valid prediction for HiQ_model.g30842.t1
Valid prediction for HiQ_model.g30828.t1
Valid prediction for snap_scaffold_20-snap.1799-T1
Valid prediction for snap_scaffold_20-snap.1815-T1
Couldn't classify 109763, 110215
Sorry, prediction pasa_asmbl_25977.p1 fails validation.
(AAT)	 TC	109763-110215	GT	AGG
(ATC)	 AG	110587-110669	GT	AAG
(GTA)	 AG	110944-111100	GT	AGG
(GAG)	 AG	111600-111764	GT	AGG
(TTT)	 AG	112017-112142	GT	TGG
(AGA)	 AG	112571-112791	GT	AGG
(CCA)	 AG	112991-113028	GT	ACG
(AGG)	 AG	113261-113367	AC	AGA
add_exon() Sorry, pasa_asmbl_25977.p1 112571-112791-terminal-2 is invalid.
-recovered pasa_asmbl_25977.p1, terminal, 112571, 112791
-recovered pasa_asmbl_25977.p1, terminal, 113261, 113367
-recovered pasa_asmbl_25977.p1, internal, 110587, 110669
-recovered pasa_asmbl_25977.p1, internal, 110944, 111100
-recovered pasa_asmbl_25977.p1, internal, 111600, 111764
-recovered pasa_asmbl_25977.p1, internal, 112017, 112142
-recovered pasa_asmbl_25977.p1, internal, 112571, 112791
-recovered pasa_asmbl_25977.p1, internal, 112991, 113028
Valid prediction for Augustus_model.g30843.t1
Couldn't classify 59018, 59182
Sorry, prediction pasa_asmbl_25989.p2 fails validation.
(GCC)	 CA	59018-59182	GT	TGG
(GCT)	 AG	59545-59670	GT	AGG
(TGC)	 AG	60840-60977	GG	GAG
-recovered pasa_asmbl_25989.p2, terminal, 60840, 60977
-recovered pasa_asmbl_25989.p2, internal, 59545, 59670
Valid prediction for snap_scaffold_20-snap.1785-T1
Couldn't classify 201970, 202068
Sorry, prediction pasa_asmbl_25975.p1 fails validation.
(CCG)	 AC	201970-202068	GT	AGG
(GCT)	 AG	202315-202467	GT	AGG
(GAT)	 AG	202737-202856	GT	AGG
(CTG)	 AG	203031-203181	GT	TGG
(CCA)	 AG	203453-203574	GT	TGG
(GCC)	 AG	203892-203934	GT	CGG
(AGC)	 AG	204089-204252	GA	AGG
-recovered pasa_asmbl_25975.p1, terminal, 204089, 204252
-recovered pasa_asmbl_25975.p1, internal, 202315, 202467
-recovered pasa_asmbl_25975.p1, internal, 202737, 202856
-recovered pasa_asmbl_25975.p1, internal, 203031, 203181
-recovered pasa_asmbl_25975.p1, internal, 203453, 203574
-recovered pasa_asmbl_25975.p1, internal, 203892, 203934
Valid prediction for snap_scaffold_20-snap.1809-T1
Valid prediction for GlimmerHMM_glimmerT_46429-T1
Valid prediction for GlimmerHMM_glimmerT_46437-T1
Valid prediction for GlimmerHMM_glimmerT_46424-T1
Valid prediction for GlimmerHMM_glimmerT_46417-T1
Valid prediction for snap_scaffold_20-snap.1813-T1
Valid prediction for GlimmerHMM_glimmerT_46419-T1
Valid prediction for Augustus_model.g30845.t1
Valid prediction for GlimmerHMM_glimmerT_46439-T1
Valid prediction for snap_scaffold_20-snap.1819-T1
Valid prediction for snap_scaffold_20-snap.1804-T1
Valid prediction for Augustus_model.g30835.t1
Couldn't classify 10293, 10458
Couldn't classify 11720, 11832
Sorry, prediction pasa_asmbl_25995.p1 fails validation.
(TTT)	 GT	10293-10458	GT	AGG
(ACA)	 AG	11477-11614	GT	GTG
(GGT)	 AG	11720-11832	CA	GAC
-recovered pasa_asmbl_25995.p1, internal, 11477, 11614
Couldn't classify 17447, 17461
Sorry, prediction pasa_asmbl_25992.p1 fails validation.
(CTT)	 CT	17447-17461	GT	TGG
(GAA)	 AG	17925-18070	GT	GGG
(TTC)	 AG	18199-18317	GT	AGG
(GTG)	 AG	18900-19024	GT	TGG
(CGT)	 AG	19160-19257	GT	AAG
(CAC)	 AG	19659-19786	GT	GAG
(CTT)	 AG	20158-20282	GT	GTG
(GTG)	 AG	20716-20861	GT	AGG
(CGT)	 AG	21058-21160	GT	AGG
(AAA)	 AG	21399-21541	GC	ACG
(GGA)	 AG	21771-21879	AC	GAA
add_exon() Sorry, pasa_asmbl_25992.p1 19659-19786-terminal-2 is invalid.
-recovered pasa_asmbl_25992.p1, terminal, 19659, 19786
-recovered pasa_asmbl_25992.p1, terminal, 21771, 21879
-recovered pasa_asmbl_25992.p1, internal, 17925, 18070
-recovered pasa_asmbl_25992.p1, internal, 18199, 18317
-recovered pasa_asmbl_25992.p1, internal, 18900, 19024
-recovered pasa_asmbl_25992.p1, internal, 19160, 19257
-recovered pasa_asmbl_25992.p1, internal, 19659, 19786
-recovered pasa_asmbl_25992.p1, internal, 20158, 20282
-recovered pasa_asmbl_25992.p1, internal, 20716, 20861
-recovered pasa_asmbl_25992.p1, internal, 21058, 21160
-recovered pasa_asmbl_25992.p1, internal, 21399, 21541
Valid prediction for Augustus_model.g30844.t1
Valid prediction for GlimmerHMM_glimmerT_46438-T1
Valid prediction for snap_scaffold_20-snap.1797-T1
Valid prediction for snap_scaffold_20-snap.1789-T1
Valid prediction for snap_scaffold_20-snap.1802-T1
Couldn't classify 15764, 15906
Couldn't classify 16452, 16495
Sorry, prediction pasa_asmbl_25994.p1 fails validation.
(AAA)	 AA	15764-15906	GT	AAG
(CTT)	 AG	15999-16135	GT	AGG
(CTA)	 AG	16452-16495	AG	AGA
-recovered pasa_asmbl_25994.p1, internal, 15999, 16135
Valid prediction for GlimmerHMM_glimmerT_46440-T1
Valid prediction for snap_scaffold_20-snap.1810-T1
Couldn't classify 50864, 51232
Sorry, prediction pasa_asmbl_25991.p1 fails validation.
(ATG)	 TC	50864-51232	GG	CAG
Valid prediction for snap_scaffold_20-snap.1818-T1
Valid prediction for snap_scaffold_20-snap.1806-T1
Valid prediction for snap_scaffold_20-snap.1811-T1
Valid prediction for snap_scaffold_20-snap.1786-T1
Valid prediction for GlimmerHMM_glimmerT_46432-T1
Valid prediction for GlimmerHMM_glimmerT_46428-T1
Valid prediction for CodingQuarry_transcript_30579-T1
Valid prediction for pasa_asmbl_25984.p3
Valid prediction for snap_scaffold_20-snap.1790-T1
Valid prediction for GlimmerHMM_glimmerT_46436-T1
Valid prediction for Augustus_model.g30840.t1
Valid prediction for HiQ_model.g30837.t1
Valid prediction for Augustus_model.g30848.t1
Valid prediction for snap_scaffold_20-snap.1787-T1
Valid prediction for snap_scaffold_20-snap.1808-T1
Valid prediction for Augustus_model.g30841.t1
Valid prediction for snap_scaffold_20-snap.1812-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 111395, rend_intergenic: 108855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121256, rend_intergenic: 119870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138206, rend_intergenic: 133517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140871, rend_intergenic: 139134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185699, rend_intergenic: 180742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233236
-exon list size: 411


building trellis

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33.9    
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38.5    
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47.9    
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90.6    
90.8    
91.0    
91.3    
91.5    
91.8    
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92.3    
92.5    
92.7    
93.0    
93.2    
93.5    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.1    
97.3    
97.6    
97.8    
98.1    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 111395, rend_intergenic: 108855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121256, rend_intergenic: 119870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138206, rend_intergenic: 133517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140871, rend_intergenic: 139134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185699, rend_intergenic: 180742  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support