-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_7932383-8099056

-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_41574-T1
Valid prediction for snap_scaffold_17-snap.1589-T1
Valid prediction for GlimmerHMM_glimmerT_41575-T1
Couldn't classify 89894, 90031
Sorry, prediction pasa_asmbl_18061.p1 fails validation.
(TGC)	 CT	89894-90031	GT	AGG
(GTG)	 AG	92458-92605	GT	TGG
(CTG)	 AG	94653-94750	AC	AGA
-recovered pasa_asmbl_18061.p1, terminal, 94653, 94750
-recovered pasa_asmbl_18061.p1, internal, 92458, 92605
Valid prediction for snap_scaffold_17-snap.1599-T1
Valid prediction for GeneMark_model.71571_t
Valid prediction for Augustus_model.g27850.t1
Valid prediction for Augustus_model.g27841.t1
Valid prediction for snap_scaffold_17-snap.1598-T1
Valid prediction for GeneMark_model.71583_t
Valid prediction for snap_scaffold_17-snap.1604-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1583-T1
Valid prediction for GeneMark_model.71573_t
Valid prediction for GlimmerHMM_glimmerT_41572-T1
Valid prediction for GeneMark_model.71566_t
Valid prediction for snap_scaffold_17-snap.1585-T1
Valid prediction for GlimmerHMM_glimmerT_41566-T1
Valid prediction for GlimmerHMM_glimmerT_41557-T1
Valid prediction for GeneMark_model.71541_t
Valid prediction for snap_scaffold_17-snap.1588-T1
Valid prediction for snap_scaffold_17-snap.1586-T1
Valid prediction for HiQ_model.g27860.t1
Valid prediction for pasa_asmbl_18064.p1
Valid prediction for GeneMark_model.71582_t
Valid prediction for GeneMark_model.71564_t
Valid prediction for GlimmerHMM_glimmerT_41554-T1
Valid prediction for Augustus_model.g27859.t1
Couldn't classify 97391, 97489
Couldn't classify 99153, 99201
Sorry, prediction pasa_asmbl_18062.p1 fails validation.
(CCT)	 GC	97391-97489	GT	AGG
(ATC)	 AG	98345-98502	GT	AGG
(AAT)	 AG	99153-99201	AG	GCA
-recovered pasa_asmbl_18062.p1, internal, 98345, 98502
Valid prediction for snap_scaffold_17-snap.1602-T1
Valid prediction for GlimmerHMM_glimmerT_41571-T1
Valid prediction for GlimmerHMM_glimmerT_41570-T1
Valid prediction for GeneMark_model.71552_t
Valid prediction for GeneMark_model.71575_t
Valid prediction for snap_scaffold_17-snap.1573-T1
Valid prediction for snap_scaffold_17-snap.1594-T1
Valid prediction for GlimmerHMM_glimmerT_41565-T1
Valid prediction for GeneMark_model.71577_t
Valid prediction for snap_scaffold_17-snap.1606-T1
Valid prediction for snap_scaffold_17-snap.1575-T1
Valid prediction for Augustus_model.g27854.t1
Valid prediction for CodingQuarry_transcript_22000-T1
Valid prediction for GeneMark_model.71585_t
Couldn't classify 103976, 104113
Sorry, prediction pasa_asmbl_18063.p1 fails validation.
(TGC)	 CT	103976-104113	GT	AGG
(GTG)	 AG	104703-104850	GT	TGG
(CGG)	 AG	105338-105435	TC	AAT
-recovered pasa_asmbl_18063.p1, terminal, 105338, 105435
-recovered pasa_asmbl_18063.p1, internal, 104703, 104850
Valid prediction for pasa_asmbl_18066.p1
Valid prediction for Augustus_model.g27862.t1
Valid prediction for GeneMark_model.71543_t
Valid prediction for GlimmerHMM_glimmerT_41563-T1
Valid prediction for GeneMark_model.71562_t
Valid prediction for snap_scaffold_17-snap.1581-T1
Valid prediction for Augustus_model.g27848.t1
Valid prediction for snap_scaffold_17-snap.1572-T1
Valid prediction for GeneMark_model.71580_t
Valid prediction for GeneMark_model.71569_t
Valid prediction for GeneMark_model.71548_t
Valid prediction for GlimmerHMM_glimmerT_41567-T1
Valid prediction for CodingQuarry_transcript_21999-T1
Valid prediction for GeneMark_model.71560_t
Valid prediction for GlimmerHMM_glimmerT_41561-T1
Valid prediction for snap_scaffold_17-snap.1590-T1
Valid prediction for GeneMark_model.71556_t
Valid prediction for GeneMark_model.71567_t
Valid prediction for GeneMark_model.71558_t
Valid prediction for snap_scaffold_17-snap.1600-T1
Valid prediction for GeneMark_model.71539_t
Valid prediction for Augustus_model.g27855.t1
Valid prediction for snap_scaffold_17-snap.1596-T1
Valid prediction for GeneMark_model.71545_t
Valid prediction for snap_scaffold_17-snap.1574-T1
Couldn't classify 67823, 67980
Couldn't classify 71393, 71441
Sorry, prediction pasa_asmbl_18059.p1 fails validation.
(CAG)	 CA	67823-67980	GT	AGG
(AAG)	 AG	69407-69604	GT	AGG
(GAT)	 AG	71393-71441	AG	GCA
-recovered pasa_asmbl_18059.p1, internal, 69407, 69604
Valid prediction for GlimmerHMM_glimmerT_41556-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 GeneMark_model.71572_t
Valid prediction for snap_scaffold_17-snap.1579-T1
Valid prediction for CodingQuarry_transcript_21992-T1
Valid prediction for CodingQuarry_transcript_21997-T1
Valid prediction for GeneMark_model.71540_t
Valid prediction for GeneMark_model.71584_t
Valid prediction for GeneMark_model.71553_t
Valid prediction for pasa_asmbl_19104.p1
Valid prediction for GeneMark_model.71544_t
Valid prediction for pasa_asmbl_19111.p1
Valid prediction for GeneMark_model.71570_t
Valid prediction for snap_scaffold_17-snap.1592-T1
Valid prediction for GlimmerHMM_glimmerT_41558-T1
Valid prediction for GeneMark_model.71549_t
Valid prediction for GeneMark_model.71538_t
Valid prediction for GeneMark_model.71576_t
Valid prediction for Augustus_model.g27847.t1
Valid prediction for snap_scaffold_17-snap.1576-T1
Valid prediction for snap_scaffold_17-snap.1607-T1
Valid prediction for HiQ_model.g27856.t1
Valid prediction for snap_scaffold_17-snap.1595-T1
Valid prediction for Augustus_model.g27861.t1
Valid prediction for GeneMark_model.71547_t
Valid prediction for Augustus_model.g27852.t1
Valid prediction for GeneMark_model.71574_t
Valid prediction for GeneMark_model.71568_t
Valid prediction for snap_scaffold_17-snap.1587-T1
Valid prediction for CodingQuarry_transcript_21994-T1
Valid prediction for GeneMark_model.71557_t
Valid prediction for snap_scaffold_17-snap.1605-T1
Valid prediction for CodingQuarry_transcript_21998-T1
Valid prediction for snap_scaffold_17-snap.1578-T1
Valid prediction for GeneMark_model.71546_t
Valid prediction for GeneMark_model.71551_t
Valid prediction for snap_scaffold_17-snap.1593-T1
Valid prediction for GlimmerHMM_glimmerT_41573-T1
Valid prediction for snap_scaffold_17-snap.1597-T1
Valid prediction for GlimmerHMM_glimmerT_41560-T1
Valid prediction for Augustus_model.g27845.t1
Valid prediction for pasa_asmbl_19109.p1
Valid prediction for snap_scaffold_17-snap.1582-T1
Valid prediction for snap_scaffold_17-snap.1601-T1
Valid prediction for HiQ_model.g27849.t1
Valid prediction for snap_scaffold_17-snap.1591-T1
Couldn't classify 58623, 58757
Sorry, prediction pasa_asmbl_19110.p1 fails validation.
(CTT)	 GT	58623-58757	GT	TGG
(GTG)	 AG	59053-59161	GT	TGG
(GCT)	 AG	59444-59685	GT	AGG
(GTT)	 AG	59855-60094	AC	GAA
-recovered pasa_asmbl_19110.p1, terminal, 59855, 60094
-recovered pasa_asmbl_19110.p1, internal, 59053, 59161
-recovered pasa_asmbl_19110.p1, internal, 59444, 59685
Valid prediction for snap_scaffold_17-snap.1584-T1
Valid prediction for CodingQuarry_transcript_21995-T1
Valid prediction for GlimmerHMM_glimmerT_41555-T1
Valid prediction for HiQ_model.g27857.t1
Valid prediction for GlimmerHMM_glimmerT_41559-T1
Valid prediction for Augustus_model.g27851.t1
Valid prediction for HiQ_model.g27846.t1
Valid prediction for GeneMark_model.71563_t
Valid prediction for GlimmerHMM_glimmerT_41569-T1
Couldn't classify 102282, 102325
Couldn't classify 102554, 102599
Sorry, prediction CodingQuarry_transcript_21996-T1 fails validation.
(ATG)	 CG	99756-99764	GT	ACG
(AGA)	 AG	99857-99909	GT	GGG
(TAT)	 AG	99989-100094	GT	AGG
(ATC)	 AG	100200-100272	GT	GAG
(ACA)	 AG	100367-100458	GT	ATG
(AAA)	 AG	100558-100640	GT	AAG
(GTA)	 AG	100726-100864	GT	CGG
(AAA)	 AG	100966-101034	GT	AGG
(GAG)	 AG	101115-101182	GT	GGG
(AAC)	 AG	101289-101396	GT	AAG
(AGA)	 AG	101490-101559	GT	GGG
(GAG)	 AG	101733-101897	GT	AGG
(CCC)	 AG	102036-102146	GT	CCG
(GAA)	 AG	102282-102325	CA	AAC
(GCT)	 AA	102554-102599	GT	AGG
(GAG)	 AG	102787-102864	AG	AGA
-recovered CodingQuarry_transcript_21996-T1, initial, 99756, 99764
-recovered CodingQuarry_transcript_21996-T1, terminal, 102787, 102864
-recovered CodingQuarry_transcript_21996-T1, internal, 99857, 99909
-recovered CodingQuarry_transcript_21996-T1, internal, 99989, 100094
-recovered CodingQuarry_transcript_21996-T1, internal, 100200, 100272
-recovered CodingQuarry_transcript_21996-T1, internal, 100367, 100458
-recovered CodingQuarry_transcript_21996-T1, internal, 100558, 100640
-recovered CodingQuarry_transcript_21996-T1, internal, 100726, 100864
-recovered CodingQuarry_transcript_21996-T1, internal, 100966, 101034
-recovered CodingQuarry_transcript_21996-T1, internal, 101115, 101182
-recovered CodingQuarry_transcript_21996-T1, internal, 101289, 101396
-recovered CodingQuarry_transcript_21996-T1, internal, 101490, 101559
-recovered CodingQuarry_transcript_21996-T1, internal, 101733, 101897
-recovered CodingQuarry_transcript_21996-T1, internal, 102036, 102146
Valid prediction for snap_scaffold_17-snap.1577-T1
Valid prediction for GlimmerHMM_glimmerT_41564-T1
Valid prediction for GlimmerHMM_glimmerT_41562-T1
Valid prediction for HiQ_model.g27858.t1
Valid prediction for GeneMark_model.71565_t
Valid prediction for GeneMark_model.71581_t
Valid prediction for GeneMark_model.71550_t
Valid prediction for GlimmerHMM_glimmerT_41576-T1
Valid prediction for snap_scaffold_17-snap.1603-T1
Valid prediction for GeneMark_model.71559_t
Valid prediction for GeneMark_model.71555_t
Valid prediction for GeneMark_model.71561_t
Valid prediction for snap_scaffold_17-snap.1580-T1
Valid prediction for GeneMark_model.71578_t
Valid prediction for CodingQuarry_transcript_21993-T1
Valid prediction for GlimmerHMM_glimmerT_41568-T1
Valid prediction for pasa_asmbl_19106.p1
Valid prediction for Augustus_model.g27843.t1
Valid prediction for GeneMark_model.71579_t
Valid prediction for GeneMark_model.71542_t
Valid prediction for snap_scaffold_17-snap.1571-T1
Valid prediction for HiQ_model.g27844.t1
Valid prediction for Augustus_model.g27853.t1
Valid prediction for Augustus_model.g27842.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10312, rend_intergenic: 4073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77156, rend_intergenic: 70352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87960, rend_intergenic: 84928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95220, rend_intergenic: 88808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105435, rend_intergenic: 99435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112646, rend_intergenic: 110618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125503, rend_intergenic: 119569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138962, rend_intergenic: 134045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147720, rend_intergenic: 141776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153141, rend_intergenic: 147749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162399, rend_intergenic: 156391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166674
-exon list size: 556


building trellis

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98.6    
98.7    
98.9    
99.1    
99.3    
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99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 10312, rend_intergenic: 4073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77156, rend_intergenic: 70352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87960, rend_intergenic: 84928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95220, rend_intergenic: 88808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105435, rend_intergenic: 99435  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112646, rend_intergenic: 110618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125503, rend_intergenic: 119569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138962, rend_intergenic: 134045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147720, rend_intergenic: 141776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153141, rend_intergenic: 147749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162399, rend_intergenic: 156391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support