-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_10452689-10586608

-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 GeneMark_model.44211_t
Valid prediction for HiQ_model.g17336.t1
Valid prediction for GlimmerHMM_glimmerT_25835-T1
Valid prediction for GeneMark_model.44236_t
Couldn't classify 92980, 93546
Sorry, prediction pasa_asmbl_4695.p1 fails validation.
(CCC)	 AT	92980-93546	GC	AGG
Valid prediction for GeneMark_model.44223_t
Valid prediction for Augustus_model.g17331.t1
Valid prediction for snap_scaffold_10-snap.2038-T1
Valid prediction for GeneMark_model.44221_t
Valid prediction for GlimmerHMM_glimmerT_25825-T1
Valid prediction for GeneMark_model.44216_t
Valid prediction for GeneMark_model.44227_t
Valid prediction for GlimmerHMM_glimmerT_25819-T1
Valid prediction for snap_scaffold_10-snap.2050-T1
Valid prediction for snap_scaffold_10-snap.2041-T1
Couldn't classify 120024, 120101
Sorry, prediction pasa_asmbl_4700.p1 fails validation.
(ATG)	 TT	110952-111098	GT	AGG
(GTG)	 AG	114018-114206	GT	AGG
(GTG)	 AG	114340-115032	GT	AGG
(GAC)	 AG	115521-115656	GT	AGG
(AGG)	 AG	115870-116021	GT	AGG
(CAT)	 AG	116109-116663	GT	AGG
(GTG)	 AG	116766-116873	GT	AGG
(ATA)	 AG	116972-117270	GT	AGG
(GAT)	 AG	117349-117499	GT	AGG
(ATG)	 AG	117574-117693	GT	AGG
(GAA)	 AG	117856-117985	GT	AGG
(ATA)	 AG	118322-118452	GT	AGG
(GAC)	 AG	118563-118678	GT	AGG
(GTC)	 AG	118816-119175	GT	GAG
(ACT)	 AG	119524-119638	GT	TGG
(GAG)	 AG	119829-119936	GT	GGG
(AGG)	 AG	120024-120101	CA	CCC
-recovered pasa_asmbl_4700.p1, initial, 110952, 111098
-recovered pasa_asmbl_4700.p1, initial, 117574, 117693
-recovered pasa_asmbl_4700.p1, terminal, 117856, 117985
-recovered pasa_asmbl_4700.p1, internal, 114018, 114206
-recovered pasa_asmbl_4700.p1, internal, 114340, 115032
-recovered pasa_asmbl_4700.p1, internal, 115521, 115656
-recovered pasa_asmbl_4700.p1, internal, 115870, 116021
-recovered pasa_asmbl_4700.p1, internal, 116109, 116663
-recovered pasa_asmbl_4700.p1, internal, 116766, 116873
-recovered pasa_asmbl_4700.p1, internal, 116972, 117270
-recovered pasa_asmbl_4700.p1, internal, 117349, 117499
-recovered pasa_asmbl_4700.p1, internal, 117574, 117693
-recovered pasa_asmbl_4700.p1, internal, 117856, 117985
-recovered pasa_asmbl_4700.p1, internal, 118322, 118452
-recovered pasa_asmbl_4700.p1, internal, 118563, 118678
-recovered pasa_asmbl_4700.p1, internal, 118816, 119175
-recovered pasa_asmbl_4700.p1, internal, 119524, 119638
-recovered pasa_asmbl_4700.p1, internal, 119829, 119936
Valid prediction for Augustus_model.g17334.t1
Valid prediction for GeneMark_model.44220_t
Valid prediction for GlimmerHMM_glimmerT_25830-T1
Valid prediction for Augustus_model.g17333.t1
Couldn't classify 97343, 98059
Sorry, prediction pasa_asmbl_4697.p1 fails validation.
(CTC)	 GT	97343-98059	AA	TCA
Valid prediction for GlimmerHMM_glimmerT_25837-T1
Valid prediction for GeneMark_model.44218_t
Valid prediction for GeneMark_model.44210_t
Valid prediction for GeneMark_model.44244_t
Valid prediction for snap_scaffold_10-snap.2059-T1
Valid prediction for snap_scaffold_10-snap.2052-T1
Valid prediction for snap_scaffold_10-snap.2042-T1
Valid prediction for snap_scaffold_10-snap.2055-T1
Valid prediction for CodingQuarry_transcript_5544-T1
Valid prediction for GeneMark_model.44237_t
Valid prediction for snap_scaffold_10-snap.2062-T1
Couldn't classify 88293, 88404
Couldn't classify 91598, 91653
Sorry, prediction pasa_asmbl_4694.p1 fails validation.
(AGG)	 GG	88293-88404	GT	GGG
(GGT)	 AG	90422-90487	GT	TGG
(ACT)	 AG	90658-90737	GT	GTG
(GAC)	 AG	90885-91011	GT	GGG
(ATG)	 AG	91210-91437	GT	AGG
(AGG)	 AG	91598-91653	CC	TGC
add_exon() Sorry, pasa_asmbl_4694.p1 91210-91437-initial-1 is invalid.
-recovered pasa_asmbl_4694.p1, initial, 91210, 91437
-recovered pasa_asmbl_4694.p1, internal, 90422, 90487
-recovered pasa_asmbl_4694.p1, internal, 90658, 90737
-recovered pasa_asmbl_4694.p1, internal, 90885, 91011
-recovered pasa_asmbl_4694.p1, internal, 91210, 91437
Valid prediction for GlimmerHMM_glimmerT_25831-T1
Valid prediction for GeneMark_model.44239_t
Valid prediction for snap_scaffold_10-snap.2057-T1
Valid prediction for GeneMark_model.44240_t
Valid prediction for snap_scaffold_10-snap.2051-T1
Valid prediction for snap_scaffold_10-snap.2035-T1
Valid prediction for Augustus_model.g17324.t1
Valid prediction for GlimmerHMM_glimmerT_25834-T1
Valid prediction for GeneMark_model.44232_t
Couldn't classify 99254, 101549
Sorry, prediction pasa_asmbl_4698.p1 fails validation.
(CTA)	 CA	99254-101549	GT	GGG
(GCA)	 AG	101648-101661	AG	GAA
-recovered pasa_asmbl_4698.p1, terminal, 101648, 101661
Valid prediction for GeneMark_model.44231_t
Valid prediction for GeneMark_model.44233_t
Valid prediction for GeneMark_model.44214_t
Valid prediction for snap_scaffold_10-snap.2054-T1
Valid prediction for GeneMark_model.44234_t
Valid prediction for Augustus_model.g17330.t1
Valid prediction for GeneMark_model.44229_t

-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 snap_scaffold_10-snap.2040-T1
Valid prediction for GeneMark_model.44241_t
Couldn't classify 84967, 85053
Sorry, prediction pasa_asmbl_3645.p1 fails validation.
(ACA)	 AC	84967-85053	GT	TAG
(ATC)	 AG	85302-85484	GT	TGG
(TCG)	 AG	85678-85951	GT	CAG
(GCT)	 AG	86081-86199	GT	GGG
(GCT)	 AG	86277-86399	GT	AGG
(GTC)	 AG	86564-86788	CT	AGC
-recovered pasa_asmbl_3645.p1, terminal, 86564, 86788
-recovered pasa_asmbl_3645.p1, internal, 85302, 85484
-recovered pasa_asmbl_3645.p1, internal, 85678, 85951
-recovered pasa_asmbl_3645.p1, internal, 86081, 86199
-recovered pasa_asmbl_3645.p1, internal, 86277, 86399
Valid prediction for GlimmerHMM_glimmerT_25821-T1
Couldn't classify 48061, 48744
Sorry, prediction pasa_asmbl_3655.p1 fails validation.
(TAC)	 CG	48061-48744	AA	CTA
Valid prediction for GlimmerHMM_glimmerT_25832-T1
Valid prediction for snap_scaffold_10-snap.2048-T1
Valid prediction for snap_scaffold_10-snap.2058-T1
Valid prediction for GlimmerHMM_glimmerT_25829-T1
Valid prediction for Augustus_model.g17322.t1
Valid prediction for HiQ_model.g17326.t1
Valid prediction for CodingQuarry_transcript_5541-T1
Valid prediction for GlimmerHMM_glimmerT_25824-T1
Valid prediction for snap_scaffold_10-snap.2053-T1
Valid prediction for snap_scaffold_10-snap.2037-T1
Valid prediction for snap_scaffold_10-snap.2036-T1
Valid prediction for GlimmerHMM_glimmerT_25818-T1
Couldn't classify 24702, 24776
Couldn't classify 24913, 25134
Sorry, prediction pasa_asmbl_3971.p1 fails validation.
(GCG)	 AG	24702-24776	GT	AGG
(TTG)	 AG	24913-25134	GT	GGG
-recovered pasa_asmbl_3971.p1, internal, 24702, 24776
-recovered pasa_asmbl_3971.p1, internal, 24913, 25134
Valid prediction for GlimmerHMM_glimmerT_25839-T1
Valid prediction for GeneMark_model.44212_t
Valid prediction for snap_scaffold_10-snap.2061-T1
Valid prediction for GeneMark_model.44235_t
Valid prediction for snap_scaffold_10-snap.2049-T1
Valid prediction for snap_scaffold_10-snap.2063-T1
Couldn't classify 64939, 65064
Couldn't classify 65765, 65841
Sorry, prediction pasa_asmbl_3652.p1 fails validation.
(GGC)	 AG	64939-65064	GT	AGG
(GTG)	 AG	65351-65573	GT	AGG
(GCA)	 AG	65765-65841	GA	ACG
-recovered pasa_asmbl_3652.p1, internal, 64939, 65064
-recovered pasa_asmbl_3652.p1, internal, 65351, 65573
Valid prediction for GlimmerHMM_glimmerT_25820-T1
Valid prediction for Augustus_model.g17327.t1
Valid prediction for GeneMark_model.44243_t
Couldn't classify 121891, 121903
Sorry, prediction pasa_asmbl_3644.p1 fails validation.
(GAA)	 CT	121891-121903	GT	AGG
(CTA)	 AG	122011-122159	GT	AGG
(AGT)	 AG	122247-122356	GT	AAG
(ATT)	 AG	122469-122616	AT	AAA
-recovered pasa_asmbl_3644.p1, terminal, 122469, 122616
-recovered pasa_asmbl_3644.p1, internal, 122011, 122159
-recovered pasa_asmbl_3644.p1, internal, 122247, 122356
Valid prediction for Augustus_model.g17332.t1
Valid prediction for GeneMark_model.44242_t
Valid prediction for GeneMark_model.44215_t
Valid prediction for GeneMark_model.44238_t
Valid prediction for snap_scaffold_10-snap.2039-T1
Valid prediction for GeneMark_model.44245_t
Valid prediction for GlimmerHMM_glimmerT_25828-T1
Valid prediction for GeneMark_model.44228_t
Valid prediction for GeneMark_model.44224_t
Valid prediction for GeneMark_model.44230_t
Valid prediction for snap_scaffold_10-snap.2046-T1
Valid prediction for Augustus_model.g17323.t1
Valid prediction for snap_scaffold_10-snap.2045-T1
Valid prediction for Augustus_model.g17329.t1
Valid prediction for GeneMark_model.44217_t
Valid prediction for Augustus_model.g17337.t1
Valid prediction for snap_scaffold_10-snap.2060-T1
Valid prediction for GlimmerHMM_glimmerT_25833-T1
Valid prediction for GlimmerHMM_glimmerT_25836-T1
Valid prediction for snap_scaffold_10-snap.2056-T1
Valid prediction for GlimmerHMM_glimmerT_25827-T1
Valid prediction for GeneMark_model.44219_t
Couldn't classify 49057, 49137
Couldn't classify 49406, 49708
Sorry, prediction pasa_asmbl_3654.p1 fails validation.
(AAC)	 AC	49057-49137	GT	AGG
(GAT)	 AG	49406-49708	AA	AGA
Valid prediction for Augustus_model.g17321.t1
Valid prediction for CodingQuarry_transcript_5543-T1
Valid prediction for snap_scaffold_10-snap.2044-T1
Couldn't classify 84353, 84407
Sorry, prediction pasa_asmbl_3646.p1 fails validation.
(ATG)	 AT	82947-82949	GT	TGG
(ATG)	 AG	83208-83327	GT	ATG
(GAA)	 AG	83515-83653	GT	GGG
(GCC)	 AG	83782-83935	GT	AGG
(GTT)	 AG	84043-84204	GT	AGG
(GAT)	 AG	84353-84407	CA	AGC
-recovered pasa_asmbl_3646.p1, initial, 82947, 82949
-recovered pasa_asmbl_3646.p1, initial, 83208, 83327
-recovered pasa_asmbl_3646.p1, internal, 83208, 83327
-recovered pasa_asmbl_3646.p1, internal, 83515, 83653
-recovered pasa_asmbl_3646.p1, internal, 83782, 83935
-recovered pasa_asmbl_3646.p1, internal, 84043, 84204
Valid prediction for GeneMark_model.44225_t
Valid prediction for GeneMark_model.44213_t
Valid prediction for snap_scaffold_10-snap.2034-T1
Valid prediction for GlimmerHMM_glimmerT_25838-T1
Valid prediction for GeneMark_model.44226_t
Valid prediction for GlimmerHMM_glimmerT_25826-T1
Valid prediction for Augustus_model.g17335.t1
Valid prediction for GlimmerHMM_glimmerT_25823-T1
Valid prediction for snap_scaffold_10-snap.2047-T1
Valid prediction for snap_scaffold_10-snap.2043-T1
Valid prediction for CodingQuarry_transcript_5542-T1
Valid prediction for Augustus_model.g17328.t1
Valid prediction for GlimmerHMM_glimmerT_25822-T1
Valid prediction for GeneMark_model.44222_t
Valid prediction for Augustus_model.g17325.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25434, rend_intergenic: 20095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27936, rend_intergenic: 27049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48697, rend_intergenic: 47133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74077, rend_intergenic: 69894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109252, rend_intergenic: 105903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115192, rend_intergenic: 110952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121291, rend_intergenic: 115517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128115, rend_intergenic: 122040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 133920
-exon list size: 467


building trellis

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33.3    
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35.8    
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36.2    
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38.8    
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99.6    
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-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 25434, rend_intergenic: 20095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27936, rend_intergenic: 27049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48697, rend_intergenic: 47133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74077, rend_intergenic: 69894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109252, rend_intergenic: 105903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115192, rend_intergenic: 110952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121291, rend_intergenic: 115517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128115, rend_intergenic: 122040  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support