-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_1767729-1922788

-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.10202_t
Valid prediction for GeneMark_model.10217_t
Valid prediction for snap_scaffold_3-snap.449-T1
Valid prediction for snap_scaffold_3-snap.431-T1
Valid prediction for snap_scaffold_3-snap.447-T1
Valid prediction for snap_scaffold_3-snap.455-T1
Valid prediction for GeneMark_model.10200_t
Valid prediction for snap_scaffold_3-snap.452-T1
Valid prediction for GlimmerHMM_glimmerT_6210-T1
Valid prediction for HiQ_model.g4080.t1
Valid prediction for GlimmerHMM_glimmerT_6223-T1
Valid prediction for Augustus_model.g4084.t1
Valid prediction for GlimmerHMM_glimmerT_6209-T1
Valid prediction for CodingQuarry_transcript_45976-T1
Valid prediction for GlimmerHMM_glimmerT_6215-T1
Valid prediction for Augustus_model.g4074.t1
Valid prediction for snap_scaffold_3-snap.459-T1
Valid prediction for Augustus_model.g4085.t1
Valid prediction for GeneMark_model.10223_t
Couldn't classify 62673, 62892
Sorry, prediction pasa_asmbl_39842.p1 fails validation.
(ATG)	 AA	57318-57439	GT	AGG
(GGG)	 AG	58414-58626	GT	TAG
(CGC)	 AG	59578-59716	GT	AGG
(CCT)	 AG	61632-61758	GT	GGG
(CAC)	 AG	61899-61947	GT	TGG
(GAG)	 AG	62083-62262	GT	GAG
(AGA)	 AG	62673-62892	GG	CCG
-recovered pasa_asmbl_39842.p1, initial, 57318, 57439
-recovered pasa_asmbl_39842.p1, internal, 58414, 58626
-recovered pasa_asmbl_39842.p1, internal, 59578, 59716
-recovered pasa_asmbl_39842.p1, internal, 61632, 61758
-recovered pasa_asmbl_39842.p1, internal, 61899, 61947
-recovered pasa_asmbl_39842.p1, internal, 62083, 62262
Valid prediction for GeneMark_model.10196_t
Valid prediction for GeneMark_model.10212_t
Valid prediction for Augustus_model.g4083.t1
Valid prediction for Augustus_model.g4077.t1
Valid prediction for snap_scaffold_3-snap.442-T1
Valid prediction for GeneMark_model.10189_t
Valid prediction for snap_scaffold_3-snap.429-T1
Valid prediction for snap_scaffold_3-snap.454-T1
Valid prediction for GlimmerHMM_glimmerT_6219-T1
Valid prediction for HiQ_model.g4078.t1
Valid prediction for GeneMark_model.10191_t
Valid prediction for GlimmerHMM_glimmerT_6211-T1
Valid prediction for snap_scaffold_3-snap.446-T1
Valid prediction for GlimmerHMM_glimmerT_6217-T1
Valid prediction for GlimmerHMM_glimmerT_6212-T1
Valid prediction for GlimmerHMM_glimmerT_6221-T1
Valid prediction for GeneMark_model.10221_t
Valid prediction for snap_scaffold_3-snap.437-T1
Valid prediction for snap_scaffold_3-snap.457-T1
Valid prediction for snap_scaffold_3-snap.439-T1
Valid prediction for Augustus_model.g4076.t1
Valid prediction for CodingQuarry_transcript_45980-T1
Valid prediction for GlimmerHMM_glimmerT_6204-T1
Couldn't classify 1723, 2331
Sorry, prediction pasa_asmbl_39837.p1 fails validation.
(GTG)	 TG	1723-2331	TT	AGT
Valid prediction for GeneMark_model.10194_t
Valid prediction for GeneMark_model.10188_t
Valid prediction for GlimmerHMM_glimmerT_6203-T1
Valid prediction for GeneMark_model.10213_t
Valid prediction for GeneMark_model.10218_t
Valid prediction for GlimmerHMM_glimmerT_6208-T1
Valid prediction for GeneMark_model.10210_t
Valid prediction for HiQ_model.g4072.t1
Valid prediction for snap_scaffold_3-snap.453-T1
Couldn't classify 40944, 41036
Sorry, prediction GeneMark_model.10198_t fails validation.
(ATG)	 TG	39640-39681	GC	CGG
(GGG)	 AG	39705-40391	GT	TGG
(GAG)	 AG	40485-40797	GT	TGG
(GTG)	 AG	40944-41036	GT	TAG
-recovered GeneMark_model.10198_t, initial, 39640, 39681
-recovered GeneMark_model.10198_t, internal, 39705, 40391
-recovered GeneMark_model.10198_t, internal, 40485, 40797
-recovered GeneMark_model.10198_t, internal, 40944, 41036
Valid prediction for Augustus_model.g4082.t1
Valid prediction for GlimmerHMM_glimmerT_6207-T1
Valid prediction for snap_scaffold_3-snap.432-T1
Valid prediction for CodingQuarry_transcript_45978-T1
Valid prediction for GeneMark_model.10204_t
Valid prediction for Augustus_model.g4075.t1
Valid prediction for GeneMark_model.10208_t
Couldn't classify 8741, 9082
Sorry, prediction pasa_asmbl_39838.p1 fails validation.
(GGA)	 AA	8741-9082	GT	AGG
(GCC)	 AG	9363-9434	GT	ATG
(CTG)	 AG	9544-9670	GT	TGG
(GGC)	 AG	9823-9970	GT	GAG
(GTT)	 AG	10170-10248	CA	AAC
-recovered pasa_asmbl_39838.p1, terminal, 10170, 10248
-recovered pasa_asmbl_39838.p1, internal, 9363, 9434
-recovered pasa_asmbl_39838.p1, internal, 9544, 9670
-recovered pasa_asmbl_39838.p1, internal, 9823, 9970
Valid prediction for Augustus_model.g4081.t1
Valid prediction for snap_scaffold_3-snap.435-T1
Valid prediction for snap_scaffold_3-snap.456-T1
Valid prediction for GlimmerHMM_glimmerT_6206-T1
Valid prediction for Augustus_model.g4086.t1
Valid prediction for GeneMark_model.10187_t
Valid prediction for GeneMark_model.10219_t
Valid prediction for pasa_asmbl_39846.p1
Valid prediction for CodingQuarry_transcript_45979-T1
Valid prediction for snap_scaffold_3-snap.450-T1
Valid prediction for GeneMark_model.10225_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: -)Couldn't classify 146571, 146702
Sorry, prediction pasa_asmbl_38682.p1 fails validation.
(GTC)	 TG	146571-146702	GT	TGG
(CGA)	 AG	146802-146956	GT	AGG
(GAC)	 AG	147041-147110	GT	AGG
(GAT)	 AG	147234-147278	GT	AGG
(GAA)	 AG	147386-147523	GT	ACG
(GTG)	 AG	148123-148210	GT	AGG
(GAG)	 AG	148381-148497	GT	TGG
(CCT)	 AG	148626-148906	TG	GAT
-recovered pasa_asmbl_38682.p1, terminal, 148626, 148906
-recovered pasa_asmbl_38682.p1, internal, 146802, 146956
-recovered pasa_asmbl_38682.p1, internal, 147041, 147110
-recovered pasa_asmbl_38682.p1, internal, 147234, 147278
-recovered pasa_asmbl_38682.p1, internal, 147386, 147523
-recovered pasa_asmbl_38682.p1, internal, 148123, 148210
-recovered pasa_asmbl_38682.p1, internal, 148381, 148497
Valid prediction for GeneMark_model.10220_t
Valid prediction for GeneMark_model.10201_t
Valid prediction for GeneMark_model.10195_t
Valid prediction for GeneMark_model.10197_t
Valid prediction for HiQ_model.g4073.t1
Couldn't classify 84676, 85065
Couldn't classify 86757, 87027
Sorry, prediction pasa_asmbl_38685.p1 fails validation.
(TTA)	 TT	84676-85065	GT	AGG
(AAC)	 AG	86273-86502	GT	AGG
(AGC)	 AG	86757-87027	CT	AGC
-recovered pasa_asmbl_38685.p1, internal, 86273, 86502
Valid prediction for snap_scaffold_3-snap.441-T1
Valid prediction for snap_scaffold_3-snap.438-T1
Valid prediction for snap_scaffold_3-snap.461-T1
Valid prediction for snap_scaffold_3-snap.451-T1
Valid prediction for snap_scaffold_3-snap.434-T1
Valid prediction for GeneMark_model.10214_t
Valid prediction for GeneMark_model.10216_t
Valid prediction for snap_scaffold_3-snap.440-T1
Valid prediction for GeneMark_model.10190_t
Valid prediction for snap_scaffold_3-snap.458-T1
Valid prediction for GeneMark_model.10211_t
Valid prediction for Augustus_model.g4087.t1
Valid prediction for GeneMark_model.10186_t
Valid prediction for GeneMark_model.10205_t
Valid prediction for GeneMark_model.10203_t
Valid prediction for GlimmerHMM_glimmerT_6220-T1
Valid prediction for GlimmerHMM_glimmerT_6214-T1
Valid prediction for snap_scaffold_3-snap.443-T1
Valid prediction for snap_scaffold_3-snap.430-T1
Valid prediction for snap_scaffold_3-snap.436-T1
Valid prediction for GlimmerHMM_glimmerT_6216-T1
Valid prediction for GeneMark_model.10222_t
Valid prediction for GeneMark_model.10192_t
Valid prediction for GlimmerHMM_glimmerT_6213-T1
Valid prediction for snap_scaffold_3-snap.444-T1
Couldn't classify 108302, 108316
Sorry, prediction GeneMark_model.10199_t fails validation.
(ATG)	 TG	106549-106563	GC	CTG
(CTT)	 AG	106635-106768	GT	GGG
(AGA)	 AG	106790-106798	GT	GGG
(AGA)	 AG	106820-106828	GT	GGG
(ACA)	 AG	106850-106888	GT	GGG
(AGA)	 AG	106912-107007	GT	TTG
(AGG)	 AG	107198-107203	GT	GGG
(GAG)	 AG	107257-107475	GT	TCG
(AGG)	 AG	107555-107560	GT	GGG
(ACA)	 AG	107588-107605	GT	GGG
(ACA)	 AG	107646-107663	GT	GGG
(AGG)	 AG	107703-107708	GT	GGG
(AGA)	 AG	107744-107753	GT	GGG
(GGA)	 AG	107785-107798	GT	GGG
(AGA)	 AG	108302-108316	GT	GAG
-recovered GeneMark_model.10199_t, initial, 106549, 106563
-recovered GeneMark_model.10199_t, internal, 106635, 106768
-recovered GeneMark_model.10199_t, internal, 106790, 106798
-recovered GeneMark_model.10199_t, internal, 106820, 106828
-recovered GeneMark_model.10199_t, internal, 106850, 106888
-recovered GeneMark_model.10199_t, internal, 106912, 107007
-recovered GeneMark_model.10199_t, internal, 107198, 107203
-recovered GeneMark_model.10199_t, internal, 107257, 107475
-recovered GeneMark_model.10199_t, internal, 107555, 107560
-recovered GeneMark_model.10199_t, internal, 107588, 107605
-recovered GeneMark_model.10199_t, internal, 107646, 107663
-recovered GeneMark_model.10199_t, internal, 107703, 107708
-recovered GeneMark_model.10199_t, internal, 107744, 107753
-recovered GeneMark_model.10199_t, internal, 107785, 107798
-recovered GeneMark_model.10199_t, internal, 108302, 108316
Valid prediction for GeneMark_model.10215_t
Valid prediction for CodingQuarry_transcript_45977-T1
Valid prediction for GeneMark_model.10206_t
Valid prediction for snap_scaffold_3-snap.433-T1
Valid prediction for snap_scaffold_3-snap.448-T1
Valid prediction for GlimmerHMM_glimmerT_6222-T1
Valid prediction for HiQ_model.g4079.t1
Valid prediction for GlimmerHMM_glimmerT_6202-T1
Valid prediction for GlimmerHMM_glimmerT_6205-T1
Valid prediction for GlimmerHMM_glimmerT_6218-T1
Valid prediction for snap_scaffold_3-snap.445-T1
Valid prediction for snap_scaffold_3-snap.460-T1
Valid prediction for GeneMark_model.10209_t
Valid prediction for GeneMark_model.10193_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18304, rend_intergenic: 11992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22578, rend_intergenic: 19740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32885, rend_intergenic: 30654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38788, rend_intergenic: 33433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54396, rend_intergenic: 38893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62913, rend_intergenic: 59355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95848, rend_intergenic: 94640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 155060
-exon list size: 465


building trellis

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33.8    
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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 18304, rend_intergenic: 11992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22578, rend_intergenic: 19740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32885, rend_intergenic: 30654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38788, rend_intergenic: 33433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54396, rend_intergenic: 38893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62913, rend_intergenic: 59355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95848, rend_intergenic: 94640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support