-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_1594578-1749823

-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.101088_t
Valid prediction for GeneMark_model.101081_t
Valid prediction for snap_scaffold_27-snap.379-T1
Valid prediction for snap_scaffold_27-snap.381-T1
Valid prediction for GlimmerHMM_glimmerT_58072-T1
Valid prediction for snap_scaffold_27-snap.393-T1
Valid prediction for snap_scaffold_27-snap.374-T1
Valid prediction for snap_scaffold_27-snap.391-T1
Valid prediction for snap_scaffold_27-snap.369-T1
Valid prediction for snap_scaffold_27-snap.358-T1
Valid prediction for GeneMark_model.101095_t
Valid prediction for snap_scaffold_27-snap.395-T1
Valid prediction for GlimmerHMM_glimmerT_58076-T1
Valid prediction for GeneMark_model.101073_t
Valid prediction for snap_scaffold_27-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_58084-T1
Valid prediction for GlimmerHMM_glimmerT_58059-T1
Valid prediction for snap_scaffold_27-snap.383-T1
Valid prediction for GeneMark_model.101086_t
Valid prediction for snap_scaffold_27-snap.372-T1
Valid prediction for snap_scaffold_27-snap.376-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58056-T1
Valid prediction for GlimmerHMM_glimmerT_58066-T1
Valid prediction for GlimmerHMM_glimmerT_58079-T1
Valid prediction for snap_scaffold_27-snap.397-T1
Valid prediction for GlimmerHMM_glimmerT_58075-T1
Valid prediction for snap_scaffold_27-snap.361-T1
Valid prediction for GeneMark_model.101103_t
Valid prediction for snap_scaffold_27-snap.380-T1
Valid prediction for snap_scaffold_27-snap.359-T1
Valid prediction for GlimmerHMM_glimmerT_58086-T1
Valid prediction for GeneMark_model.101085_t
Valid prediction for Augustus_model.g38681.t1
Valid prediction for snap_scaffold_27-snap.387-T1
Valid prediction for GeneMark_model.101079_t
Valid prediction for snap_scaffold_27-snap.384-T1
Valid prediction for GeneMark_model.101078_t
Valid prediction for GlimmerHMM_glimmerT_58061-T1
Valid prediction for GeneMark_model.101099_t
Valid prediction for GeneMark_model.101097_t
Valid prediction for snap_scaffold_27-snap.389-T1
Valid prediction for snap_scaffold_27-snap.366-T1
Valid prediction for snap_scaffold_27-snap.398-T1
Valid prediction for GeneMark_model.101076_t
Valid prediction for GeneMark_model.101069_t
Valid prediction for GeneMark_model.101087_t
Valid prediction for snap_scaffold_27-snap.367-T1
Valid prediction for snap_scaffold_27-snap.364-T1
Valid prediction for GeneMark_model.101101_t
Valid prediction for GlimmerHMM_glimmerT_58073-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 Augustus_model.g38676.t1
Valid prediction for Augustus_model.g38686.t1
Valid prediction for snap_scaffold_27-snap.386-T1
Valid prediction for GlimmerHMM_glimmerT_58065-T1
Valid prediction for GeneMark_model.101102_t
Valid prediction for GeneMark_model.101065_t
Valid prediction for GlimmerHMM_glimmerT_58087-T1
Valid prediction for GeneMark_model.101093_t
Valid prediction for snap_scaffold_27-snap.373-T1
Couldn't classify 104485, 104696
Couldn't classify 107929, 107979
Sorry, prediction pasa_asmbl_36727.p1 fails validation.
(CAA)	 CG	104485-104696	GT	AGG
(ATA)	 AG	104858-104973	GT	CCG
(ATA)	 AG	105281-105392	GT	TCG
(GTG)	 AG	105499-105668	GT	ACG
(ACA)	 AG	107223-107338	GT	AGG
(AAA)	 AG	107929-107979	CA	ACC
-recovered pasa_asmbl_36727.p1, internal, 104858, 104973
-recovered pasa_asmbl_36727.p1, internal, 105281, 105392
-recovered pasa_asmbl_36727.p1, internal, 105499, 105668
-recovered pasa_asmbl_36727.p1, internal, 107223, 107338
Valid prediction for GlimmerHMM_glimmerT_58063-T1
Valid prediction for GeneMark_model.101091_t
Valid prediction for GeneMark_model.101071_t
Valid prediction for GeneMark_model.101089_t
Valid prediction for GlimmerHMM_glimmerT_58068-T1
Valid prediction for GeneMark_model.101075_t
Valid prediction for GeneMark_model.101082_t
Couldn't classify 90696, 90711
Sorry, prediction pasa_asmbl_36728.p1 fails validation.
(GTC)	 AC	90696-90711	GT	AGG
(TCC)	 AG	90935-91065	GT	AGG
(AAA)	 AG	91600-91759	GT	GGG
(AGA)	 AG	92100-92283	GT	AGG
(GTA)	 AG	92528-92643	GT	AGG
(TCC)	 AG	92770-92887	GT	AGG
(GTG)	 AG	93372-93580	GT	CTG
(CTC)	 AG	93802-93896	GT	AGG
(AAG)	 AG	94236-94368	GT	GGG
(GTC)	 AG	94612-94716	GT	GAG
(CTA)	 AG	95230-95340	GT	GGG
(GTC)	 AG	95592-95736	GT	AGG
(TGG)	 AG	95828-95979	GT	AGG
(CTC)	 AG	96348-96451	GT	ACG
(TGT)	 AG	96704-96826	GT	ACG
(ACA)	 AG	97249-97360	GT	GGG
(GGG)	 AG	97552-97651	GT	ATG
(GTA)	 AG	97904-98009	GT	AGG
(CGC)	 AG	98155-98372	GT	AGG
(CCC)	 AG	99423-99567	GC	GAG
-recovered pasa_asmbl_36728.p1, terminal, 99423, 99567
-recovered pasa_asmbl_36728.p1, internal, 90935, 91065
-recovered pasa_asmbl_36728.p1, internal, 91600, 91759
-recovered pasa_asmbl_36728.p1, internal, 92100, 92283
-recovered pasa_asmbl_36728.p1, internal, 92528, 92643
-recovered pasa_asmbl_36728.p1, internal, 92770, 92887
-recovered pasa_asmbl_36728.p1, internal, 93372, 93580
-recovered pasa_asmbl_36728.p1, internal, 93802, 93896
-recovered pasa_asmbl_36728.p1, internal, 94236, 94368
-recovered pasa_asmbl_36728.p1, internal, 94612, 94716
-recovered pasa_asmbl_36728.p1, internal, 95230, 95340
-recovered pasa_asmbl_36728.p1, internal, 95592, 95736
-recovered pasa_asmbl_36728.p1, internal, 95828, 95979
-recovered pasa_asmbl_36728.p1, internal, 96348, 96451
-recovered pasa_asmbl_36728.p1, internal, 96704, 96826
-recovered pasa_asmbl_36728.p1, internal, 97249, 97360
-recovered pasa_asmbl_36728.p1, internal, 97552, 97651
-recovered pasa_asmbl_36728.p1, internal, 97904, 98009
-recovered pasa_asmbl_36728.p1, internal, 98155, 98372
-recovered pasa_asmbl_36728.p1, internal, 99423, 99567
Valid prediction for Augustus_model.g38687.t1
Valid prediction for Augustus_model.g38677.t1
Valid prediction for pasa_asmbl_36719.p2
Couldn't classify 133334, 134191
Sorry, prediction pasa_asmbl_36723.p1 fails validation.
(CCC)	 CC	133334-134191	AG	GCA
Valid prediction for GlimmerHMM_glimmerT_58058-T1
Valid prediction for snap_scaffold_27-snap.378-T1
Valid prediction for snap_scaffold_27-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_58077-T1
Valid prediction for snap_scaffold_27-snap.362-T1
Valid prediction for CodingQuarry_transcript_41690-T1
Valid prediction for snap_scaffold_27-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_58074-T1
Valid prediction for GeneMark_model.101092_t
Valid prediction for GeneMark_model.101077_t
Valid prediction for GlimmerHMM_glimmerT_58080-T1
Valid prediction for snap_scaffold_27-snap.382-T1
Valid prediction for GlimmerHMM_glimmerT_58069-T1
Valid prediction for snap_scaffold_27-snap.370-T1
Valid prediction for Augustus_model.g38685.t1
Valid prediction for snap_scaffold_27-snap.371-T1
Valid prediction for snap_scaffold_27-snap.375-T1
Valid prediction for Augustus_model.g38679.t1
Valid prediction for GlimmerHMM_glimmerT_58078-T1
Valid prediction for Augustus_model.g38682.t1
Valid prediction for snap_scaffold_27-snap.392-T1
Valid prediction for GeneMark_model.101104_t
Valid prediction for snap_scaffold_27-snap.385-T1
Valid prediction for GeneMark_model.101066_t
Valid prediction for GeneMark_model.101100_t
Valid prediction for GlimmerHMM_glimmerT_58083-T1
Valid prediction for GeneMark_model.101096_t
Valid prediction for Augustus_model.g38675.t1
Valid prediction for GeneMark_model.101080_t
Valid prediction for GeneMark_model.101084_t
Valid prediction for GeneMark_model.101074_t
Valid prediction for snap_scaffold_27-snap.363-T1
Valid prediction for Augustus_model.g38680.t1
Valid prediction for GlimmerHMM_glimmerT_58081-T1
Valid prediction for GeneMark_model.101064_t
Valid prediction for snap_scaffold_27-snap.390-T1
Valid prediction for snap_scaffold_27-snap.388-T1
Valid prediction for GeneMark_model.101098_t
Valid prediction for GlimmerHMM_glimmerT_58057-T1
Valid prediction for GlimmerHMM_glimmerT_58060-T1
Valid prediction for GlimmerHMM_glimmerT_58071-T1
Valid prediction for GlimmerHMM_glimmerT_58062-T1
Valid prediction for GlimmerHMM_glimmerT_58082-T1
Valid prediction for pasa_asmbl_36730.p2
Valid prediction for Augustus_model.g38684.t1
Valid prediction for GlimmerHMM_glimmerT_58067-T1
Valid prediction for Augustus_model.g38683.t1
Valid prediction for GlimmerHMM_glimmerT_58064-T1
Valid prediction for GeneMark_model.101094_t
Valid prediction for GeneMark_model.101068_t
Valid prediction for GeneMark_model.101090_t
Valid prediction for GlimmerHMM_glimmerT_58085-T1
Valid prediction for GlimmerHMM_glimmerT_58070-T1
Valid prediction for snap_scaffold_27-snap.360-T1
Valid prediction for Augustus_model.g38678.t1
Valid prediction for GeneMark_model.101070_t
Valid prediction for GeneMark_model.101067_t
Valid prediction for snap_scaffold_27-snap.368-T1
Couldn't classify 108696, 108765
Sorry, prediction pasa_asmbl_36725.p1 fails validation.
(GTG)	 TC	108696-108765	GT	ACG
(CAA)	 AG	108968-109078	GT	AGG
(GTC)	 AG	109462-109624	GT	AGG
(TGA)	 AG	110004-110071	GT	AGG
(AAC)	 AG	110713-110819	GT	ACG
(TGT)	 AG	110942-111064	GT	ACG
(GCT)	 AG	111222-111333	GT	GGG
(GTA)	 AG	111607-111706	GT	ATG
(GTT)	 AG	111934-112039	GT	AGG
(GCC)	 AG	112789-112989	GG	GAG
-recovered pasa_asmbl_36725.p1, terminal, 110004, 110071
-recovered pasa_asmbl_36725.p1, terminal, 112789, 112989
-recovered pasa_asmbl_36725.p1, internal, 108968, 109078
-recovered pasa_asmbl_36725.p1, internal, 109462, 109624
-recovered pasa_asmbl_36725.p1, internal, 110004, 110071
-recovered pasa_asmbl_36725.p1, internal, 110713, 110819
-recovered pasa_asmbl_36725.p1, internal, 110942, 111064
-recovered pasa_asmbl_36725.p1, internal, 111222, 111333
-recovered pasa_asmbl_36725.p1, internal, 111607, 111706
-recovered pasa_asmbl_36725.p1, internal, 111934, 112039
Valid prediction for snap_scaffold_27-snap.396-T1
Valid prediction for GeneMark_model.101072_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7558, rend_intergenic: 6809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9964, rend_intergenic: 8290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21880, rend_intergenic: 19744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27448, rend_intergenic: 26001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30535, rend_intergenic: 28993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34665, rend_intergenic: 32703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40782, rend_intergenic: 35066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54548, rend_intergenic: 43896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61410, rend_intergenic: 55680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68137, rend_intergenic: 62110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74300, rend_intergenic: 73171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81442, rend_intergenic: 77724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91435, rend_intergenic: 87367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102649, rend_intergenic: 97390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154344, rend_intergenic: 129675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 155246
-exon list size: 585


building trellis

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89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 7558, rend_intergenic: 6809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9964, rend_intergenic: 8290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21880, rend_intergenic: 19744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27448, rend_intergenic: 26001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30535, rend_intergenic: 28993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34665, rend_intergenic: 32703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40782, rend_intergenic: 35066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54548, rend_intergenic: 43896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61410, rend_intergenic: 55680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68137, rend_intergenic: 62110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74300, rend_intergenic: 73171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81442, rend_intergenic: 77724  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91435, rend_intergenic: 87367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102649, rend_intergenic: 97390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154344, rend_intergenic: 129675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support