-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_1457562-1713263

-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 pasa_asmbl_1494.p1
Valid prediction for HiQ_model.g165.t1
Valid prediction for GlimmerHMM_glimmerT_217-T1
Valid prediction for snap_scaffold_1-snap.288-T1
Couldn't classify 160480, 160518
Couldn't classify 160772, 160832
Sorry, prediction CodingQuarry_transcript_2535-T1 fails validation.
(ATG)	 AG	153900-153953	GT	AGG
(CAT)	 AG	156441-156516	GT	AGG
(GGG)	 AG	156721-156781	GT	AGG
(GAA)	 AG	156988-157110	GT	AAG
(TGT)	 AG	157348-157421	GT	AGG
(GAT)	 AG	158029-158099	GT	AGG
(GAC)	 AG	158185-158259	GT	AGG
(TCT)	 AG	158482-158548	GT	TGG
(AAG)	 AG	158965-159050	GT	CTG
(GAT)	 AG	159406-159482	GT	GGG
(TCA)	 AG	160480-160518	GA	GTG
(TTT)	 GA	160772-160832	GA	AAG
-recovered CodingQuarry_transcript_2535-T1, initial, 153900, 153953
-recovered CodingQuarry_transcript_2535-T1, internal, 153900, 153953
-recovered CodingQuarry_transcript_2535-T1, internal, 156441, 156516
-recovered CodingQuarry_transcript_2535-T1, internal, 156721, 156781
-recovered CodingQuarry_transcript_2535-T1, internal, 156988, 157110
-recovered CodingQuarry_transcript_2535-T1, internal, 157348, 157421
-recovered CodingQuarry_transcript_2535-T1, internal, 158029, 158099
-recovered CodingQuarry_transcript_2535-T1, internal, 158185, 158259
-recovered CodingQuarry_transcript_2535-T1, internal, 158482, 158548
-recovered CodingQuarry_transcript_2535-T1, internal, 158965, 159050
-recovered CodingQuarry_transcript_2535-T1, internal, 159406, 159482
Valid prediction for GlimmerHMM_glimmerT_208-T1
Valid prediction for GeneMark_model.253_t
Valid prediction for snap_scaffold_1-snap.271-T1
Valid prediction for snap_scaffold_1-snap.273-T1
Couldn't classify 106344, 106738
Sorry, prediction pasa_asmbl_1491.p1 fails validation.
(CGC)	 GT	106344-106738	GT	TGG
(GAT)	 AG	107239-107366	GT	GGG
(ATG)	 AG	107556-107644	GC	AGG
(CCC)	 AG	107808-108437	TG	AGT
add_exon() Sorry, pasa_asmbl_1491.p1 107556-107644-initial-1 is invalid.
-recovered pasa_asmbl_1491.p1, initial, 107556, 107644
-recovered pasa_asmbl_1491.p1, terminal, 107808, 108437
-recovered pasa_asmbl_1491.p1, internal, 107239, 107366
-recovered pasa_asmbl_1491.p1, internal, 107556, 107644
Valid prediction for GeneMark_model.221_t
Valid prediction for GeneMark_model.252_t
Valid prediction for GeneMark_model.229_t
Valid prediction for GlimmerHMM_glimmerT_212-T1
Valid prediction for snap_scaffold_1-snap.295-T1
Valid prediction for GlimmerHMM_glimmerT_223-T1
Valid prediction for CodingQuarry_transcript_2533-T1
Valid prediction for snap_scaffold_1-snap.278-T1
Valid prediction for Augustus_model.g161.t1
Valid prediction for snap_scaffold_1-snap.267-T1
Valid prediction for GeneMark_model.240_t
Valid prediction for snap_scaffold_1-snap.269-T1
Valid prediction for snap_scaffold_1-snap.292-T1
Couldn't classify 99813, 100004
Couldn't classify 101358, 101477
Sorry, prediction pasa_asmbl_1487.p1 fails validation.
(AGG)	 CC	99813-100004	GT	AGG
(GAG)	 AG	100422-100505	GT	GCG
(ACA)	 AG	100995-101219	GT	CTG
(GAG)	 AG	101358-101477	CC	GCC
-recovered pasa_asmbl_1487.p1, internal, 100422, 100505
-recovered pasa_asmbl_1487.p1, internal, 100995, 101219
Valid prediction for Augustus_model.g158.t1
Couldn't classify 96136, 96327
Couldn't classify 99112, 99229
Sorry, prediction pasa_asmbl_1486.p1 fails validation.
(GTG)	 CA	96136-96327	GT	AGG
(GCC)	 AG	97364-97402	GT	AGG
(AAC)	 AG	97514-97816	GT	AGG
(TTA)	 AG	98065-98213	GT	AAG
(GCC)	 AG	99112-99229	GT	AGG
-recovered pasa_asmbl_1486.p1, internal, 97364, 97402
-recovered pasa_asmbl_1486.p1, internal, 97514, 97816
-recovered pasa_asmbl_1486.p1, internal, 98065, 98213
-recovered pasa_asmbl_1486.p1, internal, 99112, 99229
Couldn't classify 69630, 69790
Sorry, prediction pasa_asmbl_1480.p1 fails validation.
(GGA)	 AG	69630-69790	GT	AGG
(TCT)	 AG	70092-70239	GT	GGG
(GAC)	 AG	70380-70444	GT	AGG
(GTA)	 AG	70581-70656	GT	GGG
(AAT)	 AG	70926-71000	GT	AGG
(ATC)	 AG	71231-71335	CA	GAC
-recovered pasa_asmbl_1480.p1, terminal, 71231, 71335
-recovered pasa_asmbl_1480.p1, internal, 69630, 69790
-recovered pasa_asmbl_1480.p1, internal, 70092, 70239
-recovered pasa_asmbl_1480.p1, internal, 70380, 70444
-recovered pasa_asmbl_1480.p1, internal, 70581, 70656
-recovered pasa_asmbl_1480.p1, internal, 70926, 71000
Valid prediction for Augustus_model.g157.t1
Valid prediction for GeneMark_model.256_t
Valid prediction for GeneMark_model.232_t
Valid prediction for Augustus_model.g160.t1
Valid prediction for GeneMark_model.242_t
Valid prediction for snap_scaffold_1-snap.286-T1
Valid prediction for GeneMark_model.224_t
Valid prediction for GeneMark_model.246_t
Valid prediction for Augustus_model.g172.t1
Valid prediction for Augustus_model.g171.t1
Valid prediction for CodingQuarry_transcript_2530-T1
Valid prediction for snap_scaffold_1-snap.293-T1
Valid prediction for snap_scaffold_1-snap.294-T1
Valid prediction for GeneMark_model.223_t
Valid prediction for GlimmerHMM_glimmerT_211-T1
Valid prediction for GeneMark_model.234_t
Valid prediction for GlimmerHMM_glimmerT_227-T1
Valid prediction for GlimmerHMM_glimmerT_215-T1
Valid prediction for GeneMark_model.238_t
Valid prediction for CodingQuarry_transcript_2534-T1
Valid prediction for snap_scaffold_1-snap.274-T1
Valid prediction for GeneMark_model.258_t
Valid prediction for snap_scaffold_1-snap.266-T1
Valid prediction for snap_scaffold_1-snap.285-T1
Valid prediction for GeneMark_model.260_t
Valid prediction for Augustus_model.g169.t1
Valid prediction for pasa_asmbl_1482.p1
Valid prediction for snap_scaffold_1-snap.270-T1
Valid prediction for snap_scaffold_1-snap.281-T1
Valid prediction for snap_scaffold_1-snap.287-T1
Valid prediction for snap_scaffold_1-snap.282-T1
Valid prediction for GlimmerHMM_glimmerT_222-T1
Valid prediction for GeneMark_model.228_t
Valid prediction for GeneMark_model.250_t
Valid prediction for GeneMark_model.248_t
Valid prediction for Augustus_model.g159.t1
Valid prediction for GeneMark_model.236_t
Valid prediction for GeneMark_model.230_t
Valid prediction for GlimmerHMM_glimmerT_219-T1
Valid prediction for GeneMark_model.227_t
Valid prediction for GlimmerHMM_glimmerT_224-T1
Valid prediction for CodingQuarry_transcript_2531-T1
Valid prediction for Augustus_model.g166.t1
Valid prediction for snap_scaffold_1-snap.289-T1
Valid prediction for Augustus_model.g170.t1
Valid prediction for snap_scaffold_1-snap.276-T1
Valid prediction for snap_scaffold_1-snap.280-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.251_t
Valid prediction for Augustus_model.g162.t1
Valid prediction for GlimmerHMM_glimmerT_226-T1
Valid prediction for GlimmerHMM_glimmerT_207-T1
Valid prediction for GeneMark_model.226_t
Valid prediction for snap_scaffold_1-snap.268-T1
Valid prediction for GeneMark_model.247_t
Valid prediction for GeneMark_model.233_t
Valid prediction for GeneMark_model.255_t
Valid prediction for GeneMark_model.254_t
Valid prediction for GeneMark_model.245_t
Valid prediction for GeneMark_model.239_t
Valid prediction for snap_scaffold_1-snap.279-T1
Valid prediction for GlimmerHMM_glimmerT_213-T1
Valid prediction for GeneMark_model.257_t
Valid prediction for snap_scaffold_1-snap.283-T1
Valid prediction for GeneMark_model.249_t
Valid prediction for snap_scaffold_1-snap.290-T1
Valid prediction for Augustus_model.g167.t1
Valid prediction for GeneMark_model.235_t
Valid prediction for GeneMark_model.225_t
Valid prediction for GlimmerHMM_glimmerT_220-T1
Valid prediction for GlimmerHMM_glimmerT_218-T1
Valid prediction for GlimmerHMM_glimmerT_209-T1
Valid prediction for GlimmerHMM_glimmerT_210-T1
Valid prediction for Augustus_model.g163.t1
Valid prediction for GeneMark_model.237_t
Valid prediction for GeneMark_model.222_t
Valid prediction for snap_scaffold_1-snap.284-T1
Valid prediction for Augustus_model.g168.t1
Valid prediction for GlimmerHMM_glimmerT_225-T1
Valid prediction for snap_scaffold_1-snap.291-T1
Couldn't classify 106758, 107162
Sorry, prediction pasa_asmbl_78.p1 fails validation.
(ATG)	 AG	106758-107162	GG	GCG
Valid prediction for snap_scaffold_1-snap.277-T1
Valid prediction for GeneMark_model.220_t
Valid prediction for GlimmerHMM_glimmerT_214-T1
Valid prediction for snap_scaffold_1-snap.272-T1
Valid prediction for GeneMark_model.259_t
Valid prediction for snap_scaffold_1-snap.275-T1
Valid prediction for GlimmerHMM_glimmerT_206-T1
Valid prediction for GeneMark_model.241_t
Valid prediction for Augustus_model.g164.t1
Valid prediction for GeneMark_model.243_t
Valid prediction for GlimmerHMM_glimmerT_216-T1
Valid prediction for GlimmerHMM_glimmerT_221-T1
Valid prediction for pasa_asmbl_75.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40719, rend_intergenic: 29149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57770, rend_intergenic: 52645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71335, rend_intergenic: 68130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98217, rend_intergenic: 93713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 255702
-exon list size: 483


building trellis

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98.4    
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98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 40719, rend_intergenic: 29149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57770, rend_intergenic: 52645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71335, rend_intergenic: 68130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98217, rend_intergenic: 93713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support