-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_1980356-2131682

-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 snap_scaffold_28-snap.511-T1
Valid prediction for Augustus_model.g39709.t1
Valid prediction for snap_scaffold_28-snap.501-T1
Valid prediction for GeneMark_model.104153_t
Valid prediction for snap_scaffold_28-snap.485-T1
Valid prediction for pasa_asmbl_38017.p1
Valid prediction for snap_scaffold_28-snap.509-T1
Valid prediction for GlimmerHMM_glimmerT_59671-T1
Valid prediction for snap_scaffold_28-snap.497-T1
Valid prediction for snap_scaffold_28-snap.483-T1
Valid prediction for snap_scaffold_28-snap.510-T1
Valid prediction for snap_scaffold_28-snap.520-T1
Valid prediction for snap_scaffold_28-snap.491-T1
Valid prediction for GlimmerHMM_glimmerT_59676-T1
Valid prediction for GlimmerHMM_glimmerT_59659-T1
Valid prediction for GlimmerHMM_glimmerT_59673-T1
Valid prediction for GlimmerHMM_glimmerT_59672-T1
Valid prediction for GeneMark_model.104137_t
Valid prediction for snap_scaffold_28-snap.486-T1
Valid prediction for GlimmerHMM_glimmerT_59677-T1
Valid prediction for GlimmerHMM_glimmerT_59663-T1
Valid prediction for GlimmerHMM_glimmerT_59664-T1
Valid prediction for GeneMark_model.104152_t
Valid prediction for GeneMark_model.104160_t
Valid prediction for GeneMark_model.104154_t
Valid prediction for Augustus_model.g39712.t1
Valid prediction for snap_scaffold_28-snap.478-T1
Valid prediction for GlimmerHMM_glimmerT_59652-T1
Valid prediction for GeneMark_model.104134_t
Valid prediction for snap_scaffold_28-snap.480-T1
Valid prediction for Augustus_model.g39698.t1
Valid prediction for snap_scaffold_28-snap.498-T1
Valid prediction for snap_scaffold_28-snap.500-T1
Valid prediction for Augustus_model.g39704.t1
Couldn't classify 137208, 137281
Sorry, prediction pasa_asmbl_38019.p1 fails validation.
(ATG)	 AA	136414-136559	GT	TGG
(CCC)	 AG	136764-136904	GT	CAG
(AGT)	 AG	137039-137121	GT	AGG
(GTT)	 AG	137208-137281	AA	GGA
-recovered pasa_asmbl_38019.p1, initial, 136414, 136559
-recovered pasa_asmbl_38019.p1, internal, 136764, 136904
-recovered pasa_asmbl_38019.p1, internal, 137039, 137121
Valid prediction for Augustus_model.g39696.t1
Valid prediction for GeneMark_model.104145_t
Valid prediction for GeneMark_model.104146_t
Valid prediction for snap_scaffold_28-snap.484-T1
Valid prediction for GlimmerHMM_glimmerT_59651-T1
Valid prediction for GlimmerHMM_glimmerT_59658-T1
Valid prediction for GlimmerHMM_glimmerT_59654-T1
Valid prediction for GeneMark_model.104139_t
Valid prediction for GlimmerHMM_glimmerT_59670-T1
Valid prediction for Augustus_model.g39701.t1
Valid prediction for GeneMark_model.104142_t
Valid prediction for GeneMark_model.104155_t
Valid prediction for snap_scaffold_28-snap.477-T1
Valid prediction for GeneMark_model.104140_t
Valid prediction for snap_scaffold_28-snap.499-T1
Valid prediction for GeneMark_model.104151_t
Valid prediction for Augustus_model.g39700.t1
Valid prediction for CodingQuarry_transcript_43453-T1
Valid prediction for snap_scaffold_28-snap.487-T1
Couldn't classify 118960, 119461
Couldn't classify 122488, 122508
Sorry, prediction pasa_asmbl_38015.p1 fails validation.
(CGC)	 CA	118960-119461	GT	AGG
(GTT)	 AG	120037-120261	GT	CGG
(TGT)	 AG	120402-120497	GT	TGG
(GAG)	 AG	120606-120642	GT	AGG
(AAG)	 AG	120886-120961	GT	AGG
(TCA)	 AG	122488-122508	GT	TGG
-recovered pasa_asmbl_38015.p1, internal, 120037, 120261
-recovered pasa_asmbl_38015.p1, internal, 120402, 120497
-recovered pasa_asmbl_38015.p1, internal, 120606, 120642
-recovered pasa_asmbl_38015.p1, internal, 120886, 120961
-recovered pasa_asmbl_38015.p1, internal, 122488, 122508
Valid prediction for GeneMark_model.104156_t
Valid prediction for snap_scaffold_28-snap.513-T1
Valid prediction for Augustus_model.g39697.t1
Valid prediction for snap_scaffold_28-snap.488-T1
Valid prediction for GeneMark_model.104136_t
Valid prediction for GeneMark_model.104144_t
Valid prediction for snap_scaffold_28-snap.517-T1
Couldn't classify 138855, 139101
Sorry, prediction pasa_asmbl_38023.p1 fails validation.
(GAT)	 CA	138855-139101	GT	AGG
(GTC)	 AG	139265-139386	GT	AGG
(GAC)	 AG	139546-139671	GT	AGG
(GTG)	 AG	139860-139936	GT	AAG
(ATG)	 AG	140032-140132	GT	AGG
(AGA)	 AG	140264-140364	GA	AAG
-recovered pasa_asmbl_38023.p1, initial, 140032, 140132
-recovered pasa_asmbl_38023.p1, terminal, 140264, 140364
-recovered pasa_asmbl_38023.p1, internal, 139265, 139386
-recovered pasa_asmbl_38023.p1, internal, 139546, 139671
-recovered pasa_asmbl_38023.p1, internal, 139860, 139936
-recovered pasa_asmbl_38023.p1, internal, 140032, 140132
Couldn't classify 70212, 70268
Couldn't classify 71293, 71389
Sorry, prediction pasa_asmbl_38507.p1 fails validation.
(GAT)	 AG	70212-70268	GT	CTG
(AGC)	 AG	70370-70420	GT	ATG
(CTG)	 AG	70755-70927	GT	AAG
(GTC)	 AG	71293-71389	AG	AGA
-recovered pasa_asmbl_38507.p1, internal, 70212, 70268
-recovered pasa_asmbl_38507.p1, internal, 70370, 70420
-recovered pasa_asmbl_38507.p1, internal, 70755, 70927
Valid prediction for GlimmerHMM_glimmerT_59674-T1
Valid prediction for GlimmerHMM_glimmerT_59662-T1
Valid prediction for snap_scaffold_28-snap.504-T1
Valid prediction for GlimmerHMM_glimmerT_59655-T1
Valid prediction for HiQ_model.g39710.t1
Valid prediction for GlimmerHMM_glimmerT_59653-T1
Valid prediction for GeneMark_model.104158_t
Valid prediction for snap_scaffold_28-snap.493-T1
Valid prediction for snap_scaffold_28-snap.512-T1
Couldn't classify 125451, 125540
Sorry, prediction CodingQuarry_transcript_43452-T1 fails validation.
(ATG)	 CA	125032-125045	GT	TGG
(CTG)	 CA	125451-125540	GT	GAG
(CTT)	 AG	125670-125748	GT	AGG
(GTG)	 AG	126000-126171	GT	CGG
(AAA)	 AG	126318-126397	GT	AGG
(CAA)	 AG	126661-126806	GT	GGG
(AGG)	 AG	126969-127134	GT	AGG
(CAT)	 AG	127229-127448	GT	AGG
(CGG)	 AG	127569-127678	GT	GGG
(CAC)	 AG	127804-127992	GT	CGG
(GCG)	 AG	128252-128492	GT	GCG
(TGG)	 AG	128687-128769	GT	AGG
(ATC)	 AG	128909-129029	GT	AGG
(GTG)	 AG	129123-129220	GT	AGG
(ATG)	 AG	129350-129424	GT	AGG
(ATC)	 AG	129799-129904	GT	CGG
(GTT)	 AG	130103-130289	GT	AGG
(GCA)	 AG	130417-130573	GT	AGG
(GCC)	 AG	130685-130771	TC	AGT
-recovered CodingQuarry_transcript_43452-T1, initial, 125032, 125045
-recovered CodingQuarry_transcript_43452-T1, initial, 129350, 129424
-recovered CodingQuarry_transcript_43452-T1, terminal, 130685, 130771
-recovered CodingQuarry_transcript_43452-T1, internal, 125670, 125748
-recovered CodingQuarry_transcript_43452-T1, internal, 126000, 126171
-recovered CodingQuarry_transcript_43452-T1, internal, 126318, 126397
-recovered CodingQuarry_transcript_43452-T1, internal, 126661, 126806
-recovered CodingQuarry_transcript_43452-T1, internal, 126969, 127134
-recovered CodingQuarry_transcript_43452-T1, internal, 127229, 127448
-recovered CodingQuarry_transcript_43452-T1, internal, 127569, 127678
-recovered CodingQuarry_transcript_43452-T1, internal, 127804, 127992
-recovered CodingQuarry_transcript_43452-T1, internal, 128252, 128492
-recovered CodingQuarry_transcript_43452-T1, internal, 128687, 128769
-recovered CodingQuarry_transcript_43452-T1, internal, 128909, 129029
-recovered CodingQuarry_transcript_43452-T1, internal, 129123, 129220
-recovered CodingQuarry_transcript_43452-T1, internal, 129350, 129424
-recovered CodingQuarry_transcript_43452-T1, internal, 129799, 129904
-recovered CodingQuarry_transcript_43452-T1, internal, 130103, 130289
-recovered CodingQuarry_transcript_43452-T1, internal, 130417, 130573
Valid prediction for GlimmerHMM_glimmerT_59656-T1
Valid prediction for snap_scaffold_28-snap.492-T1
Valid prediction for Augustus_model.g39695.t1
Valid prediction for snap_scaffold_28-snap.514-T1
Valid prediction for Augustus_model.g39699.t1
Valid prediction for snap_scaffold_28-snap.518-T1
Valid prediction for snap_scaffold_28-snap.503-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 snap_scaffold_28-snap.481-T1
Valid prediction for GlimmerHMM_glimmerT_59678-T1
Valid prediction for snap_scaffold_28-snap.519-T1
Valid prediction for snap_scaffold_28-snap.508-T1
Valid prediction for Augustus_model.g39707.t1
Valid prediction for GlimmerHMM_glimmerT_59680-T1
Valid prediction for snap_scaffold_28-snap.515-T1
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.104135_t
Valid prediction for Augustus_model.g39706.t1
Valid prediction for snap_scaffold_28-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_59667-T1
Valid prediction for snap_scaffold_28-snap.502-T1
Valid prediction for snap_scaffold_28-snap.495-T1
Valid prediction for snap_scaffold_28-snap.506-T1
Valid prediction for GlimmerHMM_glimmerT_59669-T1
Valid prediction for snap_scaffold_28-snap.507-T1
Valid prediction for GeneMark_model.104138_t
Valid prediction for snap_scaffold_28-snap.482-T1
Valid prediction for GeneMark_model.104161_t
Valid prediction for Augustus_model.g39705.t1
Valid prediction for Augustus_model.g39713.t1
Valid prediction for Augustus_model.g39702.t1
Valid prediction for GeneMark_model.104150_t
Valid prediction for GlimmerHMM_glimmerT_59660-T1
Valid prediction for CodingQuarry_transcript_43454-T1
Valid prediction for GeneMark_model.104162_t
Valid prediction for GlimmerHMM_glimmerT_59666-T1
Valid prediction for GeneMark_model.104157_t
Valid prediction for snap_scaffold_28-snap.489-T1
Valid prediction for GeneMark_model.104148_t
Valid prediction for GeneMark_model.104141_t
Valid prediction for GlimmerHMM_glimmerT_59668-T1
Valid prediction for Augustus_model.g39711.t1
Valid prediction for snap_scaffold_28-snap.496-T1
Couldn't classify 9818, 9960
Sorry, prediction pasa_asmbl_37338.p1 fails validation.
(ATG)	 AC	8833-8849	GT	AGG
(AAT)	 AG	9097-9211	GT	GAG
(TAC)	 AG	9315-9451	GT	GGG
(ATT)	 AG	9585-9697	GT	AGG
(GTG)	 AG	9818-9960	CA	TCC
-recovered pasa_asmbl_37338.p1, initial, 8833, 8849
-recovered pasa_asmbl_37338.p1, internal, 9097, 9211
-recovered pasa_asmbl_37338.p1, internal, 9315, 9451
-recovered pasa_asmbl_37338.p1, internal, 9585, 9697
Valid prediction for Augustus_model.g39715.t1
Valid prediction for GlimmerHMM_glimmerT_59665-T1
Valid prediction for Augustus_model.g39703.t1
Valid prediction for HiQ_model.g39714.t1
Valid prediction for GlimmerHMM_glimmerT_59675-T1
Valid prediction for snap_scaffold_28-snap.490-T1
Valid prediction for Augustus_model.g39708.t1
Valid prediction for GlimmerHMM_glimmerT_59661-T1
Valid prediction for GlimmerHMM_glimmerT_59657-T1
Valid prediction for GeneMark_model.104159_t
Valid prediction for snap_scaffold_28-snap.505-T1
Valid prediction for snap_scaffold_28-snap.516-T1
Valid prediction for snap_scaffold_28-snap.521-T1
Valid prediction for snap_scaffold_28-snap.494-T1
Valid prediction for GeneMark_model.104143_t
Valid prediction for GeneMark_model.104147_t
Valid prediction for GlimmerHMM_glimmerT_59679-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16116, rend_intergenic: 14232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43944, rend_intergenic: 42797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84463, rend_intergenic: 81932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130771, rend_intergenic: 123741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 151327
-exon list size: 487


building trellis

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99.2    
99.4    
99.6    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 16116, rend_intergenic: 14232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43944, rend_intergenic: 42797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84463, rend_intergenic: 81932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130771, rend_intergenic: 123741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support