Open zhanglucas opened 5 years ago
Hi, I'm trying to run the dev version of FusorSV with the testing data provided by you guys and I keep running into this Keyerror: I'm using the Gr37 masks provided in the data folder and hg19 reference genome.
GenomeSTRiP-------------------------------------------------------------------------------- sample=HG00096 t=INV prec=0.0 rec=0.0 f1=0.0 j=0.0 Hydra-------------------------------------------------------------------------------- sample=HG00096 t=INV prec=0.555555555556 rec=0.0588235294118 f1=0.106382978723 j=0.00119748349257 Lumpy-------------------------------------------------------------------------------- sample=HG00096 t=INV prec=0.666666666667 rec=0.127659574468 f1=0.214285714286 j=0.0039733084823 fusorSV-------------------------------------------------------------------------------- sample=HG00096 t=INV prec=0.666666666667 rec=0.461538461538 f1=0.545454545455 j=0.0256974368127 BreakSeq-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 BreakDancer-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 Tigra-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 cnMOPS-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 CNVnator-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 Delly-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 GenomeSTRiP-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 Hydra-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 Lumpy-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 fusorSV-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 BreakSeq-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 BreakDancer-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 Tigra-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 cnMOPS-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 CNVnator-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 Delly-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 GenomeSTRiP-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 Hydra-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 Lumpy-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 fusorSV-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 writing VCF for HG00096 Traceback (most recent call last): File "/u/home/l/lukezhan/FusorSV/FusorSV.py", line 334, in apply_model_to_samples out_dir+'/vcf/'+sname+'_S'+str(f_id)+'.vcf',sname,target_key=k) #VCF File "/u/home/l/lukezhan/FusorSV/svu_utils.py", line 154, in genome_to_vcf ref_seq[refname][D[i][0]].seq[D[i][1]], #REF KeyError: '1'
My command line looks like this: python /u/home/l/lukezhan/FusorSV/FusorSV.py \ -r /u/home/l/lukezhan/refgenome/hg19.fasta \ -i /u/home/l/lukezhan/meta_caller_RC1/HG00096 \ -a /u/home/l/lukezhan/FusorSV/data/human_g1k_v37_decoy_ucsc_segmental_dups.json \ -o /u/scratch/l/lukezhan/FusorOut \ -f /u/home/l/lukezhan/FusorSV/data/models/default.pickle \ -p 4 \ -z /u/home/l/lukezhan/FusorSV/data/human_g1k_v37_decoy_coordinates.json \
What am I doing wrong?
Hi, I'm trying to run the dev version of FusorSV with the testing data provided by you guys and I keep running into this Keyerror: I'm using the Gr37 masks provided in the data folder and hg19 reference genome.
GenomeSTRiP-------------------------------------------------------------------------------- sample=HG00096 t=INV prec=0.0 rec=0.0 f1=0.0 j=0.0 Hydra-------------------------------------------------------------------------------- sample=HG00096 t=INV prec=0.555555555556 rec=0.0588235294118 f1=0.106382978723 j=0.00119748349257 Lumpy-------------------------------------------------------------------------------- sample=HG00096 t=INV prec=0.666666666667 rec=0.127659574468 f1=0.214285714286 j=0.0039733084823 fusorSV-------------------------------------------------------------------------------- sample=HG00096 t=INV prec=0.666666666667 rec=0.461538461538 f1=0.545454545455 j=0.0256974368127 BreakSeq-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 BreakDancer-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 Tigra-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 cnMOPS-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 CNVnator-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 Delly-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 GenomeSTRiP-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 Hydra-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 Lumpy-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 fusorSV-------------------------------------------------------------------------------- sample=HG00096 t=TRA prec=0.0 rec=0.0 f1=0.0 j=0.0 BreakSeq-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 BreakDancer-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 Tigra-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 cnMOPS-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 CNVnator-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 Delly-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 GenomeSTRiP-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 Hydra-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 Lumpy-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 fusorSV-------------------------------------------------------------------------------- sample=HG00096 t=BND prec=0.0 rec=0.0 f1=0.0 j=0.0 writing VCF for HG00096 Traceback (most recent call last): File "/u/home/l/lukezhan/FusorSV/FusorSV.py", line 334, in apply_model_to_samples out_dir+'/vcf/'+sname+'_S'+str(f_id)+'.vcf',sname,target_key=k) #VCF File "/u/home/l/lukezhan/FusorSV/svu_utils.py", line 154, in genome_to_vcf ref_seq[refname][D[i][0]].seq[D[i][1]], #REF KeyError: '1'
My command line looks like this: python /u/home/l/lukezhan/FusorSV/FusorSV.py \ -r /u/home/l/lukezhan/refgenome/hg19.fasta \ -i /u/home/l/lukezhan/meta_caller_RC1/HG00096 \ -a /u/home/l/lukezhan/FusorSV/data/human_g1k_v37_decoy_ucsc_segmental_dups.json \ -o /u/scratch/l/lukezhan/FusorOut \ -f /u/home/l/lukezhan/FusorSV/data/models/default.pickle \ -p 4 \ -z /u/home/l/lukezhan/FusorSV/data/human_g1k_v37_decoy_coordinates.json \
What am I doing wrong?