Open maxineliu opened 2 years ago
I have a VCF file that consists of structural variant records. I'm trying to convert vcf to gds, but failed.
The command I used is: seqVCF2GDS("/Users/path/12bufo.vcf.gz", "12bufo.gds", storage.option="ZIP_RA", parallel=8L)
The error msg is:
Fri Aug 19 02:45:43 2022 Variant Call Format (VCF) Import: file(s): 12bufo.vcf.gz (1.0G) file format: VCFv4.2 genome reference: <unknown> the number of sets of chromosomes (ploidy): 2 the number of samples: 12 genotype storage: bit2 compression method: ZIP_RA # of samples: 12 calculating the total number of variants ... # of variants: 3,036,302 >>> writing to 8 files: <<< 12bufo_tmp01_1570f70c78cda [1 .. 379,544] 12bufo_tmp02_1570f3cf0760e [379,545 .. 759,088] 12bufo_tmp03_1570f4ed6b063 [759,089 .. 1,138,632] 12bufo_tmp04_1570f70d65c04 [1,138,633 .. 1,518,176] 12bufo_tmp05_1570f933447c [1,518,177 .. 1,897,720] 12bufo_tmp06_1570f4d52d9c [1,897,721 .. 2,277,264] 12bufo_tmp07_1570f47a55f3e [2,277,265 .. 2,656,808] 12bufo_tmp08_1570f3a100431 [2,656,809 .. 3,036,302] Error in .DynamicForkCall(njobs, njobs, .fun = function(.jobidx, ...) { : Error in seqVCF2GDS(vcf.fn, ptmpfn[i], header = oldheader, storage.option = storage.option, : Invalid float conversion 'None,0,8,8,8' FILE: /Users/maxineliu/work/bufo/vcf_analysis.dir/12bufo.vcf.gz LINE: 794, COLUMN: 8, PRECISE;SVTYPE=BND;SUPPORT=3;COVERAGE=None,0,8,8,8
So I modified my command: seqVCF2GDS("/Users/path/12bufo.vcf.gz", "12bufo.gds", storage.option=seqStorageOption(float.mode="float64"), parallel=8L)
Return changed but still has errors:
Fri Aug 19 02:53:04 2022 Variant Call Format (VCF) Import: file(s): 12bufo.vcf.gz (1.0G) file format: VCFv4.2 genome reference: <unknown> the number of sets of chromosomes (ploidy): 2 the number of samples: 12 genotype storage: bit2 compression method: customized # of samples: 12 calculating the total number of variants ... # of variants: 3,036,302 >>> writing to 8 files: <<< 12bufo_tmp01_1570f54acdfc [1 .. 379,544] 12bufo_tmp02_1570f72195e1a [379,545 .. 759,088] 12bufo_tmp03_1570f5f71377b [759,089 .. 1,138,632] 12bufo_tmp04_1570f1f19d31 [1,138,633 .. 1,518,176] 12bufo_tmp05_1570f1d86fcf6 [1,518,177 .. 1,897,720] 12bufo_tmp06_1570f949899f [1,897,721 .. 2,277,264] 12bufo_tmp07_1570f3aea2a7c [2,277,265 .. 2,656,808] 12bufo_tmp08_1570f638b511b [2,656,809 .. 3,036,302] Error in .DynamicForkCall(njobs, njobs, .fun = function(.jobidx, ...) { : Error in match.arg(scenario) : 'arg' should be one of “general”, “imputation”
What should I do to avoid this kind of error?
Thanks in advance, Maxine
Cannot recognize None in COVERAGE=None,0,8,8,8. None should be replaced by . in the VCF file!
None
COVERAGE=None,0,8,8,8
.
I have a VCF file that consists of structural variant records. I'm trying to convert vcf to gds, but failed.
The command I used is: seqVCF2GDS("/Users/path/12bufo.vcf.gz", "12bufo.gds", storage.option="ZIP_RA", parallel=8L)
The error msg is:
So I modified my command: seqVCF2GDS("/Users/path/12bufo.vcf.gz", "12bufo.gds", storage.option=seqStorageOption(float.mode="float64"), parallel=8L)
Return changed but still has errors:
What should I do to avoid this kind of error?
Thanks in advance, Maxine