Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/061caba38cfe63e5f0a7ddcd662672/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/061caba38cfe63e5f0a7ddcd662672/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/4beeef7561e559a12847bcd3f66452/HCC1395_BL.deconflicted_germline.vcf.gz
==> STAGING COMPLETE (4 inputs)


VCFtools - 0.1.16
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
	--gzvcf HCC1395_BL.deconflicted_germline.vcf.gz
	--out HCC1395_BL.deconflicted_germline
	--TsTv-by-count

Using zlib version: 1.2.11
Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in INFO entry: ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency, for each ALT allele, in the same order as listed">
Warning: Expected at least 2 parts in FORMAT entry: ID=SUPPRESS_DECONFLICT,Description="Variant in CHIP/germline grey zone with no COSMIC rescue, or ambiguous germline/somatic — suppressed from both outputs">
Warning: Expected at least 2 parts in INFO entry: ID=DECONFLICT_ASSIGNED,Number=1,Type=String,Description="Category assigned by deconfliction: CHIP, GERMLINE, SUPPRESS, or SUSPECT">
Warning: Expected at least 2 parts in INFO entry: ID=DECONFLICT_ASSIGNED,Number=1,Type=String,Description="Category assigned by deconfliction: CHIP, GERMLINE, SUPPRESS, or SUSPECT">
Warning: Expected at least 2 parts in INFO entry: ID=DECONFLICT_ASSIGNED,Number=1,Type=String,Description="Category assigned by deconfliction: CHIP, GERMLINE, SUPPRESS, or SUSPECT">
After filtering, kept 1 out of 1 Individuals
Outputting Ts/Tv by Alternative Allele Count
After filtering, kept 354 out of a possible 354 Sites
Run Time = 1.00 seconds
ls: *.vcf: No such file or directory
ls: *.bcf: No such file or directory
ls: *.frq: No such file or directory
ls: *.frq.count: No such file or directory
ls: *.idepth: No such file or directory
ls: *.ldepth: No such file or directory
ls: *.ldepth.mean: No such file or directory
ls: *.gdepth: No such file or directory
ls: *.hap.ld: No such file or directory
ls: *.geno.ld: No such file or directory
ls: *.geno.chisq: No such file or directory
ls: *.list.hap.ld: No such file or directory
ls: *.list.geno.ld: No such file or directory
ls: *.interchrom.hap.ld: No such file or directory
ls: *.interchrom.geno.ld: No such file or directory
ls: *.TsTv: No such file or directory
ls: *.TsTv.summary: No such file or directory
ls: *.TsTv.qual: No such file or directory
ls: *.FILTER.summary: No such file or directory
ls: *.sites.pi: No such file or directory
ls: *.windowed.pi: No such file or directory
ls: *.weir.fst: No such file or directory
ls: *.het: No such file or directory
ls: *.hwe: No such file or directory
ls: *.Tajima.D: No such file or directory
ls: *.ifreqburden: No such file or directory
ls: *.LROH: No such file or directory
ls: *.relatedness: No such file or directory
ls: *.relatedness2: No such file or directory
ls: *.lqual: No such file or directory
ls: *.imiss: No such file or directory
ls: *.lmiss: No such file or directory
ls: *.snpden: No such file or directory
ls: *.kept.sites: No such file or directory
ls: *.removed.sites: No such file or directory
ls: *.singletons: No such file or directory
ls: *.indel.hist: No such file or directory
ls: *.hapcount: No such file or directory
ls: *.mendel: No such file or directory
ls: *.FORMAT: No such file or directory
ls: *.INFO: No such file or directory
ls: *.012: No such file or directory
ls: *.012.indv: No such file or directory
ls: *.012.pos: No such file or directory
ls: *.impute.hap: No such file or directory
ls: *.impute.hap.legend: No such file or directory
ls: *.impute.hap.indv: No such file or directory
ls: *.ldhat.sites: No such file or directory
ls: *.ldhat.locs: No such file or directory
ls: *.BEAGLE.GL: No such file or directory
ls: *.BEAGLE.PL: No such file or directory
ls: *.ped: No such file or directory
ls: *.map: No such file or directory
ls: *.tped: No such file or directory
ls: *.tfam: No such file or directory
ls: *.diff.sites_in_files: No such file or directory
ls: *.diff.indv_in_files: No such file or directory
ls: *.diff.sites: No such file or directory
ls: *.diff.indv: No such file or directory
ls: *.diff.discordance.matrix: No such file or directory
ls: *.diff.switch: No such file or directory