Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/3a4ffda5299442d064a73cc328d6f8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/3a4ffda5299442d064a73cc328d6f8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/a153d47a3d6e5236a4c5afd5f3f898/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.vcf.gz
  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
==> STAGING COMPLETE (4 inputs)


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

Parameters as interpreted:
	--gzvcf HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.vcf.gz
	--out HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels
	--TsTv-by-qual

Using zlib version: 1.2.11
Warning: Expected at least 2 parts in FORMAT entry: ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2">
Warning: Expected at least 2 parts in FORMAT entry: ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2">
Warning: Expected at least 2 parts in FORMAT entry: ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2">
Warning: Expected at least 2 parts in INFO entry: ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}.">
Warning: Expected at least 2 parts in INFO entry: ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}.">
Warning: Expected at least 2 parts in INFO entry: ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}.">
Warning: Expected at least 2 parts in INFO entry: ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}.">
Warning: Expected at least 2 parts in INFO entry: ID=QSI,Number=1,Type=Integer,Description="Quality score for any somatic variant, ie. for the ALT haplotype to be present at a significantly different frequency in the tumor and normal">
After filtering, kept 2 out of 2 Individuals
Outputting Ts/Tv By Quality
After filtering, kept 35 out of a possible 35 Sites
Run Time = 0.00 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.count: 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