vcftools counts output not written to file
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2.4 years ago

I am trying to write a counts file using vcftools. Whether the output file is actually written depends on the prefix that I supply in the --out option. The .log file, however, does get written. Below I am pasting the contents of two log files written after my command. They only differ in the name of the prefix that I supply. What am I doing wrong?

The version that does write output

VCFtools - 0.1.15 (C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:

--gzvcf /Users/xxx/Documents/Ch1/anc_data/all2019.vcf.gz
--chr 9
--to-bp 22486683
--keep anc_partPop_assignments/BNC2/16802118/EF/AA_anc.sample
--counts
--out /Users/xxx/Documents/Ch1/partition1/anc_target/counts/BNC2_16802118_EF_AA
--remove-indels
--from-bp 8067207

Using zlib version: 1.2.11 Keeping individuals in 'keep' list After filtering, kept 23 out of 5081 Individuals Outputting Frequency Statistics... After filtering, kept 8213 out of a possible 1233013 Sites Run Time = 259.00 seconds

The version that does not write output

VCFtools - 0.1.15 (C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:

--gzvcf /Users/xxx/Documents/Ch1/anc_data/all2019.vcf.gz
--chr 9
--to-bp 22486683
--keep anc_partPop_assignments/BNC2/16802118/EF/AA_anc.sample
--counts
--out /Users/xxx/Documents/Ch1/partition1/anc_target/counts/BNC2_16802118_EF_AA_1
--remove-indels
--from-bp 8067207

Using zlib version: 1.2.11 Keeping individuals in 'keep' list After filtering, kept 23 out of 5081 Individuals Outputting Frequency Statistics... After filtering, kept 8213 out of a possible 1233013 Sites Run Time = 273.00 seconds

vcftools vcf frequency counts SNP • 642 views
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