Downgrade conda vcftools version dependency

[pdimens]

I'm unsure if this is an actual issues, but it seems the output of freebayes doesn't jive with the vcftools (0.1.16) that's bundled with conda's dDocent recipe, as it spits out many initial warnings:

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

Parameters as interpreted:
        --vcf BFT_biallelic_noindel.recode.vcf

Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
Warning: Expected at least 2 parts in INFO entry: ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
Warning: Expected at least 2 parts in INFO entry: ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
Warning: Expected at least 2 parts in INFO entry: ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
Warning: Expected at least 2 parts in INFO entry: ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
Warning: Expected at least 2 parts in FORMAT entry: ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
Warning: Expected at least 2 parts in FORMAT entry: ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
After filtering, kept 646 out of 646 Individuals

[jpuritz]

The warnings are annoying but do not affect downstream analysis. This is a problem with VCFtools (vcftools/vcftools#129) which is no longer being developed. May have to switch to bcftools eventually.

[michellehauer]

So I keep on reading that the warnings don't matter or affect downstream analyses, but my command doesn't produce the output file I want at all. Any tips on how to resolve this?

module: loading 'R/3.4.3_mkl'
module: loading 'vcftools/0.1.16'
module: loading 'bcftools/1.9'

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

Parameters as interpreted:
        --vcf anvio_repseq.Freebayes.FINAL.recode.vcf
        --out HA_Illium13
        --indv HA_Illium13

Warning: Expected at least 2 parts in INFO entry: ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
Warning: Expected at least 2 parts in INFO entry: ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
Warning: Expected at least 2 parts in INFO entry: ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
Warning: Expected at least 2 parts in INFO entry: ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
Warning: Expected at least 2 parts in INFO entry: ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
Warning: Expected at least 2 parts in INFO entry: ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
Warning: Expected at least 2 parts in FORMAT entry: ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
Warning: Expected at least 2 parts in FORMAT entry: ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
Keeping individuals in 'keep' list
After filtering, kept 1 out of 9 Individuals
After filtering, kept 1524 out of a possible 1524 Sites
Run Time = 0.00 seconds