KING pipeline does not work #147

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1. BoPeng commented on May 16, 2020

   

   BoPeng

   on May 16, 2020

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   I have trouble installing plink because the bioconda plink uses a version of gsl that conflicts with the conda-forge version of gsl used by vtools.
2. BoPeng commented on May 16, 2020

   

   BoPeng

   on May 16, 2020

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   vtools execute KING   --jobname dummy  --var_table pass_variants   --king_path ~/bin/   --plink_path ~/bin
   
   INFO: Executing KING.king_0: Load specified snapshot if a snapshot is specified. Otherwise use the existing project.
   INFO: Executing KING.king_10: Check the existence of KING and PLINK command.
   INFO: Command /Users/bpeng/bin//king is located.
   INFO: Command /Users/bpeng/bin/plink is located.
   INFO: Executing KING.king_20: Write selected variant and samples in tped format
   INFO: Running vtools export pass_variants --format tped --samples "1" | awk '{$2=$1"_"$4;$3=0;print $0}' > /Users/bpeng/vatlab/vtools/ticket147/.vtools_cache/dummy.tped
   INFO: Executing KING.king_21: Rename tfam file to match tped file
   INFO: Running mv pass_variants.tfam /Users/bpeng/vatlab/vtools/ticket147/.vtools_cache/dummy.tfam
   INFO: Executing KING.king_30: Calculate LD pruning candidate list with a cutoff of R^2=0.5
   INFO: Running /Users/bpeng/bin/plink --tped dummy.tped --tfam dummy.tfam --indep-pairwise 50 5 0.5 --allow-no-sex --out dummy.LD.50 under /Users/bpeng/vatlab/vtools/ticket147/.vtools_cache
   INFO: Executing KING.king_31: LD pruning from pre-calculated list
   INFO: Running /Users/bpeng/bin/plink --tped dummy.tped --tfam dummy.tfam --extract dummy.LD.50.prune.in --no-parents --no-sex --no-pheno --maf 0.01 --make-bed --out dummy under /Users/bpeng/vatlab/vtools/ticket147/.vtools_cache
   INFO: Executing KING.king_41: Global ancestry inference
   INFO: Running /Users/bpeng/bin//king -b dummy.bed --mds --prefix dummy- under /Users/bpeng/vatlab/vtools/ticket147/.vtools_cache
   ERROR: Failed to execute step king_41: Output file /Users/bpeng/vatlab/vtools/ticket147/.vtools_cache/dummy-pc.txt does not exist after completion of the job.
   

   king
   KING 2.2.4 - (c) 2010-2019 Wei-Min Chen
   
   

    plink
   
   @----------------------------------------------------------@
   |        PLINK!       |     v1.07      |   10/Aug/2009     |
   |----------------------------------------------------------|
   |  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
   |----------------------------------------------------------|
   |  For documentation, citation & bug-report instructions:  |
   |        http://pngu.mgh.harvard.edu/purcell/plink/        |
   @----------------------------------------------------------@
   
   

   So the problem seems to be with the version of king.
3. BoPeng commented on May 16, 2020

   

   BoPeng

   on May 16, 2020

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   Error message is

   Genotypes stored in 1 words for each of 26 individuals.
   The number of individuals is < 1.
   

   so the previous command plink --make-bed could be doing something wrong.

   I would suggest that @enigmargs tries to understand what ~/.variant_tools/pipeline/KING.pipeline is trying to achieve and see if this is what is supposed to happen given this particular dataset.
4. enigmargs commented on May 22, 2020

   

   enigmargs

   on May 22, 2020

   Last edited by enigmargs

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   I tried exececuting steps individually on,

   • different (larger) dataset - which shows the same error as you quoted
   • King v2.2.3 which shows the following

   

   • and king v2.2.2 which shows error as below, I think in line with the WARNING mentioned in KING website that LPACK libraries are lacking below v2.2.3

   

   Is there any specific reason to use tfile format in export (instead of vcf) at King_20?
   Is it advisable to calculate PCs using PLINK and then import as phenotype field directly?

   I sincerely hope that I'm not dragging it too long!
5. gaow commented on May 22, 2020

   

   gaow

   on May 22, 2020

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   @enigmargs This pipeline not only does PCA but also does relationship analysis which is important in GWAS. Compared to PLINK, the relationship analysis using KING is more robust to the presence of population structure, and can perform pair-wise comparisons between individuals thus works for small sample size where good estimate of allele frequency is challenging.

   Perhaps for PCA/MDS analysis there is no major difference between these tools. Unfortunately we don't have a separate implementation for that.

   It seems the failure is related to LAPACK installation?