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BGI-shenzhen / LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
MIT License
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`ZLIB_1.2.9' not found #23

Closed janking1 closed 2 years ago

janking1 commented 2 years ago

Here is my error,it seems that this error comes from converting SVG 2 PNG, I have already install the "zlib 1.2.9" and using command "export LIBRARY_PATH=$LIBRARY_PATH:/WORK/scau_ljq_1/USER/szq/2022.4.15dsq_LD_haploview/lib" to set the path to "zlib 1.2.9", but it didn't work and shows the same error, I wonder is there somewhere I can truly set the path to "zlib 1.2.9":

system(paste0("./LDBlockShow ",

  • " -InPlink sub_snp_PLAG1_sub_eigen_expand_sig_3Mb_bonferroni_0.01_200k_1557_indi ",
  • " -Region 4:72694947:78692263 ",
  • " -OutPut ","sub_snp_PLAG1_sub_eigen_expand_sig_3Mb_bonferroni_0.01_200k_1557_indi ",
  • " -OutPng "
  • ))

    Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :10303

    Start Region Cal... :4 72694947 78692263; In This Region TotalSNP Number is 7184

    Start draw... SVG info: SNPNumber :7184 , SVG (width,height) = (6609.28,4885.12) Too many SNP site 7184 , I suggest that you randomly select fewer sites to reshow , and here I try to draw ... In Big SNP Number :7184 ,Para -NumGradien suggest be maxValue : 10 ,auto be it Tip: The region you inputed is greater than the Para [-NoShowLDist], and this will call LDheatmap to be a not-complete triangle. You can modify the parameter [-NoShowLDist] according to your needs. convert SVG ---> PNG ... /usr/bin/convert: /WORK/app/anaconda3/5.3.0/lib/./libuuid.so.1: no version information available (required by /usr/lib64/libSM.so.6) /usr/bin/convert: /WORK/app/zlib/1.2.8/lib/libz.so.1: version `ZLIB_1.2.9' not found (required by /WORK/app/anaconda3/5.3.0/lib/./libpng16.so.16) ALL done find blocks...

hewm2008 commented 2 years ago

Hi @janking1 you can manually convert the svg to png to see if this error is reported. convert xxx.svg xxx.png

If it reports a considerable error, it is a problem with the installation of your command convert, you can reinstall this command first.

你好 你手动将svg转png看看是否报这个错，若报相当的错，当是你的命令convert安装的问题，你可以重新安装一下这个命令看看 convert xxx.svg xxx.png

janking1 commented 2 years ago

Thanks for help, it work. It seems that it is a problem with the installation of my command convert, may I ask if there would be trouble if I convert SVG directly without using ShowLDSVG?

hewm2008 commented 2 years ago

No problem, you can manually convert svg to png format by other methods/software.