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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Can't find the [ convert ] bin in your $PATH, I try to convert svg by /home/Lingchenjin/LDBlookshow/LDBlockShow/bin/svg_kit/svg2xxx.pl #43

Open 8ling88 opened 2 months ago

8ling88 commented 2 months ago

[Lingchenjin@mu01 Example2]$ ../../bin/LDBlockShow -InVCF ../Example1/Test.vcf.gz -OutPut out -Region chr11:24100000:24200000 -InGWAS gwas.pvalue -OutPng -SeleVar 2

Detected VCF File is phased file with '|', Read VCF in Phase mode

Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :11

Start Region Cal... :chr11 24100000 24200000; In This Region TotalSNP Number is 7

find blocks... sh: /home/Lingchenjin/LDBlookshow/LDBlockShow/example/Example2/../../bin/plink: Permission denied mv: cannot stat ‘out.plink.blocks.det’: No such file or directory gzip: out.blocks: No such file or directory Warining: SVG module in Perl is missing, trying to loading the built-in [SVG.pm]... Loading SVG module done Start draw... SVG info: SNPNumber :7 , SVG (width,height) = (455,518) convert SVG ---> PNG ... Can't find the [ convert ] bin in your $PATH, I try to convert svg by /home/Lingchenjin/LDBlookshow/LDBlockShow/bin/svg_kit/svg2xxx.pl Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using 'localhost:13.0' as the value of the DISPLAY variable. at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method) at sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:65) at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:115) at java.security.AccessController.doPrivileged(Native Method) at sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:74) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:264) at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:103) at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:82) at java.awt.image.BufferedImage.createGraphics(BufferedImage.java:1181) at org.apache.batik.ext.awt.image.GraphicsUtil.createGraphics(Unknown Source) at org.apache.batik.gvt.filter.GraphicsNodeRed8Bit.genRect(Unknown Source) at org.apache.batik.gvt.filter.GraphicsNodeRed8Bit.copyData(Unknown Source) at org.apache.batik.ext.awt.image.rendered.TileCacheRed.genRect(Unknown Source) at org.apache.batik.ext.awt.image.rendered.AbstractTiledRed.drawBlockInPlace(Unknown Source) at org.apache.batik.ext.awt.image.rendered.AbstractTiledRed.drawBlock(Unknown Source) at org.apache.batik.ext.awt.image.rendered.AbstractTiledRed.copyToRasterByBlocks(Unknown Source) at org.apache.batik.ext.awt.image.rendered.AbstractTiledRed.copyData(Unknown Source) at org.apache.batik.ext.awt.image.rendered.TranslateRed.copyData(Unknown Source) at org.apache.batik.ext.awt.image.rendered.PadRed.copyData(Unknown Source) at org.apache.batik.gvt.renderer.StaticRenderer.repaint(Unknown Source) at org.apache.batik.gvt.renderer.StaticRenderer.repaint(Unknown Source) at org.apache.batik.transcoder.image.ImageTranscoder.transcode(Unknown Source) at org.apache.batik.transcoder.XMLAbstractTranscoder.transcode(Unknown Source) at org.apache.batik.transcoder.SVGAbstractTranscoder.transcode(Unknown Source) at org.apache.batik.apps.rasterizer.SVGConverter.transcode(Unknown Source) at org.apache.batik.apps.rasterizer.SVGConverter.execute(Unknown Source) at org.apache.batik.apps.rasterizer.Main.execute(Unknown Source) at org.apache.batik.apps.rasterizer.Main.main(Unknown Source) ALL done

hewm2008 commented 2 months ago

1 chmd 755 -R /home/Lingchenjin/LDBlookshow/LDBlockShow/example/Example2/../../bin/ 2 就是系统安一下 convert 命令。
【 若有root 的可以一句命令 安装好 convert 命令; sudo apt-get install ImageMagick or sudo yum install ImageMagick】 没有再用 conda 安装 . 再没有就自己一步步安。 即可以使用如果下命令转png: convert