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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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I have problem to use the software in linux #3

Closed lrj-1 closed 3 years ago

lrj-1 commented 3 years ago

$ LDBlockShow -InVCF 507sample.vcf_Chr_id.vcf -OutPut file -Region chr14:55370544:55870544 -OutPng

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

    InPut Para -Region  chromosome [chr14]  can't be found in the SNP dataset

Warining: SVG module in Perl is missing, trying to loading the built-in [SVG.pm]... Loading SVG module done Start draw... SVG info: SNPNumber :0 , SVG (width,height) = (0,0) Use of uninitialized value in subtraction (-) at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 510, line 1. Use of uninitialized value in subtraction (-) at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 510, line 1. Use of uninitialized value in subtraction (-) at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 532, line 1. Use of uninitialized value in subtraction (-) at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 532, line 1. Illegal division by zero at /public/home/yplu/biosoft/LDBlockShow-1.36/bin//ShowLDSVG line 532, line 1.

hewm2008 commented 3 years ago

It may be caused by the one of following two reasons reasons A: The region you gave has no snp sites (or the region has no snp after filtering such as maf). If so, you can enlarge the region or reduce filter conditions. reasons B: You gave the wrong chr name. First, make sure if the chr name is right . Give the correct chr name, which must be consistent with the chr name of the VCF file.

有可能是如下两个原因造成的 A :你给的这个region没有snp位点 （or 被过滤掉了 如maf 等过滤后 这个region一个snp都没有），若是这样可以把region放大,or把过滤条件降低 B：你给错了 chr名字 。 你先确认一下是不是chr名给错了，给对的chr名，要和VCF文件的chr名是一致的。

lrj-1 commented 3 years ago

thanks for your timely reply ,and I check name,but it have new number svg can't convert to png

convert SVG ---> PNG ... which: no convert in (/public/home/yplu/perl5/bin:/public/home/yplu/miniconda3/bin:/public/home/yplu/miniconda3/condabin:/public/home/yplu/myBin/bin:/public/home/software/opt/moudles/Modules/3.2.10/bin:/opt/ibm/lsf/10.1/linux3.10-glibc2.17-x86_64/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/public/home/yplu/.local/bin:/public/home/yplu/bin) Can't find the [ convert ] bin, I try to convert svg by /public/home/yplu/biosoft/LDBlockShow-1.36/bin/svg_kit/svg2xxx.pl

hewm2008 commented 3 years ago

This is just a warning and does not affect the results, mainly in the step of converting svg to png. reason : Your system does not have this command [ convert ] command solution ： you can install it[convert] yourself.

Because there is no such [convert] command on yours linux , the program calls [LDBlockShow-1.36/bin/svg_kit/svg2xxx.pl] to convert svg to png or pdf

这个只是提示而己，并不影响结果，主要在转化svg到png这一步。 原因是： 你的系统没有这个命令 convert 的命令， 解决 ： 你可以自己安装之。 or 由于没有这个命令，程序调用了 LDBlockShow-1.36/bin/svg_kit/svg2xxx.pl 把svg转为png or pdf

dawei1203 commented 3 years ago

yum install ImageMagick