Blank png files

[SquRunner]

I am attempting to plot regions along a genome. I know I have dense SNP data, but some regions work, and others don't? An example of the command for a region that does not work is:

LDBlockShow -InVCF concat.recode.vcf.gz -OutPut chr25_out_LD -Region chr25:46949317-47474693 -OutPng -NoShowLDist 1000000 -SeleVar 2
#Compress the SVG file
ShowLDSVG -InPreFix chr25_out_LD -OutPut chr25_out_LD_compressed.svg

Output File:

warning skip Indel site, there are total skip Indel sites number is : 1309

Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic sites number is :3169

Warning skip high missing site, and total skip allelic sites number is :22

Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :1164

Start Region Cal... :chr25 46949317 47474693; In This Region TotalSNP Number is 3217

In Big SNP Number :3217 ,Para -NumGradien suggest be maxValue : 10 ,auto be it convert SVG ---> PNG ... ALL done

Error File:

Start draw... SVG info: SNPNumber :3217 , SVG (width,height) = (5919.28,4375.12) Start draw... SVG info: SNPNumber :3217 , SVG (width,height) = (5919.28,4375.12) Start draw... SVG info: SNPNumber :4813 , SVG (width,height) = (6641.94,4909.26) Start draw... SVG info: SNPNumber :4813 , SVG (width,height) = (6641.94,4909.26)

Thank you for the help!

[hewm2008]

You can run the command convert xxx.svg xxx.png yourself convert xxx.svg xxx.png

[SquRunner]

Thank you for the reply! Sadly this did not working either. I still end up with a blank file. The file size increases a bit? Originally it was 7.3K but now it is 13K.

I have sence tried running a number of other regions as well, none of which are plotting.

Some throw an error:

Can't Found the Site file : chr25_out_LD.site.gz Too many SNP site 4813 , I suggest that you add the Para [-OutPng] to see the png File In Big SNP Number :4813 ,Para -NumGradien suggest be maxValue : 10 ,auto be it ALL done

And again, the command I used that resulted in this error was: LDBlockShow -InVCF dp8_concat.recode.vcf -OutPut chr25_whole_out_LD -Region chr25:1-700000 -OutPng -NoShowLDist 108720060 -SeleVar 2

[hewm2008]

svg is only 17k, which is not too big. There may be something wrong with the convert command in your linux system. I suggest you download svg to your local computer, open it with a browser, and then use other screenshot software to convert it to png format.

[SquRunner]

The svg file is actually 308M. I have tried bringing it locally, but does not like to open in the browser. The convert function seems to work for some regions, but not most.

[hewm2008]

You can retry running this command manually on a computer node with large memory.convert xxx.svg xxx.png