Question: Alternative to PGDSpider for vcf conversion
1
gravatar for QPaps04
6 months ago by
QPaps0410
QPaps0410 wrote:

Hello all, I have been trying to convert a large vcf file to GESTE_BAYE_SCAN format using PGDSpider. I have tried doing a straight conversion and also a two-step: vcf > PGD > GEST_BAYE_SCAN. The first step works. Hoever every time I try to produce the BayeScn file I get this error: ERROR 20-05 11:11:57,272 (GesteBayeScanWriter.java:write:382) -not enough memory. To increase the allowed memory see help.

I even took of the min max memory when I ran the line of code, as so: java -jar ~/bin/PGDSpider_2.1.1.5/PGDSpider2-cli.jar -inputfile ./PA_etcGBS_PGD -inputformat PGD -outputfile ./PA_etcGBS_GESTEBayeScn -outputformat GESTE_BAYE_SCAN -spid ./files/spid/PGD_to_GESTE_BAYE_SCAN.spid

Does anynone have any alternatives to PGDSpider for file conversion? Or any sugestion how I make this work? I can send you my settings in the .spid file if that is useful just let me know.

Thanks for your help in adavance, Eve

memory conversion snp next-gen vcf • 391 views
ADD COMMENTlink modified 7 weeks ago by stunts0 • written 6 months ago by QPaps0410
0
gravatar for jpr6mg
3 months ago by
jpr6mg0
jpr6mg0 wrote:

Were you ever able to figure out a workaround on this? Even when I max out the available memory on my server (512GB), the program isn't able to successfully write an output file.

ADD COMMENTlink written 3 months ago by jpr6mg0
0
gravatar for stunts
7 weeks ago by
stunts0
stunts0 wrote:

You can try to increase memory limits by running PGDSpider with java -jar -Xmx8g -jar .... In this case the -Xmx will increase the max memory usage to 8Gb. You can adjust to your limits and/or needs.

ADD COMMENTlink written 7 weeks ago by stunts0
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