Alternative to PGDSpider for vcf conversion

Question

[QPaps04]

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

Answer 1

[jpr6mg]

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.

[QPaps04]

sorry for my delay in responding - I used this in the end to get it into BayeScan format https://github.com/santiagosnchez/vcf2bayescan

Make sure you set up your population file correctly, otherwise it only discovers one popualtion. See here https://github.com/santiagosnchez/vcf2bayescan/issues/1 for my solution

Answer 2

[Francisco Pina Martins]

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.