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_18.104.22.168/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