Mitch comments

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                                            Mitch

Separating .vcf's by individual on pooled call?

Absolutely. I did samtools -r merge for all individuals from the CEU into a single pooled .bam Then ran discovery phase; perl /path/to/software/Retroseq/RetroSeq-master/bin/retroseq.pl -discover -bam TestCEU-r.bam -output CEU-r.HERVK.tab -eref HERVKfa.tab...

Separating .vcf's by individual on pooled call?

UPDATE: The Wildschutte 2016 paper took these, simplified, steps. 1. -discover phase on individual .bam's from 1kGP, to produce candidates 2. merge .bam's by population, with samtools merge 3. -call...

EasySFS runtime? Running forever?

HI Isaac, thanks for the quick response. I should have clarified `nohup ./easySFS.py -i ${vcf} -p ${id} -a -f --proj 48,48,48,48,48 &` is the frozen line I simply gave you...

EasySFS runtime? Running forever?

Hi, Yes ~275 VIRT and RES in htop. CPU% is drifting around 90-100% and MEM% ~50%. Overall memory usage is steady around ~350/503Gb with a couple other processes running as...

EasySFS runtime? Running forever?

Hi Isaac, I ran things on a set of 100k SNPs and finally got some output and it looks right! Interestingly, the output came out really quickly but the program...

EasySFS runtime? Running forever?

Hello, I upped the vcf to 1e6 snps and it seems to have run completely, produced output, in ~2hrs. But once again the job never terminated. I'm calling it completed...