Question: Freebayes command stopped due to lack of space
gravatar for amcheroo
5 months ago by
amcheroo0 wrote:

Hi, the server I am working with was out of space; I already cleaned it and it has enough space now. Before that, I was using freebayes programme for SNP calling, but as this space thing happened, it seems that the SNP calling is stopped now, cause when I use ls -lht nameofthefile.vcf the date and the hour consists on a week ago, but when I use htop, apparently it is still working. Does anyone know how to restart that command? Thank you in advance

forum freebayes snp calling • 155 views
ADD COMMENTlink modified 5 months ago by finswimmer6.7k • written 5 months ago by amcheroo0

Find its PID number and use the kill command.

(in htop you can use F9 for this)

ADD REPLYlink modified 5 months ago • written 5 months ago by jrj.healey8.3k

Thank you for your answer, but in that way, I will definitely kill the process but it wouldn't finish. I would like to restart not from zero but from the moment it stops. Is there any possible way?

ADD REPLYlink written 5 months ago by amcheroo0

I'm not familiar with FreeBayes itself, but it is quite rare that programs support 'resuming'. If you had suspended the program with Ctrl-Z, you could use fg to resume it, but if the process has been disowned I don't believe there is any way to retrieve it. You'll just have to kill it and start over (unless someone knows better than me).

ADD REPLYlink written 5 months ago by jrj.healey8.3k
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