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mroosmalen / nanosv

SV caller for nanopore data
MIT License
89 stars 22 forks source link

Busy with printing to vcf... #62

Open ndierckx opened 4 years ago

ndierckx commented 4 years ago

Hi,

Is it normal that it is almost 2 days stuck on "Busy with printing to vcf..."?

jaesvi commented 4 years ago

Not really, it should not be the most computationally intense step. But of course it depends on your sample and coverage, and the number of breakpoints expected.

ndierckx commented 4 years ago

I don't think virtual memory is a problem and everything progresses relatively fast, but it gets stuck every time at "Busy with printing to vcf..." without any errors

ndierckx commented 4 years ago

Anything wrong with the command I use? NanoSV -s samtools -b file.bed -o file.vcf file.bam

Amanda2018genetics commented 1 year ago

I don't think virtual memory is a problem and everything progresses relatively fast, but it gets stuck every time at "Busy with printing to vcf..." without any errors

Hi, I was stuck in 'busy with printing to vcf ..." for more than 12 hours. Is that normal ? And how did you solve the problem ? thanks.

ndierckx commented 1 year ago

Hi, sorry forgot to answer. Never really resolved the problem, but sometimes after waiting a very long time, it did finish...