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HenrikBengtsson / CostelloPSCNSeq

R package: Parent-specific Copy-number Estimation Pipeline using HT-Seq Data
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Chr 1-25: Need to increase to `vmem=2gb` in .future.R #10

Closed HenrikBengtsson closed 7 years ago

HenrikBengtsson commented 7 years ago

While testing with chr 1-22, X, Y, and M, I ran into the following in the 2.sequenza.R step:

$ tail /home/henrik/projects/CostelloJ-PSCN-Seq_tests/.future/20170626_111627-54Dsqf/sample_1_38265500/logs/joba810736cd1202b8e75d829f18ca5d611.log
[...]
 Chromosome 'M'...done
pileup2seqz...done
=>> PBS: job killed: vmem 1076252672 exceeded limit 1073741824

The solution should be to bump up from vmem=1gb to vmem=2gb in .future.R.

I'll update this in this repository; there'll be other updates too soon, so you shouldn't have to do anything unless you wanna to it already now.

HenrikBengtsson commented 7 years ago

Confirming that bumping up to vmem=2gb works.