Hi all,
I'm processing a large set of SNP6 samples (1020) and performing CBS
segmentations afterwards. It's a very lengthy process and the annoying part
is that it systematically crashes on the last sample, see code and output
below:
# Run CBS paired segmentation with pooled normal samples
cbs <- CbsModel(cesN, cesN1.ref)
fit(cbs, verbose=verbose)
print(cbs)
# Export CBS regions
pathname <- writeRegions(cbs, verbose=verbose)
20170831 06:57:51| Pathname:
> cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/YKG-1,chr25,6c653767ed90d29ad5254a760d8f3952.xdr
> 20170831 06:57:51| Already done. Skipping.
> 20170831 06:57:51|Array #1018 ('YKG-1') of 1019 on chromosome 25...done
> 20170831 07:01:07|Genomic-signal tags:
> 20170831 07:01:07|Reference tags: 6c653767ed90d29ad5254a760d8f3952
> 20170831 07:01:08|Array #1019 ('YMB-1-E') of 1019 on chromosome 1...
> 20170831 07:01:08| Pathname:
> cbsData/gdsc_all,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6/YMB-1-E,chr01,6c653767ed90d29ad5254a760d8f3952.xdr
> 20170831 07:01:08| Already done. Skipping.
> Error: empty (zero-byte) input file
> Execution halted
At first I thought it was a problem of the sample, but that is not the case
as I could process it separately. In fact, at this stage all the samples
seem to be processed. Also strange is that the script works and exports the
regions for subsets of the data-set.
Any suggestion in how to export these would be much appreciated?
Thank you,
P.S: I'm using the multithreaded option of aroma
# - Setup configurations
# options(mc.cores = 10)
print(future::availableCores())
# Multithreaded
future::plan('multiprocess')
# Increase ram
setOption(aromaSettings, 'memory/ram', 600.0)
# Logs
log <- verbose <- Arguments$getVerbose(-4, timestamp=TRUE)
# Reduce decimal places to minimize space
options(digits=4)
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