Hi,
does the error occur when you run:
fit(cbs, verbose=verbose)
or did that complete successfully and you get the error while running:
pathname <- writeRegions(cbs, verbose=verbose)
If you run interactively, what does traceback() output if called
immediately after the error occurs?
Also, see if
fit(cbs, arrays = 1019:1020, chromosomes = c(1, 25), verbose = verbose)
or alternatively,
pathname <- writeRegions(cbs, arrays = 1019:1020, chromosomes = c(1,
25), verbose=verbose)
gives the same error. Then you can get to traceback() a bit sooner.
/Henrik
PS. I assume that you already know that rerunning the commands will
not redo the actual analysis; already processed samples will be
skipped - though with 1020 samples it might still take some time.
On Thu, Aug 31, 2017 at 1:26 AM, Emanuel Gonçalves
<emanuelvgoncal...@gmail.com> wrote:
> 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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