Hi Henrik,
does the error occur when you run:
>
> fit(cbs, verbose=verbose)
>
Yes, because I never got the "print(cbs)" output
> 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?
>
Unfortunately, I can't run this interactively because even though the
samples are already preprocessed it takes almost a day to load everything.
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.
I changed the code accordingly:
fit(cbs, arrays=1019:1020, chromosomes=c(1, 25), verbose=verbose)
It ran without throwing any error (I tried before the same with a subset of
~100 samples and it also worked).
It seems to be a specific problem when all the 1020 samples are ran
together. I've placed a try/catch with the traceback().
# Run CBS paired segmentation with pooled normal samples
cbs <- CbsModel(cesN, cesN1.ref)
out <- tryCatch(
{
fit(cbs, arrays=1019:1020, chromosomes=c(1, 25), verbose=verbose)
},
error=function() {
message('Try/catch: error')
traceback()
},
warning=function() {
message('Try/catch: warning')
traceback()
},
finally={
message('Try/catch: finally')
traceback()
}
)
print(cbs)
I started the script with all the samples (without "arrays=1019:1020") as
before.
What surprised me is that the script continued to the writeRegions call and
it started to export all the samples.
pathname <- writeRegions(cbs, verbose=verbose)
> # Export CBS regions
> > pathname <- writeRegions(cbs, verbose=verbose)
> 20170831 21:53:10|Array #1 ('201T') of 1019...
> 20170831 21:53:10| Extracting regions from all fits...
> 20170831 21:53:10| Obtaining CN model fits (or fit if missing)...
> 20170831 21:57:15| Obtaining CN model fits (or fit if missing)...done
> 20170831 21:57:15| Extracting regions for chromosome #1...
> 20170831 21:57:15| Extracting regions for chromosome #1...done
> 20170831 21:57:15| Extracting regions for chromosome #2...
> 20170831 21:57:15| Extracting regions for chromosome #2...done
> 20170831 21:57:15| Extracting regions for chromosome #3...
> 20170831 21:57:15| Extracting regions for chromosome #3...done
Does it mean it will export all the samples processed so far? Can I export
everything without re-calling the fit function from CbsModel?
Thanks a lot,
> 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
> <[email protected] <javascript:>> 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)
> >
> >
> > --
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
> >
> >
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--
--
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