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Question: BSmooth 'names' attribute must be the same length as the vector
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gravatar for ravi.tharakan
29 days ago by
ravi.tharakan0 wrote:

Hi All. I'm having a problem while running BSmooth in the bsseq package. I have 25 WGBS samples, human, which I've processed using Bismark, and I have read the coverage files using read.bismark. However, when I try to run BSmooth, I get the following error:

> Meth.cov.fit <- BSmooth(Meth.cov, mc.cores = 32, verbose = TRUE)
[BSmooth] preprocessing ... done in 37.1 sec
[BSmooth] smoothing by 'sample' (mc.cores = 32, mc.preschedule = FALSE)
[BSmooth] smoothing done in 17656.1 sec
Error in names(object) <- nm :
'names' attribute [25] must be the same length as the vector [2]

Here is the session info:

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.8 (Final)`
Matrix products: default
BLAS/LAPACK: /usr/local/OpenBLAS/0.2.19/gcc-4.9.1/lib/libopenblas_nehalemp-r0.2.19.so`
`locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C `
`attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base `
`other attached packages:
[1] bsseq_1.12.2 SummarizedExperiment_1.6.5 DelayedArray_0.2.7 matrixStats_0.52.2
[5] Biobase_2.36.2 GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 IRanges_2.10.5
[9] S4Vectors_0.14.7 BiocGenerics_0.22.1 `
`loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 XVector_0.16.0 zlibbioc_1.22.0 munsell_0.4.3 colorspace_1.3-2
[6] lattice_0.20-35 plyr_1.8.4 tools_3.4.0 grid_3.4.0 data.table_1.10.4-2
[11] R.oo_1.21.0 gtools_3.5.0 permute_0.9-4 Matrix_1.2-11 GenomeInfoDbData_0.99.0
[16] R.utils_2.5.0 bitops_1.0-6 RCurl_1.95-4.8 limma_3.33.13 compiler_3.4.0
[21] R.methodsS3_1.7.1 scales_0.5.0 locfit_1.5-9.1

I am running R on a Linux cluster but using Rstudio through Xming, if that helps. Any help would be really appreciated, I'm quite puzzled by this.

ADD COMMENTlink modified 26 days ago • written 29 days ago by ravi.tharakan0
0
gravatar for Peter Hickey
29 days ago by
Peter Hickey290
Johns Hopkins University, Baltimore, USA
Peter Hickey290 wrote:

Hi Ravi,

I have seen this error before when running on a cluster with a large value of mc.cores. Unfortunately, I don't know the exact cause (I suspect one of the jobs dies, possibly because it runs out of memory). I have been able to get around this by reducing to, say, mc.cores = 8. Does this work in your case?

Cheers, Pete

ADD COMMENTlink written 29 days ago by Peter Hickey290

Hi Pete, thanks for your help. mc.cores = 8 does work, at least it solves the error, but now the session dies because R overruns memory, even when I allocate 200 GB RAM and only smooth one chromosome. It seems like you're right about this being a memory problem.

Best, Ravi

ADD REPLYlink written 25 days ago by ravi.tharakan0

That does sound unusual; smoothing is memory intensive but shouldn't be that bad. This is CpG methylation, correct? And you're running it with Meth.cov.fit <- BSmooth(Meth.cov, mc.cores = 32, verbose = TRUE)?

ADD REPLYlink written 25 days ago by Peter Hickey290

Yes, CpG methylation; the code is like this:

chr1_Meth.cov <- chrSelectBSseq(Meth.cov, seqnames = 'chr1')
chr1_Meth.cov.fit <- BSmooth(chr1_Meth.cov, mc.cores = 8, verbose = TRUE)

I don't know if this is relevant, but another odd thing I noticed is that when I run

sum(rowSums(getCoverage(Meth.cov)) == 0) I get 0, which I understand means I have nowhere in the genome that has no coverage in at least one sample. I am not sure if that's plausible, so I wonder if there is something going on with my files.

Also, if it helps, my Meth.cov BSseq object is of length 58165645.

ADD REPLYlink modified 25 days ago • written 25 days ago by ravi.tharakan0
your zero-coverage sounds weird. On Tue, Oct 24, 2017 at 10:34 PM, ravi.tharakan [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User ravi.tharakan <https: support.bioconductor.org="" u="" 14221=""/> wrote Comment: > BSmooth 'names' attribute must be the same length as the vector > <https: support.bioconductor.org="" p="" 101916="" #102101="">: > > Yes, CpG methylation; the code is like this: > > chr1_Meth.cov <- chrSelectBSseq(Meth.cov, seqnames = 'chr1') > chr1_Meth.cov.fit <- BSmooth(chr1_Meth.cov, mc.cores = 8, verbose = TRUE) > > I don't know if this is relevant, but another odd thing I noticed is that > when I run > > sum(rowSums(getCoverage(Meth.cov)) == 0) I get 0, which I understand > means I have nowhere in the genome that has no coverage in at least one > sample. I am not sure if that's plausible, so I wonder if there is > something going on with my files. > > ------------------------------ > > Post tags: bsseq, bsmooth > > You may reply via email or visit https://support.bioconductor. > org/p/101916/#102101 >
ADD REPLYlink written 25 days ago by Kasper Daniel Hansen6.3k

Yes, it does sound a little odd. Especially since you have unstranded CpGs (my guess based on having 58,165,645 rows = 2 * 24 million CpGs in hg19)

ADD REPLYlink modified 25 days ago • written 25 days ago by Peter Hickey290
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