BSmooth 'names' attribute must be the same length as the vector
1
0
Entering edit mode
@ravitharakan-14221
Last seen 7.1 years ago

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.

bsseq bsmooth • 2.1k views
ADD COMMENT
0
Entering edit mode
Peter Hickey ▴ 740
@petehaitch
Last seen 21 days ago
WEHI, Melbourne, Australia

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode
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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 875 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6