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BSmooth - Error in env[[as.character(i)]] <- value : wrong args for environment subassignment #110
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The root cause is this:
which means that one of the parallel jobs failed. |
Could you call
traceback()
right after the error and send the output?
…On Tue, Apr 5, 2022 at 5:35 AM Aleksa Krsmanović ***@***.***> wrote:
I'm coming across a problem while trying to analyze WGBS data from CD4 and
CD8 T cells (3 vs 3 samples). I used the following code:
bsseq_obj = BSseq(chr = chr, pos = position, M = M, Cov = C, sampleNames = sample_names)
replicate = c(seq(1,length(group1_sample_list)), seq(1,length(group2_sample_list)))
bsseq::pData(bsseq_obj) = data.frame(row.names = sample_names, replicate, tissue)
bsseq_obj = renameSeqlevels(bsseq_obj, mapSeqlevels(seqlevels(bsseq_obj), "UCSC"))
bsseq_obj = bsseq_obj[seqnames(bsseq_obj)=="chr19",]
bs.fit = BSmooth(bsseq_obj)
For testing purposes, I am only focusing on chr 19 with 1057376 CpG sites
in total.
The error appears after calling BSmooth:
Error in env[[as.character(i)]] <- value :
wrong args for environment subassignment
In addition: Warning message:
In parallel::mccollect(wait = FALSE, timeout = 1) :
1 parallel job did not deliver a result
BiocManager::valid() returns TRUE. I am using Ubuntu 20.04 with R version
4.1.3
Thank you very much for your time.
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Best,
Kasper
|
I'm coming across a problem while trying to analyze WGBS data from CD4 and CD8 T cells (3 vs 3 samples). I used the following code:
For testing purposes, I am only focusing on chr 19 with 1057376 CpG sites in total.
The error appears after calling BSmooth:
BiocManager::valid()
returns TRUE.Thank you very much for your time.
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