Question: Minfi issue: return code from pthread_create() is 22
1
gravatar for jshouse
12 weeks ago by
jshouse10
jshouse10 wrote:

I went to estimate cell counts from a 450k RGSet with

    estimateCellCounts(RGSet, referencePlatform = c("IlluminaHumanMethylation450k"))

I got the following:

> cellCounts <- estimateCellCounts(RGSet, referencePlatform = c("IlluminaHumanMethylation450k")) 
[estimateCellCounts] Combining user data with reference (flow sorted) data. 'stringsAsFactors' is ignored
[estimateCellCounts] Processing user and reference data together.
[preprocessQuantile] Mapping to genome.
[preprocessQuantile] Fixing outliers.
[preprocessQuantile] Quantile normalizing. Error in normalize.quantiles(mat[Index2, ]) :   
 ERROR; return code from pthread_create() is 22

I tried to find this error but did not get anything that seemed helpful.

My sessionInfo:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 19.04

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] 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] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 FlowSorted.Blood.450k_1.22.0                      
 [3] haven_2.1.1                                        gridExtra_2.3                                     
 [5] sva_3.32.1                                         genefilter_1.66.0                                 
 [7] mgcv_1.8-28                                        nlme_3.1-140                                      
 [9] lmtest_0.9-37                                      zoo_1.8-6                                         
[11] sandwich_2.5-1                                     MASS_7.3-51.1                                     
[13] data.table_1.12.2                                  R.utils_2.9.0                                     
[15] R.oo_1.22.0                                        R.methodsS3_1.7.1                                 
[17] foreign_0.8-71                                     IlluminaHumanMethylation450kmanifest_0.4.0        
[19] compare_0.2-6                                      minfi_1.30.0                                      
[21] bumphunter_1.26.0                                  locfit_1.5-9.1                                    
[23] iterators_1.0.10                                   foreach_1.4.4                                     
[25] Biostrings_2.52.0                                  XVector_0.24.0                                    
[27] SummarizedExperiment_1.14.0                        DelayedArray_0.10.0                               
[29] BiocParallel_1.18.0                                matrixStats_0.54.0                                
[31] Biobase_2.44.0                                     GenomicRanges_1.36.0                              
[33] GenomeInfoDb_1.20.0                                IRanges_2.18.1                                    
[35] S4Vectors_0.22.0                                   BiocGenerics_0.30.0                               
[37] forcats_0.4.0                                      stringr_1.4.0                                     
[39] dplyr_0.8.3                                        purrr_0.3.2                                       
[41] readr_1.3.1                                        tidyr_0.8.3                                       
[43] tibble_2.1.3                                       ggplot2_3.2.0                                     
[45] tidyverse_1.2.1                                    knitr_1.23    
minfi 450k • 223 views
ADD COMMENTlink modified 27 days ago by lucy0 • written 12 weeks ago by jshouse10
Answer: Minfi issue: return code from pthread_create() is 22
1
gravatar for jdshih
11 weeks ago by
jdshih20
jdshih20 wrote:

I had the same error using oligo and affy, and the source of the error appears to be openblas >= 0.3.4. You can see in your R session history that you are using openblas 0.3.5.

For now, I'd replace openblas with blas until this problem is fixed upstream and the change is propagated to your OS distribution.

See https://support.bioconductor.org/p/117119/#123061

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by jdshih20
Answer: Minfi issue: return code from pthread_create() is 22
0
gravatar for lucy
27 days ago by
lucy0
lucy0 wrote:

After digging through the code, I found the error occurs when minfi calls normalize.quantiles.use.target from the preprocessCore library. There is an issue regarding the blas error on the preprocessCore github.

To work around it, this solution by the preprocessCore author worked for me (linux, ubuntu, conda setup). Basically, clone the current github, and install the library without threading:

git clone https://github.com/bmbolstad/preprocessCore.git
cd preprocessCore/
R CMD INSTALL --configure-args="--disable-threading"  .
ADD COMMENTlink written 27 days ago by lucy0
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