Question: Oligo RMA normalization : ERROR; return code from pthread_create() is 22
0
gravatar for RV
8 months ago by
RV10
RV10 wrote:

I am trying to use oligo::rma for a HTA feature set from a linux environment and right after background correction, following is trace back – Background correcting

Error in basicRMA(pms, pnVec, normalize, background): ERROR; return code from pthread_create() is 22

Traceback:

1. oligo::rma(in_data, target = "core")
2. oligo::rma(in_data, target = "core")
3. .local(object, ...)
4. basicRMA(pms, pnVec, normalize, background)

When I run the same command for the same files in a windows Rstudio and it runs just fine. I have over 1500 samples, and need to use the linux env to process it all.

I appreciate your help!

Attached is the sessionInfo -

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

Matrix products: default
BLAS/LAPACK: /home/linuxbrew/.linuxbrew/Cellar/openblas/0.3.4/lib/libopenblasp-r0.3.4.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] 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
[8] methods   base

other attached packages:
 [1] pd.hta.2.0_3.12.2   DBI_1.0.0           RSQLite_2.1.1
 [4] oligo_1.46.0        Biostrings_2.50.2   XVector_0.22.0
 [7] IRanges_2.16.0      S4Vectors_0.20.1    Biobase_2.42.0
[10] oligoClasses_1.44.0 BiocGenerics_0.28.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0                  compiler_3.5.2
 [3] BiocManager_1.30.4          GenomeInfoDb_1.18.1
 [5] bitops_1.0-6                iterators_1.0.10
 [7] tools_3.5.2                 zlibbioc_1.28.0
 [9] digest_0.6.18               bit_1.1-14
[11] memoise_1.1.0               preprocessCore_1.44.0
[13] lattice_0.20-38             ff_2.2-14
[15] pkgconfig_2.0.2             Matrix_1.2-15
[17] foreach_1.4.4               DelayedArray_0.8.0
[19] GenomeInfoDbData_1.2.0      affxparser_1.54.0
[21] bit64_0.9-7                 grid_3.5.2
[23] BiocParallel_1.16.5         blob_1.1.1
[25] codetools_0.2-16            matrixStats_0.54.0
[27] GenomicRanges_1.34.0        splines_3.5.2
[29] SummarizedExperiment_1.12.0 RCurl_1.95-4.11
[31] affyio_1.52.0
ADD COMMENTlink modified 12 weeks ago by jdshih20 • written 8 months ago by RV10

If you're running it on a cluster environment (running Red Hat), then you may be up against restrictions in place by your system administrator. Are you just running it from the command line on the server?

ADD REPLYlink written 8 months ago by Kevin Blighe200

Hi Kevin, Apologies for the delayed reply. No, I am running it in a Red Hat server. It works just fine on a local command line.

Thanks!

ADD REPLYlink written 7 months ago by RV10

Hi Kevin, Apologies for the delayed reply. No, I am running it in a Red Hat server. It works just fine on a local command line.

Thanks!

ADD REPLYlink written 7 months ago by RV10
Answer: Oligo RMA normalization : ERROR; return code from pthread_create() is 22
0
gravatar for jdshih
12 weeks ago by
jdshih20
jdshih20 wrote:

I struggled with the same error with oligo and affy for the past few days, resulting in a loss of not so insignificant amount of hair.

The error occurs in libpthread.so, one of the shared libraries of glibc. Error code 22 indicates EINVAL (Invalid argument):

$ errno 22
EINVAL 22 Invalid argument

The cause of this error seems to originate from libopenblasp-r0.3.4.so. (I still have the same issue with openblas 0.3.6.) The default stack size may be too small: https://github.com/xianyi/OpenBLAS/issues/1936

You can wait for this problem to be fixed upstream and propagated to your OS distribution, but for now, I'd replace openblas with blas.

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by jdshih20
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