Oligo RMA normalization : ERROR; return code from pthread_create() is 22
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RV ▴ 10
@rv-18712
Last seen 2.8 years ago

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
microarray normalization oligo HTA • 2.9k views
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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?

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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!

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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!

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jdshih ▴ 20
@jdshih-19709
Last seen 2.5 years ago

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.

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I solved this problem downgrading the version of openblas to 0.3.3.

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