Error when running the pcrelate function

[AmandaHWChong]

Hi,

I have been trying run pcrelate(), however I am receiving this error:

Error in if (idx <= length(redo.index)) idx <- redo.index[idx] else idx <- idx - : argument is of length zero Calls: pcrelate ... .reducer_add -> .reducer_add -> .map_index -> .map_index In addition: Warning message: In parallel::mccollect(wait = FALSE, timeout = 1) : 1 parallel job did not deliver a result

Do you have any advice on how to troubleshoot this issue?

[smgogarten]

This seems like an error in parallelization, so try running with a single thread by including the argument BPPARAM=BiocParallel::SerialParam().

[AmandaHWChong]

It works! Perfect, thank you for your help!

[rbutleriii]

Hi @smgogarten , getting the same error.

> mypcrelate <- pcrelate(gds,
  pcs = mypcair$vectors[,1:8],
  training.set = mypcair$unrels
)
Using 18 CPU cores
676 samples to be included in the analysis...
Betas for 8 PC(s) will be calculated using 647 samples in training.set...
Running PC-Relate analysis for 676 samples using 488830 SNPs in 49 blocks...
Error in if (idx <= length(redo.index)) idx <- redo.index[idx] else idx <- idx -  :
  argument is of length zero
In addition: Warning messages:
1: In parallel::mccollect(wait = TRUE) :
  5 parallel jobs did not deliver results
2: In parallel::mccollect(wait = FALSE, timeout = 1) :
  1 parallel job did not deliver a result

Running it in serial does work, but is there a timeline for fixing the parallel? It would be ...very desired for a dataset of typical size these days. I am wondering if it is a call somewhere where mccollect having wait = FALSE just exits before several blocks are finished?

> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] data.table_1.15.4   BiocParallel_1.38.0 Matrix_1.6-5
[4] GWASTools_1.50.0    Biobase_2.64.0      BiocGenerics_0.50.0
[7] GENESIS_2.34.0      SNPRelate_1.38.0    gdsfmt_1.40.0

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1        dplyr_1.1.4             blob_1.2.4
 [4] Biostrings_2.72.1       fastmap_1.2.0           rpart_4.1.23
 [7] lifecycle_1.0.4         survival_3.7-0          RSQLite_2.3.7
[10] magrittr_2.0.3          compiler_4.4.1          rlang_1.1.4
[13] tools_4.4.1             utf8_1.2.4              bit_4.0.5
[16] SeqArray_1.44.0         purrr_1.0.2             GWASExactHW_1.2
[19] nnet_7.3-19             grid_4.4.1              stats4_4.4.1
[22] fansi_1.0.6             jomo_2.7-6              mice_3.16.0
[25] iterators_1.0.14        MASS_7.3-61             cli_3.6.3
[28] crayon_1.5.3            generics_0.1.3          httr_1.4.7
[31] minqa_1.2.7             DBI_1.2.3               DNAcopy_1.78.0
[34] cachem_1.1.0            zlibbioc_1.50.0         operator.tools_1.6.3
[37] splines_4.4.1           parallel_4.4.1          XVector_0.44.0
[40] vctrs_0.6.5             boot_1.3-30             glmnet_4.1-8
[43] sandwich_3.1-0          jsonlite_1.8.8          SparseM_1.84-2
[46] IRanges_2.38.1          S4Vectors_0.42.1        quantsmooth_1.70.0
[49] bit64_4.0.5             mitml_0.4-5             foreach_1.5.2
[52] tidyr_1.3.1             glue_1.7.0              nloptr_2.1.1
[55] pan_1.9                 codetools_0.2-19        shape_1.4.6.1
[58] GenomeInfoDb_1.40.1     GenomicRanges_1.56.1    UCSC.utils_1.0.0
[61] lmtest_0.9-40           lme4_1.1-35.5           tibble_3.2.1
[64] pillar_1.9.0            quantreg_5.98           GenomeInfoDbData_1.2.12
[67] R6_2.5.1                SeqVarTools_1.42.0      formula.tools_1.7.1
[70] lattice_0.22-5          backports_1.5.0         memoise_2.0.1
[73] broom_1.0.6             MatrixModels_0.5-3      Rcpp_1.0.13
[76] nlme_3.1-165            mgcv_1.9-1              logistf_1.26.0
[79] zoo_1.8-12              pkgconfig_2.0.3