name.fail-IBD.IDs not found

[wiedenhoeft]

Using version 0.3.2, I am running perIndividualQC(..., do.evaluate_check_relatedness=TRUE) successfully. When I try to run cleanData(...), I get the error
filterRelated is TRUE but file name.fail-IBD.IDs does not exist. I have tried to create the file separately as well using exclude_relatedness <- check_relatedness(indir=indir, qcdir=qcdir, name=name, interactive=TRUE, path2plink=path2plink), but it only creates name.imiss and name.lmiss and a bunch of other files, but no name.fail-IBD.IDs. I am assuming that perhaps no related individuals were found, however, this case should be handled, e.g. by creating an empty file.

[HannahVMeyer]

Could you please provide the output of sessionInfo(). When you do create an empty file, do you still get the same error?

I will not have time to look at this right now, will follow up in week August 3rd.

/ooo tomorrow until next week

Thanks

[wiedenhoeft]

When I create an empty file, it fails upon trying to read it: Read individual IDs that failed relatedness check Error in data.table::fread(paste(out, ".fail-IBD.IDs", sep = ""), data.table = FALSE, : Input is either empty, fully whitespace, or skip has been set after the last non-whitespace.

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

Matrix products: default
BLAS: /SAN/software/R/R-3.6.0/lib/libRblas.so
LAPACK: /SAN/software/R/R-3.6.0/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] ggplot2_3.3.2 plinkQC_0.3.2

loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 pillar_1.4.6 compiler_3.6.0 plyr_1.8.6 R.methodsS3_1.8.0
[6] R.utils_2.9.2 tools_3.6.0 sys_3.3 digest_0.6.25 lifecycle_0.2.0
[11] tibble_3.0.3 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.7 rstudioapi_0.11
[16] ggrepel_0.8.2 yaml_2.2.1 gridExtra_2.3 UpSetR_1.4.0 withr_2.1.2
[21] dplyr_1.0.0 generics_0.0.2 vctrs_0.3.2 grid_3.6.0 cowplot_1.0.0
[26] tidyselect_1.1.0 getopt_1.20.3 glue_1.4.1 optparse_1.6.6 data.table_1.12.8
[31] R6_2.4.1 polyclip_1.10-0 tweenr_1.0.1 purrr_0.3.4 farver_2.0.3
[36] magrittr_1.5 MASS_7.3-51.6 scales_1.1.1 ellipsis_0.3.1 ggforce_0.3.2
[41] colorspace_1.4-1 labeling_0.3 munsell_0.5.0 crayon_1.3.4 R.oo_1.23.0

[wiedenhoeft]

As far as I can tell, there seems to be the more general issue that the software does not handle cases when nothing fails. For instance, running sex_check(interactive=TRUE) yields Error in FUN(X[[i]], ...) : object 'x' not found in cases when sex_check(interactive=FALSE) yields
`$fail_sex
NULL

$mixup
NULL

$p_sexcheck`

This also makes perIndividualQC() fail with Combine fail IDs into name.fail.IDs

[HannahVMeyer]

I addressed the above in issue #30 on the development branch. I am adding some more tests for the original problem described above and will push to the development branch of this repos.

[HannahVMeyer]

Could you try installing the development version:

library(devtools)
install_github("meyer-lab-cshl/plinkQC", ref="dev" )

and see if it solves your issue? I will then move it over to the master branch and submit to CRAN

Thanks.

[wiedenhoeft]

It runs without error now, thank you so much :-)