bschilder
commented
2 years ago That's odd, axel should be faster if anything because it uses multithreading for downloads. Did you have any other processes running on some cores that might have clogged up axel? I find htop is pretty useful for assessing this.
I'll make an edit to make sure download_method gets passed to to the "UKB MAF" step.
michaelofrancis
As the title says, it is getting to this line of output and then hanging indefinitely. I was having some issues with axel for the LD downloading part which is why I switched to wget. I don't see a way to bypass axel for this part.
Log of input/output attached. echolocatoR_log_MF_03122022.txt
R SESSION INFO
R: sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-conda-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)
Matrix products: default BLAS/LAPACK: /home/mf91122/.conda/envs/echoR/lib/libopenblasp-r0.3.18.so
locale: [1] C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] echolocatoR_0.2.2
loaded via a namespace (and not attached): [1] Rcpp_1.0.8 XVector_0.34.0 GenomeInfoDb_1.30.1
[4] pillar_1.7.0 compiler_4.0.5 R.methodsS3_1.8.1
[7] R.utils_2.11.0 tools_4.0.5 bitops_1.0-7
[10] zlibbioc_1.40.0 jsonlite_1.8.0 lifecycle_1.0.1
[13] tibble_3.1.6 gtable_0.3.0 lattice_0.20-45
[16] pkgconfig_2.0.3 png_0.1-7 rlang_0.4.12
[19] Matrix_1.4-0 DBI_1.1.2 parallel_4.0.5
[22] GenomeInfoDbData_1.2.7 dplyr_1.0.7 Biostrings_2.62.0
[25] IRanges_2.28.0 S4Vectors_0.32.3 generics_0.1.2
[28] vctrs_0.3.8 rappdirs_0.3.3 rprojroot_2.0.2
[31] stats4_4.0.5 grid_4.0.5 tidyselect_1.1.1
[34] here_1.0.1 reticulate_1.24 glue_1.5.0
[37] data.table_1.14.2 R6_2.5.1 fansi_1.0.0
[40] BiocParallel_1.28.3 seqminer_8.4 ggplot2_3.3.5
[43] purrr_0.3.4 magrittr_2.0.2 GenomicRanges_1.46.1
[46] scales_1.1.1 Rsamtools_2.6.0 ellipsis_0.3.2
[49] BiocGenerics_0.40.0 assertthat_0.2.1 colorspace_2.0-3
[52] utf8_1.2.2 RCurl_1.98-1.6 munsell_0.5.0
[55] crayon_1.5.0 R.oo_1.24.0