Error with addReproduciblePeakSet() in finding MACS2

[cristanchoa]

Hi, thanks for the great package.

I am tweaking some data I have and need to remake an ArchR projects with new peak set. I ran the addReproduciblePeakSet() command below and it is now having difficulty using MACS2. I had MACS2 2.1.4 installed when I first got the following error asking to update the version. So I did upgrade the newest version of 2.2.8 but am still getting the same error. Appreciate any insight!

Ana

R command:

hypoxia_proj_filt <- addReproduciblePeakSet(

• ArchRProj = hypoxia_proj_filt,
• groupBy = "celltype.condition",
• pathToMacs2 ="/home/cristanchoa/.local/lib/python3.8/site-packages/MACS2", force = TRUE, maxPeaks = 10*10^7
• ) Warning in system2(path, "callpeak -h", stdout = TRUE, stderr = TRUE) : running command ''/home/cristanchoa/.local/lib/python3.8/site-packages/MACS2' callpeak -h 2>&1' had status 126 Warning in system2(path, " --version", stdout = TRUE, stderr = TRUE) : running command ''/home/cristanchoa/.local/lib/python3.8/site-packages/MACS2' --version 2>&1' had status 126 Error in .checkMacs2Options(pathToMacs2) : Macs2 Path (/home/cristanchoa/.local/lib/python3.8/site-packages/MACS2) is out of date (version sh: /home/cristanchoa/.local/lib/python3.8/site-packages/MACS2: Is a directory) and does not have --shift option. Please update (https://github.com/taoliu/MACS) and provide new path!

MACS installation [cristanchoa@m-2-02 ~]$ pip install MACS2 Defaulting to user installation because normal site-packages is not writeable Collecting MACS2 Using cached MACS2-2.2.8.tar.gz (358 kB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata ... done Requirement already satisfied: numpy>=1.17 in /cm/shared/easybuild/software/Python/3.8.2-GCCcore-9.3.0/lib/python3.8/site-packages (from MACS2) (1.20.3) Building wheels for collected packages: MACS2 Building wheel for MACS2 (PEP 517) ... done Created wheel for MACS2: filename=MACS2-2.2.8-cp38-cp38-linux_x86_64.whl size=1879223 sha256=f488973299d2f773605a3b3552f1bfab8adc19e91cfa3ddbf165de222dbada08 Stored in directory: /home/cristanchoa/.cache/pip/wheels/83/4c/10/e386bf54cb5bed55c4547b3bf0042a211ed2f50b19483ea38d Successfully built MACS2 Installing collected packages: MACS2 Successfully installed MACS2-2.2.8 [cristanchoa@m-2-02 ~]$ pip install MACS2 Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: MACS2 in ./.local/lib/python3.8/site-packages (2.2.8) Requirement already satisfied: numpy>=1.17 in /cm/shared/easybuild/software/Python/3.8.2-GCCcore-9.3.0/lib/python3.8/site-packages (from MACS2) (1.20.3)

Session Info sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux 8.2 (Ootpa)

Matrix products: default BLAS: /cm/shared/apps_chop/R/4.1.2/lib64/R/lib/libRblas.so LAPACK: /cm/shared/apps_chop/R/4.1.2/lib64/R/lib/libRlapack.so

Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 grid stats graphics grDevices utils datasets methods base

other attached packages: [1] uwot_0.1.14 nabor_0.5.0 BSgenome.Mmusculus.UCSC.mm10_1.4.3 [4] BSgenome_1.62.0 rtracklayer_1.54.0 Biostrings_2.62.0
[7] XVector_0.34.0 SeuratObject_4.1.3 Seurat_4.3.0
[10] Signac_1.9.0 rhdf5_2.38.1 SummarizedExperiment_1.24.0
[13] Biobase_2.54.0 MatrixGenerics_1.6.0 Rcpp_1.0.10
[16] Matrix_1.5-3 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
[19] IRanges_2.28.0 S4Vectors_0.32.4 BiocGenerics_0.40.0
[22] matrixStats_0.63.0 data.table_1.14.6 stringr_1.5.0
[25] plyr_1.8.8 magrittr_2.0.3 ggplot2_3.4.0
[28] gtable_0.3.1 gtools_3.9.4 gridExtra_2.3
[31] ArchR_1.0.2

loaded via a namespace (and not attached): [1] fastmatch_1.1-3 igraph_1.4.2 lazyeval_0.2.2 sp_1.6-0
[5] splines_4.1.2 BiocParallel_1.28.3 listenv_0.9.0 scattermore_0.8
[9] digest_0.6.31 htmltools_0.5.5 fansi_1.0.4 tensor_1.5
[13] cluster_2.1.2 ROCR_1.0-11 globals_0.16.2 spatstat.sparse_3.0-1
[17] colorspace_2.1-0 ggrepel_0.9.2 xfun_0.39 dplyr_1.0.10
[21] crayon_1.5.2 RCurl_1.98-1.9 jsonlite_1.8.4 progressr_0.13.0
[25] spatstat.data_3.0-1 survival_3.5-5 zoo_1.8-12 glue_1.6.2
[29] polyclip_1.10-4 zlibbioc_1.40.0 leiden_0.4.3 DelayedArray_0.20.0
[33] Rhdf5lib_1.16.0 future.apply_1.10.0 abind_1.4-5 scales_1.2.1
[37] DBI_1.1.3 spatstat.random_3.1-4 miniUI_0.1.1.1 viridisLite_0.4.2
[41] xtable_1.8-4 reticulate_1.28 htmlwidgets_1.6.2 httr_1.4.5
[45] RColorBrewer_1.1-3 ellipsis_0.3.2 ica_1.0-3 farver_2.1.1
[49] XML_3.99-0.12 pkgconfig_2.0.3 deldir_1.0-6 utf8_1.2.3
[53] labeling_0.4.2 tidyselect_1.2.0 rlang_1.0.6 reshape2_1.4.4
[57] later_1.3.1 munsell_0.5.0 tools_4.1.2 cli_3.4.1
[61] generics_0.1.3 ggridges_0.5.4 evaluate_0.20 fastmap_1.1.1
[65] yaml_2.3.6 goftest_1.2-3 knitr_1.42 fitdistrplus_1.1-11
[69] purrr_1.0.1 RANN_2.6.1 pbapply_1.7-0 future_1.32.0
[73] nlme_3.1-162 mime_0.12 RcppRoll_0.3.0 compiler_4.1.2
[77] rstudioapi_0.14 plotly_4.10.1 png_0.1-8 spatstat.utils_3.0-2
[81] tibble_3.2.1 stringi_1.7.12 lattice_0.21-8 vctrs_0.5.1
[85] pillar_1.9.0 lifecycle_1.0.3 rhdf5filters_1.6.0 spatstat.geom_3.1-0
[89] lmtest_0.9-40 RcppAnnoy_0.0.20 cowplot_1.1.1 bitops_1.0-7
[93] irlba_2.3.5.1 httpuv_1.6.9 patchwork_1.1.2 BiocIO_1.4.0
[97] R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20 parallelly_1.35.0
[101] codetools_0.2-18 MASS_7.3-54 assertthat_0.2.1 rjson_0.2.21
[105] withr_2.5.0 GenomicAlignments_1.30.0 sctransform_0.3.5 Rsamtools_2.10.0
[109] GenomeInfoDbData_1.2.7 tidyr_1.2.1 rmarkdown_2.21 Cairo_1.5-12.2
[113] Rtsne_0.16 spatstat.explore_3.1-0 shiny_1.7.4 restfulr_0.0.15

[rcorces]

Hi @cristanchoa! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
It is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment, all of which are extremely challenging to troubleshoot. As such, we require reproducible examples (preferably using the tutorial dataset) from users who want assistance. If you cannot reproduce your error, we will not be able to help. Before going through the work of making a reproducible example, search the previous Issues, Discussions, function definitions, or the ArchR manual and you will likely find the answers you are looking for. If your post does not contain a reproducible example, it is unlikely to receive a response.
In addition to a reproducible example, you must do the following things before we help you, unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Did you post your log file? If not, add it now. 3.__ Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[paupaiz]

I was facing the same error after upgrading to MACS2 v2.2.8. I resolved it by: pip install --upgrade --force-reinstall MACS2 adding the path to my R environment: Sys.setenv(PATH = paste(pathToMacs2, Sys.getenv("PATH"), sep = ":")) (Check path was correctly added: Sys.getenv("PATH")) Restarting R

If this doesn't work, check chmod of the MACS executable. You should be able to run which macs2 and /path/to/macs2 callpeak -h successfully from CLI

[cristanchoa]

Thanks! Adding the path worked but only when I added the old path to an old version of R. I'm guessing there is something odd about my local HPC cluster that is being upgraded to a new version of linux and R by my instiution. I'm getting a new error now, which I suspect is a local environment issue, but I'm going to post it here in case anyone else has seen something similar and knows what needs to be fixed.

It starts working fine, but then when almost finished I get several: "ERROR Found in .writeCoverageToBed for LogFile = ArchRLogs/ArchR-addReproduciblePeakSet-1dffa626867ca0-Date-2023-05-29_Time-01-30-37.log"

From: Pau Paiz @.> Sent: Sunday, May 28, 2023 8:35 AM To: GreenleafLab/ArchR @.> Cc: Cristancho, Ana G @.>; Mention @.> Subject: [External]Re: [GreenleafLab/ArchR] Error with addReproduciblePeakSet() in finding MACS2 (Issue #1961)

I was facing the same error after upgrading to MACS2 v2.2.8. I resolved it by: pip install --upgrade --force-reinstall MACS2 adding the path to my R environment: Sys.setenv(PATH = paste(pathToMacs2, Sys.getenv("PATH"), sep = ":")) (Check path was correctly added: Sys.getenv("PATH")) Restarting R

If this doesn't work, check chmod of the MACS executable. You should be able to run which macs2 and /path/to/macs2 callpeak -h successfully from CLI

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