CommandNotFoundError message at alignment step

[hariiyer16]

Dear Thomas, I am trying to setup systemPipeR for ChIP-seq analyses and keep getting following error during alignment.

`CommandNotFoundError: Your shell has not been properly configured to use 'conda deactivate'. To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

• bash
• fish
• tcsh
• xonsh
• zsh
• powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'. `

I think this is not directly a systemPipeR issue, but seems the shell script that is called from within R is not able to activate conda. I am able to activate conda interactively without issues. I tried few thins like explicitly including command to activate conda in batchtools.sge.tmpl. I would appreciate any help or suggestions.

Thank you in advance. Sincerely. Hari Easwaran

Following is info about by R session.

R version 4.1.1 Patched (2021-08-13 r80752) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: ~/core/conda/miniconda3-4.6.14/envs/svnR-4.1.x/R/4.1.x/lib64/R/lib/libRblas.so LAPACK: ~/core/conda/miniconda3-4.6.14/envs/svnR-4.1.x/R/4.1.x/lib64/R/lib/libRlapack.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] tools stats4 stats graphics grDevices datasets utils [8] methods base

other attached packages: [1] batchtools_0.9.15 ape_5.5 [3] ggplot2_3.3.5 systemPipeR_1.27.25 [5] ShortRead_1.51.0 GenomicAlignments_1.29.0 [7] SummarizedExperiment_1.23.1 Biobase_2.53.0 [9] MatrixGenerics_1.5.3 matrixStats_0.60.1 [11] BiocParallel_1.27.3 Rsamtools_2.9.1 [13] Biostrings_2.61.2 XVector_0.33.0 [15] GenomicRanges_1.45.0 GenomeInfoDb_1.29.3 [17] IRanges_2.27.0 S4Vectors_0.31.0 [19] BiocGenerics_0.39.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.7 lattice_0.20-44 prettyunits_1.1.1 [4] png_0.1-7 assertthat_0.2.1 digest_0.6.27 [7] utf8_1.2.2 R6_2.5.1 backports_1.2.1 [10] pillar_1.6.2 progress_1.2.2 zlibbioc_1.39.0 [13] rlang_0.4.11 data.table_1.14.0 rstudioapi_0.13 [16] Matrix_1.3-4 checkmate_2.0.0 stringr_1.4.0 [19] htmlwidgets_1.5.3 RCurl_1.98-1.4 munsell_0.5.0 [22] DelayedArray_0.19.1 compiler_4.1.1 pkgconfig_2.0.3 [25] htmltools_0.5.2 tidyselect_1.1.1 tibble_3.1.4 [28] GenomeInfoDbData_1.2.6 fansi_0.5.0 crayon_1.4.1 [31] dplyr_1.0.7 withr_2.4.2 rappdirs_0.3.3 [34] bitops_1.0-7 grid_4.1.1 nlme_3.1-152 [37] gtable_0.3.0 lifecycle_1.0.0 DBI_1.1.1 [40] magrittr_2.0.1 scales_1.1.1 stringi_1.7.4 [43] hwriter_1.3.2 fs_1.5.0 latticeExtra_0.6-29 [46] brew_1.0-6 ellipsis_0.3.2 generics_0.1.0 [49] vctrs_0.3.8 RColorBrewer_1.1-2 glue_1.4.2 [52] purrr_0.3.4 hms_1.1.0 jpeg_0.1-9 [55] parallel_4.1.1 fastmap_1.1.0 yaml_2.2.1 [58] colorspace_2.0-2 base64url_1.4

[dcassol]

Hi @hariiyer16, My guess is that conda is not in the R env PATH. You can try:

systemPipeR::tryCMD("conda")

This function will show if the conda PATh is set. If it isn't, you need to export the PATH.

Please let me know if that works. All the best, Daniela

[hariiyer16]

THanks Daniela for the quick response.

tryCMD("conda") gives the following message. "All set up, proceed!"

I could work up from reading the files to indexing. So wonder why I am getting this error for bowtie2 call.

Thanks again.

[dcassol]

Hi @hariiyer16, Thank you for trying this.

In order to help you find the issue faster, I would like to ask you to share the files you are using to create the bowtie2 object. For example,

bowtie2-mapping-se.cwl
bowtie2-mapping-se.yml

Also, the R command you are using to generate the object.

To try to isolate if it is a problem with the script or the submission to the cluster, I would suggest trying to run one sample (or a dummy example) with the runCommandline function and check if the same error happens.

[hariiyer16]

Hi Daniela, runCommandline worked!!! I believe it has to do with submission job to the cluster. Will try to figure it out. In meantime, my bowtie2-mapping-se.cwl and bowtie2-mapping-se.yml files can be found at: https://gist.github.com/hariiyer16/fbc75877cc2275fa60ae9eef70351853

Thank you again. Hari

[dcassol]

Great! I checked the command line description files and everything is great. Could you also please share the batchtools.sge.tmpl file?

Thank you! Daniela

[hariiyer16]

I have included the batchtools.sge.tmpl at the same link: https://gist.github.com/hariiyer16/fbc75877cc2275fa60ae9eef70351853

Thank you.

[dcassol]

Hello @hariiyer16, I'm going to close this for now! Feel free to re-open if you have any additional questions. Cheers, Daniela