error in evaluating the argument 'x' in selecting a method for function '%in%': 'echo' not found

[ishaaq34]

I was trying to your data files to get used to the systemPipeR: Riboseq analysis. But unfortunately, I got the highlighted error message. I am not good at R so I could not figure out whether it is some basic R error or the pipeline line related.

args <- systemArgs(sysma="param/hisat2.param", mytargets="targets_trim.txt")

sysargs(args)[1] # Command-line parameters for first FASTQ file M1A "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S C:/Users/ishaa/Desktop/Bioinformatics/Ribo/riboseq/results/SRR446027_1.fastq_trim.gz.hisat.sam C:/Users/ishaa/Desktop/Bioinformatics/Ribo/riboseq/data/tair10.fasta -U C:\Users\ishaa\Desktop\Bioinformatics\Ribo\riboseq\results\SRR446027_1.fastq_trim.gz "

> moduleload(modules(args)) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function '%in%': 'echo' not found

My session information is

sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] echor_0.1.6 modules_0.10.0 dbplyr_2.1.1
[4] dplyr_1.0.6 systemPipeR_1.24.6 ShortRead_1.48.0
[7] GenomicAlignments_1.26.0 SummarizedExperiment_1.20.0 Biobase_2.50.0
[10] MatrixGenerics_1.2.1 matrixStats_0.59.0 BiocParallel_1.24.1
[13] Rsamtools_2.6.0 Biostrings_2.58.0 XVector_0.30.0
[16] GenomicRanges_1.42.0 GenomeInfoDb_1.26.7 IRanges_2.24.1
[19] S4Vectors_0.28.1 BiocGenerics_0.36.1

loaded via a namespace (and not attached): [1] colorspace_2.0-1 rjson_0.2.20 hwriter_1.3.2 ellipsis_0.3.2
[5] rstudioapi_0.13 farver_2.1.0 bit64_4.0.5 AnnotationDbi_1.52.0
[9] fansi_0.5.0 xml2_1.3.3 splines_4.0.5 cachem_1.0.6
[13] knitr_1.36 jsonlite_1.7.2 annotate_1.68.0 GO.db_3.12.1
[17] png_0.1-7 pheatmap_1.0.12 graph_1.68.0 readr_2.1.1
[21] BiocManager_1.30.16 compiler_4.0.5 httr_1.4.2 GOstats_2.56.0
[25] backports_1.4.1 assertthat_0.2.1 Matrix_1.3-2 fastmap_1.1.0
[29] limma_3.46.0 htmltools_0.5.2 prettyunits_1.1.1 tools_4.0.5
[33] gtable_0.3.0 glue_1.5.1 GenomeInfoDbData_1.2.4 Category_2.56.0
[37] rsvg_2.1.2 batchtools_0.9.15 rappdirs_0.3.3 V8_3.6.0
[41] Rcpp_1.0.7 vctrs_0.3.8 rtracklayer_1.49.5 xfun_0.28
[45] stringr_1.4.0 lifecycle_1.0.1 XML_3.99-0.6 edgeR_3.32.1
[49] zlibbioc_1.36.0 scales_1.1.1 BSgenome_1.58.0 BiocStyle_2.18.1
[53] VariantAnnotation_1.36.0 hms_1.1.0 RBGL_1.66.0 RColorBrewer_1.1-2
[57] yaml_2.2.1 curl_4.3.2 memoise_2.0.1 ggplot2_3.3.3
[61] biomaRt_2.46.3 latticeExtra_0.6-29 stringi_1.7.6 RSQLite_2.2.7
[65] genefilter_1.72.1 checkmate_2.0.0 GenomicFeatures_1.42.3 DOT_0.1
[69] rlang_0.4.12 pkgconfig_2.0.3 bitops_1.0-7 evaluate_0.14
[73] lattice_0.20-44 purrr_0.3.4 labeling_0.4.2 bit_4.0.4
[77] tidyselect_1.1.1 GSEABase_1.52.1 AnnotationForge_1.32.0 plyr_1.8.6
[81] geojsonsf_2.0.1 magrittr_2.0.1 R6_2.5.1 generics_0.1.0
[85] base64url_1.4 DelayedArray_0.16.3 DBI_1.1.1 pillar_1.6.4
[89] withr_2.4.3 survival_3.2-11 RCurl_1.98-1.3 tibble_3.1.6
[93] crayon_1.4.2 utf8_1.2.2 BiocFileCache_1.14.0 tzdb_0.2.0
[97] rmarkdown_2.11 jpeg_0.1-9 progress_1.2.2 locfit_1.5-9.4
[101] grid_4.0.5 data.table_1.14.2 blob_1.2.1 Rgraphviz_2.34.0
[105] digest_0.6.29 xtable_1.8-4 tidyr_1.1.4 brew_1.0-6
[109] openssl_1.4.5 munsell_0.5.0 viridisLite_0.4.0 askpass_1.1

[ishaaq34]

Could you please help me out. I would appreciate that much

[dcassol]

Hi @ishaaq34, thank you for using systemPipeR.

Are you running this workflow in a compute cluster environment with Environment Modules available? If not, you can ignore this because you need to have hisat2 exported on your PATH. To test, you can try:

library(systemPipeR)
tryCL(command="hisat2") 

[ishaaq34]

@dcassol thank you so much for your response. I am running this workflow on my personal computer (windows). I add Hisat2 in the path but not sure why I have been getting the error

tryCL(command="hisat2") ERROR: hisat2: COMMAND NOT FOUND. Please make sure to configure your PATH environment variable according to the software in use.

I also ran the following command

args <- systemArgs(sysma="param/hisat2.param", mytargets="targets_trim.txt")

sysargs(args)[1] # Command-line parameters for first FASTQ file M1A "hisat2 -p 4 -k 1 --min-intronlen 30 --max-intronlen 3000 -S C:/Users/ishaa/Desktop/Bioinformatics/Ribo/riboseq/results/SRR446027_1.fastq_trim.gz.hisat.sam C:/Users/ishaa/Desktop/Bioinformatics/Ribo/riboseq/data/tair10.fasta -U C:\Users\ishaa\Desktop\Bioinformatics\Ribo\riboseq\results\SRR446027_1.fastq_trim.gz "

system("hisat2-build ./data/tair10.fasta ./data/tair10.fasta") [1] 127

runCommandline(args=args) Error in runCommandline(args = args) : object 'modulecmd_path' not found

Could you please let me know where I am making mistakes

[dcassol]

Hi @ishaaq34, this command (tryCL) shows that you don't have hisat2 exported on your PATH. You can double-check the hisat2 manual to obtain and install the software locally.

Also, you are using the old param files from systemPipeR, and it is returning the wrong error message - I will fix that. But I recommend you to use the latest version of the package, with more features!

[ishaaq34]

@dcassol Thank you so much. I will try to figure it out. Appreciate your kind support very much