Closed cloudred20 closed 7 years ago
tgirke
commented
7 years ago Most likely bowtie2 is not seen from the location where you are running your R session. To debug this, make sure bowtie2 is installed on your system and then run the full sys command (bowtie2 -p 4 -k ...) from the command-line in the same directory from where you are running your R session. If this is working you can try to run it from R instead using the system or system2 function.
cloudred20
commented
7 years ago Yup... So it's working from the command line and also if I system command. What could be the possible error with runCommandline(args) and how can I debug it? Thanks a ton
tgirke
commented
7 years ago I see. In that case, you might not be using a module system on your computer. If so, you want to to drop the line specifying the software in the corresponding param file (e.g. para/bowtieSE.param) via a module system entirely or remove just the "bowtie2..." entry (leave field empty). More details on this is in the general manual here: https://goo.gl/i2fCiW.
cloudred20
commented
7 years ago Thanks. I sincerely appreciate your help.
Yours Scientifically,
Megha Lal
On Thu, Jul 6, 2017 at 3:38 PM, Thomas Girke notifications@github.com wrote:
I see. In that case, you might not be using a module system on your computer. If so, you want to to drop the line specifying the software in the corresponding param file (e.g. para/bowtieSE.param) via a module system entirely or remove just the "bowtie2..." entry (leave field empty). More details on this is in the general manual here: https://goo.gl/i2fCiW.
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Hi,
I was analyzing ChIP-seq data using systemPipeR and faced system2 error right when I started aligning the data. I thought I would run the pipeline with sample data provided under systemPipeRData. However I'm still facing trouble.
1
Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale: [1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8
[4] LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8
[7] LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] systemPipeRdata_1.5.0 systemPipeR_1.10.0 ShortRead_1.34.0
[4] GenomicAlignments_1.12.1 SummarizedExperiment_1.6.3 DelayedArray_0.2.7
[7] matrixStats_0.52.2 Biobase_2.36.2 BiocParallel_1.10.1
[10] Rsamtools_1.28.0 Biostrings_2.44.1 XVector_0.16.0
[13] GenomicRanges_1.28.3 GenomeInfoDb_1.12.2 IRanges_2.10.2
[16] S4Vectors_0.14.3 BiocGenerics_0.22.0
loaded via a namespace (and not attached): [1] Rcpp_0.12.11 locfit_1.5-9.1 lattice_0.20-35
[4] GO.db_3.4.1 digest_0.6.12 plyr_1.8.4
[7] BatchJobs_1.6 backports_1.1.0 RSQLite_2.0
[10] ggplot2_2.2.1 zlibbioc_1.22.0 rlang_0.1.1
[13] GenomicFeatures_1.28.4 lazyeval_0.2.0 annotate_1.54.0
[16] blob_1.1.0 Matrix_1.2-10 checkmate_1.8.3
[19] GOstats_2.42.0 splines_3.4.1 stringr_1.2.0
[22] pheatmap_1.0.8 RCurl_1.95-4.8 bit_1.1-12
[25] biomaRt_2.32.1 munsell_0.4.3 sendmailR_1.2-1
[28] compiler_3.4.1 rtracklayer_1.36.3 base64enc_0.1-3
[31] pkgconfig_2.0.1 BBmisc_1.11 fail_1.3
[34] tibble_1.3.3 GenomeInfoDbData_0.99.0 edgeR_3.18.1
[37] XML_3.98-1.9 AnnotationForge_1.18.0 bitops_1.0-6
[40] grid_3.4.1 RBGL_1.52.0 xtable_1.8-2
[43] GSEABase_1.38.0 gtable_0.2.0 DBI_0.7
[46] magrittr_1.5 scales_0.4.1 graph_1.54.0
[49] stringi_1.1.5 hwriter_1.3.2 genefilter_1.58.1
[52] limma_3.32.2 latticeExtra_0.6-28 brew_1.0-6
[55] rjson_0.2.15 RColorBrewer_1.1-2 tools_3.4.1
[58] bit64_0.9-7 Category_2.42.1 survival_2.41-3
[61] AnnotationDbi_1.38.1 colorspace_1.3-2 memoise_1.1.0