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modarzi
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@modarzi-16296
Last seen 4.0 years ago
Hi, I would like to download TCGA data from GDC by TCGAbiolinks package.I wrote below code for that pupose:
query <- GDCquery(project = "TCGA-SARC",sample.type = "Primary solid Tumor",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",workflow.type = "HTSeq - Counts")
GDCdownload(query)
when I run below code:
data <- GDCprepare(query)
I see below message in console:
Downloading data for project TCGA-SARC
GDCdownload will download 259 files. A total of 64.930633 MB
Downloading as: Thu_Dec_12_14_39_40_2019.tar.gz
Downloading: 65 MB
After a while and downloading 65 MB, I didn't see 'data' as R object. I see some message same as below:
ff8fba5e-f6e2-4db6-87cf-11958b27bc37/2b66a8a5-1e0a-4a4a-beb7-b2273b2ffb05.htseq.counts.gz: Can't create '\\\\?\\F:\\ff8fba5e-f6e2-4db6-87cf-11958b27bc37\\2b66a8a5-1e0a-4a4a-beb7-b2273b2ffb05.htseq.counts.gz'
tar.exe: Error exit delayed from previous errors.
I setwd()
in my F driver. now in 'F' driver I see just 2 files:
1- MANIFEST.txt
2-ThuDec121439402019.tar.gz
when I get properties of 'ThuDec121439402019.tar.gz' file I see size: 61.6 MB (64,643,687 bytes).
Now I don't know what is my problem and what should I do by this process? I appreciate it if anybody shares his/her comment with me.
> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SummarizedExperiment_1.16.0 DelayedArray_0.12.0 matrixStats_0.55.0 Biobase_2.46.0
[5] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0 IRanges_2.20.0 S4Vectors_0.24.0
[9] BiocGenerics_0.32.0 TCGAbiolinks_2.14.0 sva_3.34.0 BiocParallel_1.20.0
[13] genefilter_1.68.0 mgcv_1.8-30 nlme_3.1-141 stringr_1.4.0
[17] dplyr_0.8.3 Hmisc_4.2-0 ggplot2_3.2.1 Formula_1.2-3
[21] survival_2.44-1.1 lattice_0.20-38 impute_1.60.0 cluster_2.1.0
[25] class_7.3-15 MASS_7.3-51.4 sqldf_0.4-11 RSQLite_2.1.2
[29] gsubfn_0.7 proto_1.0.0 WGCNA_1.68 fastcluster_1.1.25
[33] dynamicTreeCut_1.63-1
loaded via a namespace (and not attached):
[1] backports_1.1.5 circlize_0.4.8 aroma.light_3.16.0 BiocFileCache_1.10.0
[5] plyr_1.8.4 selectr_0.4-1 ConsensusClusterPlus_1.50.0 lazyeval_0.2.2
[9] splines_3.6.1 robust_0.4-18.1 digest_0.6.23 foreach_1.4.7
[13] htmltools_0.4.0 GO.db_3.10.0 magrittr_1.5 checkmate_1.9.4
[17] memoise_1.1.0 fit.models_0.5-14 doParallel_1.0.15 limma_3.42.0
[21] ComplexHeatmap_2.2.0 Biostrings_2.54.0 readr_1.3.1 annotate_1.64.0
[25] R.utils_2.9.0 askpass_1.1 prettyunits_1.0.2 colorspace_1.4-1
[29] rvest_0.3.4 ggrepel_0.8.1 blob_1.2.0 rappdirs_0.3.1
[33] rrcov_1.4-7 xfun_0.10 jsonlite_1.6 tcltk_3.6.1
[37] crayon_1.3.4 RCurl_1.95-4.12 zeallot_0.1.0 zoo_1.8-6
[41] iterators_1.0.12 glue_1.3.1 survminer_0.4.6 gtable_0.3.0
[45] zlibbioc_1.32.0 XVector_0.26.0 GetoptLong_0.1.7 shape_1.4.4
[49] DEoptimR_1.0-8 scales_1.0.0 DESeq_1.38.0 mvtnorm_1.0-11
[53] edgeR_3.28.0 DBI_1.0.0 ggthemes_4.2.0 Rcpp_1.0.3
[57] xtable_1.8-4 progress_1.2.2 htmlTable_1.13.2 clue_0.3-57
[61] matlab_1.0.2 foreign_0.8-72 bit_1.1-14 km.ci_0.5-2
[65] preprocessCore_1.48.0 htmlwidgets_1.5.1 httr_1.4.1 RColorBrewer_1.1-2
[69] acepack_1.4.1 pkgconfig_2.0.3 XML_3.98-1.20 R.methodsS3_1.7.1
[73] nnet_7.3-12 dbplyr_1.4.2 locfit_1.5-9.1 tidyselect_0.2.5
[77] rlang_0.4.2 AnnotationDbi_1.48.0 munsell_0.5.0 tools_3.6.1
[81] downloader_0.4 generics_0.0.2 broom_0.5.2 knitr_1.25
[85] bit64_0.9-7 robustbase_0.93-5 survMisc_0.5.5 purrr_0.3.3
[89] EDASeq_2.20.0 R.oo_1.23.0 xml2_1.2.2 biomaRt_2.42.0
[93] compiler_3.6.1 rstudioapi_0.10 curl_4.2 png_0.1-7
[97] ggsignif_0.6.0 tibble_2.1.3 geneplotter_1.64.0 pcaPP_1.9-73
[101] stringi_1.4.3 GenomicFeatures_1.38.0 Matrix_1.2-17 KMsurv_0.1-5
[105] vctrs_0.2.0 lifecycle_0.1.0 pillar_1.4.2 GlobalOptions_0.1.1
[109] data.table_1.12.6 bitops_1.0-6 rtracklayer_1.46.0 hwriter_1.3.2
[113] R6_2.4.0 latticeExtra_0.6-28 ShortRead_1.44.0 gridExtra_2.3
[117] codetools_0.2-16 assertthat_0.2.1 chron_2.3-54 openssl_1.4.1
[121] rjson_0.2.20 withr_2.1.2 GenomicAlignments_1.22.0 Rsamtools_2.2.0
[125] GenomeInfoDbData_1.2.2 hms_0.5.2 grid_3.6.1 rpart_4.1-15
[129] tidyr_1.0.0