Error when downloading data with recount3.
1
1
Entering edit mode
Zach Brehm ▴ 20
@brehmzp
Last seen 11 months ago
Rochester, NY

I'm attempting to download some data from GTEx with recount3 and I'm getting an invalid description error when the download begins, as well as a warning that one of the URLs being referenced is not available.

> library(recount3)
> human_projects <- available_projects()
2020-10-29 09:52:51 caching file sra.recount_project.MD.gz.
2020-10-29 09:52:51 caching file gtex.recount_project.MD.gz.
2020-10-29 09:52:51 caching file tcga.recount_project.MD.gz.
> proj_info <- subset(human_projects,
+                     project == "BLOOD_VESSEL" & project_type == "data_sources"
+                     )
> rse_blood_vessel <- create_rse(proj_info)
2020-10-29 09:52:54 downloading and reading the metadata.
2020-10-29 09:52:54 caching file gtex.gtex.BLOOD_VESSEL.MD.gz.
2020-10-29 09:52:54 caching file gtex.recount_project.BLOOD_VESSEL.MD.gz.
2020-10-29 09:52:55 caching file gtex.recount_qc.BLOOD_VESSEL.MD.gz.
2020-10-29 09:52:55 caching file gtex.recount_seq_qc.BLOOD_VESSEL.MD.gz.
2020-10-29 09:52:55 downloading and reading the feature information.
2020-10-29 09:52:55 caching file human.gene_sums.G026.gtf.gz.
2020-10-29 09:52:56 downloading and reading the counts: 1398 samples across 63856 features.
Error in file(file, "rt") : invalid 'description' argument
In addition: Warning message:
The 'url' <http://idies.jhu.edu/recount3/data/human/data_sources/gtex/gene_sums/EL/BLOOD_VESSEL/gtex.gene_sums.BLOOD_VESSEL.G026.gz> does not exist or is not available. 
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 20.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
 [1] recount3_1.0.0              SummarizedExperiment_1.20.0 Biobase_2.50.0              GenomicRanges_1.42.0        GenomeInfoDb_1.26.0         IRanges_2.24.0              S4Vectors_0.28.0           
 [8] BiocGenerics_0.36.0         MatrixGenerics_1.2.0        matrixStats_0.57.0         

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.0         purrr_0.3.4              lattice_0.20-41          vctrs_0.3.4              generics_0.0.2           BiocFileCache_1.14.0     rtracklayer_1.50.0      
 [8] blob_1.2.1               XML_3.99-0.5             rlang_0.4.8              R.oo_1.24.0              pillar_1.4.6             withr_2.3.0              glue_1.4.2              
[15] DBI_1.1.0                R.utils_2.10.1           BiocParallel_1.24.0      rappdirs_0.3.1           bit64_4.0.5              dbplyr_1.4.4             sessioninfo_1.1.1       
[22] GenomeInfoDbData_1.2.4   lifecycle_0.2.0          zlibbioc_1.36.0          Biostrings_2.58.0        R.methodsS3_1.8.1        memoise_1.1.0            curl_4.3                
[29] fansi_0.4.1              Rcpp_1.0.5               DelayedArray_0.16.0      XVector_0.30.0           bit_4.0.4                Rsamtools_2.6.0          digest_0.6.27           
[36] dplyr_1.0.2              grid_4.0.3               cli_2.1.0                tools_4.0.3              bitops_1.0-6             magrittr_1.5             RCurl_1.98-1.2          
[43] tibble_3.0.4             RSQLite_2.2.1            crayon_1.3.4             pkgconfig_2.0.3          ellipsis_0.3.1           Matrix_1.2-18            data.table_1.13.2       
[50] assertthat_0.2.1         httr_1.4.2               rstudioapi_0.11          R6_2.5.0                 GenomicAlignments_1.26.0 compiler_4.0.3
recount3 • 457 views
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1
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Hi Zach,

Thanks for reporting this. We'll look into it.

Best, Leo

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1
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Hi Zach,

We found the issue and are working on resolving it. Basically, we have the data at IDIES already but some files are not in the right location. So the url that recount3 is providing is the correct one (the intended one) but we made a small mistake on the IDIES side that we are fixing right now. We'll let you know once this is resolved.

Best, Leo

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@lcolladotor
Last seen 20 days ago
United States

Hi,

Thanks for reporting this issue! It has been resolved now thanks to speedy work by Christopher Wilks. Thanks Chris!

The root problem was that we had uploaded the GTEx data to the IDIES data server but had not moved it to the paths expected by the recount3 R package. You don't need to update the R package, simply, run the commands again.

Best, Leo

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Leo's too kind, the error was all mine to start with.

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1
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Hehe, no worries Chris ^^ We all make errors like that all the time :P Thanks again Zach Brehm for reporting the issue.

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1
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Thanks Leo and Chris, I just tried it again and everything worked for me. Appreciate the help!

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