Question

Failed to read SDRF

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Entering edit mode

Ed Siefker ▴ 230

@ed-siefker-5136

Last seen 12 months ago

United States

I am trying to read RNAseq data from ArrayExpress with ArrayExpressHTS(). I am using Bioconductor 3.10.

I have prepared a transcriptome reference with prepareReference() under "reference/".

When I run ArrayExpressHTS(), it downloads the correct SDRF file then fails to read it. This happens with multiple AE identifiers. I can confirm that the SDRF downloads correctly and is found at the location it fails to read.

> aehts <-ArrayExpressHTS("E-MTAB-6071", refdir="reference/")
Mon Mar  2 14:32:09 2020 [AEHTS] PSR: /home/hatta/retina-rnaseq-mouse/E-MTAB-6071/PSR
Mon Mar  2 14:32:09 2020 [AEHTS] Backing up /home/hatta/retina-rnaseq-mouse/E-MTAB-6071/PSR to /home/hatta/retina-rnaseq-mouse/E-MTAB-6071/PSR-backup-Mon-Mar--2-14:32:09-2020-1
Mon Mar  2 14:32:09 2020 [AEHTS] Creating /home/hatta/retina-rnaseq-mouse/E-MTAB-6071/PSR
Mon Mar  2 14:32:09 2020 [AEHTS] Master Memory Usage: Start
           used  (Mb) gc trigger  (Mb) max used  (Mb)
Ncells  7248623 387.2   12066822 644.5 10957081 585.2
Vcells 12373218  94.5   22929267 175.0 15800658 120.6
Mon Mar  2 14:32:10 2020 [AEHTS] creating projects
Mon Mar  2 14:32:10 2020 [AEHTS]    Searching /home/hatta/retina-rnaseq-mouse/reference/reference_genomes/ for supported organisms
Mon Mar  2 14:32:11 2020 [AEHTS] Downloading IDF http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-6071/E-MTAB-6071.idf.txt
trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-6071/E-MTAB-6071.idf.txt'
Content type 'text/plain' length 5084 bytes
==================================================
downloaded 5084 bytes

Mon Mar  2 14:32:14 2020 [AEHTS] Downloading SDRF http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-6071/E-MTAB-6071.sdrf.txt
trying URL 'http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-6071/E-MTAB-6071.sdrf.txt'
Content type 'text/plain' length 12504 bytes (12 KB)
==================================================
downloaded 12 KB

Mon Mar  2 14:32:16 2020 [AEHTS] *** ERROR ***
Mon Mar  2 14:32:16 2020 [AEHTS] 
Mon Mar  2 14:32:16 2020 [AEHTS]     E-MTAB-6071 Failed to read SDRF /home/hatta/retina-rnaseq-mouse/E-MTAB-6071/data/E-MTAB-6071.sdrf.txt
Mon Mar  2 14:32:16 2020 [AEHTS] 
Error in mapAEtoENAviaHTTP(accession, descriptors$sdrffname) : 
> aehts <-ArrayExpressHTS("E-MTAB-6071", refdir="reference/")
>

Session info, in case it helps.

> library(BiocManager)
Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
> sessionInfo()
R version 3.6.3 RC (2020-02-21 r77847)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux bullseye/sid

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.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

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

other attached packages:
 [1] BiocManager_1.30.10    ArrayExpressHTS_1.36.0 snow_0.4-3            
 [4] Rsamtools_2.2.3        Biostrings_2.54.0      XVector_0.26.0        
 [7] GenomicRanges_1.38.0   GenomeInfoDb_1.22.0    IRanges_2.20.2        
[10] S4Vectors_0.24.3       BiocGenerics_0.32.0    sampling_2.8          

loaded via a namespace (and not attached):
 [1] bitops_1.0-6                matrixStats_0.55.0         
 [3] R2HTML_2.3.2                bit64_0.9-7                
 [5] RColorBrewer_1.1-2          progress_1.2.2             
 [7] httr_1.4.1                  tools_3.6.3                
 [9] backports_1.1.5             R6_2.4.1                   
[11] rpart_4.1-15                Hmisc_4.3-1                
[13] DBI_1.1.0                   lazyeval_0.2.2             
[15] colorspace_1.4-1            nnet_7.3-13                
[17] tidyselect_1.0.0            gridExtra_2.3              
[19] prettyunits_1.1.1           curl_4.3                   
[21] bit_1.1-15.2                compiler_3.6.3             
[23] sendmailR_1.2-1             Biobase_2.46.0             
[25] htmlTable_1.13.3            DelayedArray_0.12.2        
[27] scales_1.1.0                checkmate_2.0.0            
[29] genefilter_1.68.0           askpass_1.1                
[31] rappdirs_0.3.1              DESeq_1.38.0               
[33] stringr_1.4.0               digest_0.6.25              
[35] foreign_0.8-75              base64enc_0.1-3            
[37] jpeg_0.1-8.1                pkgconfig_2.0.3            
[39] htmltools_0.4.0             limma_3.42.2               
[41] dbplyr_1.4.2                htmlwidgets_1.5.1          
[43] rlang_0.4.5                 rstudioapi_0.11            
[45] RSQLite_2.2.0               hwriter_1.3.2              
[47] BiocParallel_1.20.1         acepack_1.4.1              
[49] dplyr_0.8.4                 RCurl_1.98-1.1             
[51] magrittr_1.5                GenomeInfoDbData_1.2.2     
[53] Formula_1.2-3               Matrix_1.2-18              
[55] Rcpp_1.0.3                  munsell_0.5.0              
[57] lifecycle_0.1.0             edgeR_3.28.1               
[59] stringi_1.4.6               MASS_7.3-51.5              
[61] SummarizedExperiment_1.16.1 zlibbioc_1.32.0            
[63] BiocFileCache_1.10.2        grid_3.6.3                 
[65] blob_1.2.1                  crayon_1.3.4               
[67] lattice_0.20-40             splines_3.6.3              
[69] annotate_1.64.0             hms_0.5.3                  
[71] locfit_1.5-9.1              knitr_1.28                 
[73] pillar_1.4.3                geneplotter_1.64.0         
[75] biomaRt_2.42.0              lpSolve_5.6.15             
[77] XML_3.99-0.3                glue_1.3.1                 
[79] ShortRead_1.44.3            latticeExtra_0.6-29        
[81] data.table_1.12.8           png_0.1-7                  
[83] vctrs_0.2.3                 gtable_0.3.0               
[85] openssl_1.4.1               purrr_0.3.3                
[87] assertthat_0.2.1            ggplot2_3.2.1              
[89] xfun_0.12                   xtable_1.8-4               
[91] svMisc_1.1.0                survival_3.1-8             
[93] tibble_2.1.3                rJava_0.9-11               
[95] GenomicAlignments_1.22.1    AnnotationDbi_1.48.0       
[97] memoise_1.1.0               cluster_2.1.0              
>

software error arrayexpressHTS • 1.4k views

ADD COMMENT • link 4.7 years ago Ed Siefker ▴ 230

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Entering edit mode

Sorry this isn't much help, but I just wanted to add that I get exactly the same error when I run that code, so it's not just your setup.

ADD REPLY • link 4.7 years ago Mike Smith ★ 6.6k

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Clues. This happens when I run 'library(ArrayExpressHTS)'

No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’
No methods found in package ‘IRanges’ for requests: ‘Rle’, ‘subseq’ when loading ‘ArrayExpressHTS’

prepareReference() fails without manually setting "location". Apparently getDefaultReferenceDir() is not defined.

I created a new site library, and reinstalled BioConductor from source. Nothing changed.

ADD REPLY • link 4.7 years ago Ed Siefker ▴ 230

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Does BiocManager::valid() provide any hints?

ADD REPLY • link 4.7 years ago Martin Morgan 25k

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Unfortunately not, traceback() might though.

Tue Mar  3 14:15:17 2020 [AEHTS] *** ERROR ***
Tue Mar  3 14:15:17 2020 [AEHTS] 
Tue Mar  3 14:15:17 2020 [AEHTS]     E-MTAB-6071 Failed to read SDRF /home/hatta/retina-rnaseq-mouse/E-MTAB-6071/data/E-MTAB-6071.sdrf.txt
Tue Mar  3 14:15:17 2020 [AEHTS] 
Error in mapAEtoENAviaHTTP(accession, descriptors$sdrffname) : 
> traceback()
4: stop()
3: mapAEtoENAviaHTTP(accession, descriptors$sdrffname)
2: createAEprojects(accession = accession, dir = dir, refdir = refdir, 
       localmode = getPipelineOption("ebilocalmode"), options = options)
1: ArrayExpressHTS("E-MTAB-6071", refdir = "reference/")
> BiocManager::valid() 
[1] TRUE
>

ADD REPLY • link 4.7 years ago Ed Siefker ▴ 230

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Entering edit mode

Stepping through the code it fails inside readSDRF(sdrffname) with the error could not find function "read.AnnotatedDataFrame"

I see the following message when the package loads:

No methods found in package ‘Biobase’ for request: ‘read.AnnotatedDataFrame’ when loading ‘ArrayExpressHTS’

So perhaps something has changed in Biobase?

ADD REPLY • link 4.7 years ago Mike Smith ★ 6.6k

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Thanks, I created a new post tagging BioBase. Maybe that will get some attention.

ADD REPLY • link 4.7 years ago Ed Siefker ▴ 230

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Entering edit mode

Did some more digging, and read.AnnotatedDataFrame’ is not a method, it's a function, but ArrayExpressHTS tries uses importMethodsFrom() in its NAMESPACE.

Switiching to use just import gets past out original error, but then I end up with

Error in url(descriptorurl) : invalid 'description' argument
In addition: Warning message:
In readLines(rundocurl) :
  incomplete final line found on 'http://www.ebi.ac.uk/ena/data/view/ERR2124678&display=xml'
structure("Error in url(descriptorurl) : invalid 'description' argument\n", class = "try-error", condition = structure(list(
    message = "invalid 'description' argument", call = url(descriptorurl)), class = c("simpleError", 
"error", "condition")))

I.m beginning to think ArrayExpressHTS might need an overhaul!

ADD REPLY • link 4.7 years ago Mike Smith ★ 6.6k

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Biobase hasn't changed recently, e.g., git blame NAMESPACE shows the last change to the relevant line of the NAMESPACE file to be in 2010.

1ef01a72 (Valerie Obenchain 2010-11-01 05:43:37 +0000 61)        readExpressionSet, read.AnnotatedDataFrame, read.MIAME, MIAME,

I don't think that this is an 'error' anyway, just a warning...

ADD REPLY • link 4.7 years ago Martin Morgan 25k