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CummeRbund Column Name Mismatch Error

Hello,

I am have issues loading in my cuffdiff output into cummeRbund. I'm using cufflinks version 2.2.1 and the most up to date CummeRbund version. I see in other posts that RSQlite might be the problem.The error I'm receiving is:

cuffData <- readCufflinks("458_all_diff", rebuild = T) Creating database 458_all_diff/cuffData.db Reading Run Info File 458_all_diff/run.info Writing runInfo Table Reading Read Group Info 458_all_diff/read_groups.info Writing replicates Table Reading 458_all_diff/genes.fpkm_tracking Checking samples table... Populating samples table... Error: Column name mismatch.

In addition: There were 50 or more warnings (use warnings() to see the first 50)

Are there any update to date fixes out there or someone who knows how to solve this issue? Any help would be much appreciated as I am trying to obtain some nice visuals like volcano plots for my lab's projects and I'm crunched for time. Any help would be much appreciated.

Bryce

rna-seq cummerbund bioconductor cufflinks cuffdiff
• 3,110 views • link
updated by Chaozhong Liu • Chaozhong Liu • written by bryce.kirby • bryce.kirby

Instead of trying to solve this error, you should instead use the new tuxedo pipeline (hisat + stringtie + ballgown).

If you really want to fix cummeRbund, you have to downgrade it and RSQLite, as described on this post (which you probably did read, I guess), or install the development version, as described on this post.

What is the output of sessionInfo()?

• 0 views • link
written by h.mon h.mon

Sorry for the late reply. Here is my sessionInfo

R version 3.4.2 (2017-09-28) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] devtools_1.13.5 cummeRbund_2.18.0 Gviz_1.20.0 rtracklayer_1.36.6 GenomicRanges_1.28.6 [6] GenomeInfoDb_1.12.3 IRanges_2.10.5 S4Vectors_0.14.7 fastcluster_1.1.24 reshape2_1.4.3
[11] ggplot2_2.2.1 RSQLite_2.0 BiocGenerics_0.22.1

loaded via a namespace (and not attached): [1] httr_1.3.1 Biobase_2.36.2 AnnotationHub_2.8.3
[4] bit64_0.9-7 splines_3.4.2 shiny_1.0.5
[7] Formula_1.2-2 interactiveDisplayBase_1.14.0 latticeExtra_0.6-28
[10] blob_1.1.0 BSgenome_1.44.2 GenomeInfoDbData_0.99.0
[13] Rsamtools_1.28.0 yaml_2.1.18 pillar_1.2.1
[16] backports_1.1.2 lattice_0.20-35 biovizBase_1.24.0
[19] digest_0.6.15 RColorBrewer_1.1-2 XVector_0.16.0
[22] checkmate_1.8.5 colorspace_1.3-2 httpuv_1.3.6.2
[25] htmltools_0.3.6 Matrix_1.2-12 plyr_1.8.4
[28] pkgconfig_2.0.1 XML_3.98-1.10 biomaRt_2.32.1
[31] zlibbioc_1.22.0 xtable_1.8-2 scales_0.5.0
[34] BiocParallel_1.10.1 htmlTable_1.11.2 tibble_1.4.2
[37] AnnotationFilter_1.0.0 withr_2.1.1 SummarizedExperiment_1.6.5
[40] GenomicFeatures_1.28.5 nnet_7.3-12 lazyeval_0.2.1
[43] mime_0.5 survival_2.41-3 magrittr_1.5
[46] memoise_1.1.0 foreign_0.8-69 BiocInstaller_1.26.1
[49] tools_3.4.2 data.table_1.10.4-3 matrixStats_0.53.1
[52] stringr_1.3.0 munsell_0.4.3 cluster_2.0.6
[55] DelayedArray_0.2.7 ensembldb_2.0.4 AnnotationDbi_1.38.2
[58] Biostrings_2.44.2 compiler_3.4.2 rlang_0.2.0
[61] RCurl_1.95-4.10 dichromat_2.0-0 rstudioapi_0.7
[64] VariantAnnotation_1.22.3 htmlwidgets_1.0 bitops_1.0-6
[67] base64enc_0.1-3 gtable_0.2.0 curl_3.1
[70] DBI_0.8 R6_2.2.2 GenomicAlignments_1.12.2
[73] gridExtra_2.3 knitr_1.20 bit_1.1-12
[76] Hmisc_4.1-1 ProtGenerics_1.8.0 stringi_1.1.7
[79] Rcpp_0.12.15 rpart_4.1-13 acepack_1.4.1

• 0 views • link
written by bryce.kirby • bryce.kirby

1 answer

Hi Bryce

I have had the same problem as you, but now I solved it by using the latest version of cummeRbund (which is somehow not automatically installed in your R). In fact, it is just the suggestion of h.mon. But the new version is not available on the website he posted now.

You can just install the latest version of cummeRbund at BioC. Here is the website: http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html

Hope you can solve the problem!

Chaozhong

• 1 views • link
written by Chaozhong Liu • Chaozhong Liu

Hi I updated everything but not get this error :

Creating database RNA-480_Output/cuffData.db Error in rsqlite_connect(dbname, loadable.extensions, flags, vfs) : Could not connect to database: unable to open database file

Any ideas? Here is my session info.

Thanks so much!

sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] cummeRbund_2.20.0 Gviz_1.22.3 rtracklayer_1.38.3 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 IRanges_2.12.0
[7] S4Vectors_0.16.0 fastcluster_1.1.24 reshape2_1.4.3 ggplot2_2.2.1 RSQLite_2.0 BiocGenerics_0.24.0 [13] BiocInstaller_1.28.0

• 1 views • link
written by bryce.kirby • bryce.kirby

Sorry, I have no idea of that. But I can give you my sessionInfo( ):

R version 3.4.4 (2018-03-15) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Sierra 10.12.5

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale: [1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8

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

other attached packages: [1] cummeRbund_2.20.0 Gviz_1.20.0 BiocInstaller_1.26.1 rtracklayer_1.36.6
[5] GenomicRanges_1.28.6 GenomeInfoDb_1.12.3 IRanges_2.10.5 S4Vectors_0.14.7
[9] fastcluster_1.1.24 reshape2_1.4.3 ggplot2_2.2.1 RSQLite_2.0
[13] BiocGenerics_0.22.1

I hope this can help!

• 1 views • link
written by Chaozhong Liu • Chaozhong Liu

Hello,

I was able to read everything in. I ended up changing the directory to the entire path of where the data was and it worked. Thanks for your help!

• 1 views • link
written by bryce.kirby • bryce.kirby

Hi Bryce I'm sorry I forgot to check messages of Biostar these days : ) Good to hear everything works well.

Chaozhong

• 0 views • link
written by Chaozhong Liu • Chaozhong Liu

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