An error has occurred. Check your logs or contact the app author for clarification.

[gene-drive]

After loading data and adjusting settings, once I click on Gene Table I get this message after a moment of waiting:
An error has occurred. Check your logs or contact the app author for clarification.

I did notice some errors after installing BEAVR-Docker in Windows. Not sure if these at all are related. Sorry for the long block below.

f42fd3b4a010: Pull complete
43fb01442cf8: Pull complete
0a1665ee6e4a: Pull complete
676e523523a7: Pull complete
689d3e105be4: Pull complete
e0f5fadec882: Pull complete
8d37b1db41dd: Pull complete
1cc449af1019: Pull complete
0e40efdf44cc: Pull complete
e817102c2c4a: Pull complete
a49e8987b780: Pull complete
6c252619daa7: Pull complete
c45851b0e365: Pull complete
c2978605d776: Pull complete
450c7521222c: Pull complete
b5286a25b6fb: Pull complete
cdd928a43f36: Pull complete
a63e41077377: Pull complete
4e6b9928835f: Pull complete
cb7a8be2b20a: Pull complete
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3cc28c10ac66: Pull complete
d67783cafca7: Pull complete
f0730fa2125f: Pull complete
532d856f96a3: Pull complete
d0561ce2f7ee: Pull complete
94122399e7c3: Pull complete
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a721a9ffaea6: Pull complete
Digest: sha256:5dc40e0ca36d169a753be5012d3afa2bf2a2e10d05d88e29e695056b08dc7761
Status: Downloaded newer image for pirunthan/beavr:latest
77be22d2817d: Downloading [======>                                            ]  26.79MB/205.7MB
*** warning - no files are being watched ***
[2022-02-09T23:56:56.579] [INFO] shiny-server - Shiny Server v1.5.13.943 (Node.js v12.14.1)
[2022-02-09T23:56:56.580] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
[2022-02-09T23:56:56.602] [WARN] shiny-server - Running as root unnecessarily is a security risk! You could be running more securely as non-root.
[2022-02-09T23:56:56.604] [INFO] shiny-server - Starting listener on http://[::]:3838
[2022-02-09T23:58:04.468] [INFO] shiny-server - Created bookmark state directory: /var/lib/shiny-server/bookmarks
[2022-02-09T23:58:04.468] [INFO] shiny-server - Created user bookmark state directory: /var/lib/shiny-server/bookmarks/shinyf5043192: Waiting
a721a9ffaea6: Waiting
*** '/var/log/shiny-server//shiny-server-shiny-20220209-235804-37607.log' has been created ***

*** /var/log/shiny-server//shiny-server-shiny-20220209-235804-37607.log ***

Listening on http://127.0.0.1:37607

Attaching package: ‘shinydashboard’

The following object is masked from ‘package:graphics’:

    box

Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.10' is out-of-date; the current release version '3.14'
  is available with R version '4.1'; see https://bioconductor.org/install

Attaching package: ‘colourpicker’

The following object is masked from ‘package:shiny’:

    runExample


Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable

Loading required package: magrittr
========================================
circlize version 0.4.8
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: http://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.
========================================


Attaching package: ‘shinyalert’

The following object is masked from ‘package:colourpicker’:

    runExample

The following object is masked from ‘package:shiny’:

    runExample

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:gridExtra’:

    combine

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:data.table’:

    first, second

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:data.table’:

    shift

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

Loading required package: AnnotationDbi



Registered S3 method overwritten by 'enrichplot':
  method               from
  fortify.enrichResult DOSE
ReactomePA v1.30.0  For help: https://guangchuangyu.github.io/ReactomePA

If you use ReactomePA in published research, please cite:
Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479

Attaching package: ‘enrichplot’

The following object is masked from ‘package:ggpubr’:

    color_palette

Loading required package: grid
========================================
ComplexHeatmap version 2.5.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
  genomic data. Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
! pheatmap() has been masked by ComplexHeatmap::pheatmap(). 90% of the arguments
   in the original pheatmap() are identically supported in the new function. You
   can still use the original function by explicitly calling pheatmap::pheatmap().


Attaching package: ‘ComplexHeatmap’

The following object is masked from ‘package:pheatmap’:

    pheatmap

Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
^AIf you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.
========================================


Attaching package: ‘shinyalert’

The following object is masked from ‘package:colourpicker’:

    runExample

The following object is masked from ‘package:shiny’:

    runExample

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:gridExtra’:

    combine

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:data.table’:

    first, second

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:data.table’:

    shift

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

Loading required package: AnnotationDbi



Registered S3 method overwritten by 'enrichplot':
  method               from
  fortify.enrichResult DOSE
ReactomePA v1.30.0  For help: https://guangchuangyu.github.io/ReactomePA

If you use ReactomePA in published research, please cite:
Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479

Attaching package: ‘enrichplot’

The following object is masked from ‘package:ggpubr’:

    color_palette

Loading required package: grid
========================================
ComplexHeatmap version 2.5.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
  genomic data. Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
! pheatmap() has been masked by ComplexHeatmap::pheatmap(). 90% of the arguments
   in the original pheatmap() are identically supported in the new function. You
   can still use the original function by explicitly calling pheatmap::pheatmap().


Attaching package: ‘ComplexHeatmap’

The following object is masked from‘package:pheatmap’:

    pheatmap

Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 134 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895
Warning: Error in mapIds_base: mapIds must have at least one key to match against.
  127: stop
  126: mapIds_base
  125: mapIds
  123: <reactive:calc_res> [/srv/shiny-server/server.R#307]
  107: calc_res
  102: exprFunc [/srv/shiny-server/server.R#351]
  101: widgetFunc
  100: func
   87: origRenderFunc
   86: renderFunc
   82: origRenderFunc
   81: output$calc_res_values
    1: runApp
```f42fd3b4a010: Pull complete
43fb01442cf8: Pull complete
0a1665ee6e4a: Pull complete
676e523523a7: Pull complete
689d3e105be4: Pull complete
e0f5fadec882: Pull complete
8d37b1db41dd: Pull complete
1cc449af1019: Pull complete
0e40efdf44cc: Pull complete
e817102c2c4a: Pull complete
a49e8987b780: Pull complete
6c252619daa7: Pull complete
c45851b0e365: Pull complete
c2978605d776: Pull complete
450c7521222c: Pull complete
b5286a25b6fb: Pull complete
cdd928a43f36: Pull complete
a63e41077377: Pull complete
4e6b9928835f: Pull complete
cb7a8be2b20a: Pull complete
764592e3618b: Pull complete
3cc28c10ac66: Pull complete
d67783cafca7: Pull complete
f0730fa2125f: Pull complete
532d856f96a3: Pull complete
d0561ce2f7ee: Pull complete
94122399e7c3: Pull complete
9972f5043192: Pull complete
a721a9ffaea6: Pull complete
Digest: sha256:5dc40e0ca36d169a753be5012d3afa2bf2a2e10d05d88e29e695056b08dc7761
Status: Downloaded newer image for pirunthan/beavr:latest
77be22d2817d: Downloading [======>                                            ]  26.79MB/205.7MB
*** warning - no files are being watched ***
[2022-02-09T23:56:56.579] [INFO] shiny-server - Shiny Server v1.5.13.943 (Node.js v12.14.1)
[2022-02-09T23:56:56.580] [INFO] shiny-server - Using config file "/etc/shiny-server/shiny-server.conf"
[2022-02-09T23:56:56.602] [WARN] shiny-server - Running as root unnecessarily is a security risk! You could be running more securely as non-root.
[2022-02-09T23:56:56.604] [INFO] shiny-server - Starting listener on http://[::]:3838
[2022-02-09T23:58:04.468] [INFO] shiny-server - Created bookmark state directory: /var/lib/shiny-server/bookmarks
[2022-02-09T23:58:04.468] [INFO] shiny-server - Created user bookmark state directory: /var/lib/shiny-server/bookmarks/shinyf5043192: Waiting
a721a9ffaea6: Waiting
*** '/var/log/shiny-server//shiny-server-shiny-20220209-235804-37607.log' has been created ***

*** /var/log/shiny-server//shiny-server-shiny-20220209-235804-37607.log ***

Listening on http://127.0.0.1:37607

Attaching package: ‘shinydashboard’

The following object is masked from ‘package:graphics’:

    box

Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.10' is out-of-date; the current release version '3.14'
  is available with R version '4.1'; see https://bioconductor.org/install

Attaching package: ‘colourpicker’

The following object is masked from ‘package:shiny’:

    runExample


Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable

Loading required package: magrittr
========================================
circlize version 0.4.8
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: http://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.
========================================


Attaching package: ‘shinyalert’

The following object is masked from ‘package:colourpicker’:

    runExample

The following object is masked from ‘package:shiny’:

    runExample

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:gridExtra’:

    combine

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:data.table’:

    first, second

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:data.table’:

    shift

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

Loading required package: AnnotationDbi



Registered S3 method overwritten by 'enrichplot':
  method               from
  fortify.enrichResult DOSE
ReactomePA v1.30.0  For help: https://guangchuangyu.github.io/ReactomePA

If you use ReactomePA in published research, please cite:
Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479

Attaching package: ‘enrichplot’

The following object is masked from ‘package:ggpubr’:

    color_palette

Loading required package: grid
========================================
ComplexHeatmap version 2.5.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
  genomic data. Bioinformatics 2016.

This message can be suppressed by:
  suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
! pheatmap() has been masked by ComplexHeatmap::pheatmap(). 90% of the arguments
   in the original pheatmap() are identically supported in the new function. You
   can still use the original function by explicitly calling pheatmap::pheatmap().


Attaching package: ‘ComplexHeatmap’

The following object is masked from ‘package:pheatmap’:

    pheatmap

Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
Warning in FUN(X[[i]], ...) :
  The tag provided is not a shiny tag. Action abort.
^AIf you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.
========================================


Attaching package: ‘shinyalert’

The following object is masked from ‘package:colourpicker’:

    runExample

The following object is masked from ‘package:shiny’:

    runExample

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from ‘package:gridExtra’:

    combine

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:data.table’:

    first, second

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object is masked from ‘package:data.table’:

    shift

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
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converting counts to integer mode
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 134 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testing
using 'apeglm' for LFC shrinkage. If used in published research, please cite:
    Zhu, A., Ibrahim, J.G., Love, M.I. (2018) Heavy-tailed prior distributions for
    sequence count data: removing the noise and preserving large differences.
    Bioinformatics. https://doi.org/10.1093/bioinformatics/bty895
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[developerpiru]

Hi gene-drive,

The error:
Warning: Error in mapIds_base: mapIds must have at least one key to match against.

usually means there is an error in one or both of the input files (sample IDs or transcript IDs). Do you mind sharing your input files so the error can be replicated? You can either post here or share privately to pperampa [at] uwo.ca.

Thanks
-Piru

[gene-drive]

I’m curious if the issue is because my read counts table uses gene names instead of ENSEMBL IDs. I’ve tried to convert the gene names to ENSEMBL IDs but I’m finding many genes in my list don’t have IDs, so I’m not sure how to fix this.

Here is my sample treatment matrix file:

	condition	replicate	genotype
ctrl_1	ctrl	1	het
ctrl_2	ctrl	2	het
ctrl_3	ctrl	3	het
ctrl_4	ctrl	4	het
ctrl_5	ctrl	5	het
ctrl_6	ctrl	6	het
KO_1	KO	1	KO
KO_2	KO	2	KO
KO_3	KO	3	KO
KO_4	KO	4	KO
KO_5	KO	5	KO
KO_6	KO	6	KO

And here are just a few lines from my read count table file:

	ctrl_1	ctrl_2	ctrl_3	ctrl_4	ctrl_5	ctrl_6	KO_1	KO_2	KO_3	KO_4	KO_5	KO_6
4933401J01Rik	0	0	0	0	0	0	0	0	0	0	0	0
Gm26206	0	0	0	0	0	0	0	0	0	0	0	0
Xkr4	0	1	0	0	8	4	1	1	9	0	0	6
Gm18956	0	0	0	0	0	0	0	0	0	0	0	0
Gm37180	0	0	0	0	0	0	0	0	0	0	0	0
Gm37363	0	0	0	0	0	0	0	0	0	0	0	0