Entering edit mode
Hello, I am trying to perform DESeq2 on Salmon indexed mouse data. I am running into the following error when trying to execute tximeta.
importing quantifications
> se <- tximeta(coldata)
reading in files with read_tsv
1 2 3 4
found matching linked transcriptome:
[ GENCODE - Mus musculus - release M27 ]
useHub=TRUE: checking for TxDb via 'AnnotationHub'
snapshotDate(): 2021-05-18
did not find matching TxDb via 'AnnotationHub'
building TxDb with 'GenomicFeatures' package
Error in makeTxDbFromGFF(txomeInfo$gtf) :
Cannot detect whether 'file' is a GFF3 or GTF file. Please use the 'format' argument to specify the format ("gff3" or
"gtf").
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] stats graphics grDevices utils datasets methods base
other attached packages:
[1] tximeta_1.10.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.24.0 bitops_1.0-7 matrixStats_0.60.1 bit64_4.0.5
[5] filelock_1.0.2 progress_1.2.2 httr_1.4.2 GenomeInfoDb_1.28.4
[9] tools_4.1.0 utf8_1.2.2 R6_2.5.1 DBI_1.1.1
[13] BiocGenerics_0.38.0 lazyeval_0.2.2 withr_2.4.2 tidyselect_1.1.1
[17] prettyunits_1.1.1 bit_4.0.4 curl_4.3.2 compiler_4.1.0
[21] Biobase_2.52.0 xml2_1.3.2 DelayedArray_0.18.0 rtracklayer_1.52.1
[25] readr_2.0.1 rappdirs_0.3.3 stringr_1.4.0 digest_0.6.27
[29] Rsamtools_2.8.0 XVector_0.32.0 pkgconfig_2.0.3 htmltools_0.5.2
[33] MatrixGenerics_1.4.3 dbplyr_2.1.1 fastmap_1.1.0 ensembldb_2.16.4
[37] rlang_0.4.11 rstudioapi_0.13 RSQLite_2.2.8 shiny_1.6.0
[41] BiocIO_1.2.0 generics_0.1.0 jsonlite_1.7.2 vroom_1.5.5
[45] BiocParallel_1.26.2 dplyr_1.0.7 RCurl_1.98-1.4 magrittr_2.0.1
[49] GenomeInfoDbData_1.2.6 Matrix_1.3-4 Rcpp_1.0.7 S4Vectors_0.30.0
[53] fansi_0.5.0 lifecycle_1.0.0 stringi_1.7.4 yaml_2.2.1
[57] SummarizedExperiment_1.22.0 zlibbioc_1.38.0 BiocFileCache_2.0.0 AnnotationHub_3.0.1
[61] grid_4.1.0 blob_1.2.2 parallel_4.1.0 promises_1.2.0.1
[65] crayon_1.4.1 lattice_0.20-44 Biostrings_2.60.2 GenomicFeatures_1.44.2
[69] hms_1.1.0 KEGGREST_1.32.0 pillar_1.6.2 GenomicRanges_1.44.0
[73] rjson_0.2.20 biomaRt_2.48.3 stats4_4.1.0 XML_3.99-0.7
[77] glue_1.4.2 BiocVersion_3.13.1 BiocManager_1.30.16 tzdb_0.1.2
[81] png_0.1-7 vctrs_0.3.8 httpuv_1.6.3 purrr_0.3.4
[85] assertthat_0.2.1 cachem_1.0.6 mime_0.11 xtable_1.8-4
[89] restfulr_0.0.13 AnnotationFilter_1.16.0 later_1.3.0 tibble_3.1.4
[93] GenomicAlignments_1.28.0 AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0
[97] tximport_1.20.0 ellipsis_0.3.2 interactiveDisplayBase_1.30.0
