Entering edit mode
Hi all. I am running tximeta with a small set of salmon alignments against gencode V29. When I run the tximeta command, however, it downloads the gencode annotation gtf, but suddenly says "cannot open URL" and dies? This was working fine several weeks ago, but suddenly it is not. I can manually download the gtf myself, and dialog box pops up which looks like the download is proceeding, but then no luck. This is driving me crazy that it suddenly stopped working...
> se <- tximeta(samples)
importing salmon quantification files
reading in files with read.delim (install 'readr' package for speed up)
1 2 3 4 5 6 7 8
found matching transcriptome:
[ GENCODE - Homo sapiens - release 43 ]
useHub=TRUE: checking for TxDb via 'AnnotationHub'
snapshotDate(): 2025-10-29
did not find matching TxDb via 'AnnotationHub'
building TxDb with 'txdbmaker' package
Import genomic features from the file as a GRanges object ...
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz'
Content type 'unknown' length 49661267 bytes (47.4 MB)
Error in .rs.downloadFile(url = resource(con), destfile = destfile) :
cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz'
In addition: Warning messages:
1: In .rs.downloadFile(url = resource(con), destfile = destfile) :
downloaded length 35621080 != reported length 49661267
2: In .rs.downloadFile(url = resource(con), destfile = destfile) :
URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz': Timeout of 60 seconds was reached
sessionInfo():
R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ensembldb_2.34.0 AnnotationFilter_1.34.0 tximport_1.38.2
[4] txdbmaker_1.6.2 GenomicFeatures_1.62.0 AnnotationDbi_1.72.0
[7] Biobase_2.70.0 GenomicRanges_1.62.1 IRanges_2.44.0
[10] Seqinfo_1.0.0 S4Vectors_0.48.0 BiocGenerics_0.56.0
[13] generics_0.1.4 BiocFileCache_3.0.0 dbplyr_2.5.2
[16] tximeta_1.28.3
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 dplyr_1.2.0
[3] blob_1.3.0 filelock_1.0.3
[5] Biostrings_2.78.0 bitops_1.0-9
[7] fastmap_1.2.0 RCurl_1.98-1.17
[9] lazyeval_0.2.2 GenomicAlignments_1.46.0
[11] XML_3.99-0.22 lifecycle_1.0.5
[13] ProtGenerics_1.42.0 KEGGREST_1.50.0
[15] RSQLite_2.4.6 magrittr_2.0.4
[17] compiler_4.5.2 rlang_1.1.7
[19] progress_1.2.3 tools_4.5.2
[21] yaml_2.3.12 rtracklayer_1.70.1
[23] prettyunits_1.2.0 S4Arrays_1.10.1
[25] bit_4.6.0 curl_7.0.0
[27] DelayedArray_0.36.0 abind_1.4-8
[29] BiocParallel_1.44.0 withr_3.0.2
[31] purrr_1.2.1 grid_4.5.2
[33] biomaRt_2.66.1 SummarizedExperiment_1.40.0
[35] cli_3.6.5 crayon_1.5.3
[37] httr_1.4.8 rjson_0.2.23
[39] DBI_1.3.0 cachem_1.1.0
[41] stringr_1.6.0 parallel_4.5.2
[43] BiocManager_1.30.27 XVector_0.50.0
[45] restfulr_0.0.16 matrixStats_1.5.0
[47] vctrs_0.7.1 Matrix_1.7-4
[49] jsonlite_2.0.0 hms_1.1.4
[51] bit64_4.6.0-1 glue_1.8.0
[53] codetools_0.2-20 stringi_1.8.7
[55] BiocVersion_3.22.0 GenomeInfoDb_1.46.2
[57] BiocIO_1.20.0 UCSC.utils_1.6.1
[59] tibble_3.3.1 pillar_1.11.1
[61] rappdirs_0.3.4 R6_2.6.1
[63] httr2_1.2.2 lattice_0.22-9
[65] AnnotationHub_4.0.0 png_0.1-8
[67] Rsamtools_2.26.0 cigarillo_1.0.0
[69] memoise_2.0.1 SparseArray_1.10.8
[71] MatrixGenerics_1.22.0 pkgconfig_2.0.3
