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I received this error:
Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) :
HDF5. File accessibility. Unable to open file.
I used Kallisto as pseudoaligner and I collected abundance files in their corresponding folder. Until this code everything worked, however I do not understand what is happening, ¿could it be associated with a deprecated line in abundance file?
Thanks in advance. I send my info R sesion beneath.
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
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Hi everyone:
I am unable to run this following code:
so<-sleuth_prep(experimental_design,
~Group,
target_mapping = t2g,
read_bootstrap_tpm = TRUE,
extra_bootstrap_summary = TRUE,
transformation_function = function(x) log2(x + 0.5),
num_cores = 1) %>%
sleuth_fit()
I received this error:
Error in H5Fopen(file, flags = flags, fapl = fapl, native = native) :
HDF5. File accessibility. Unable to open file.
I used Kallisto as pseudoaligner and I collected abundance files in their corresponding folder. Until this code everything worked, however I do not understand what is happening, ¿could it be associated with a deprecated line in abundance file?
Thanks in advance. I send my info R sesion beneath.
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=Spanish_Spain.1252 LC_CTYPE=Spanish_Spain.1252
[3] LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Spain.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.50.3 forcats_0.5.1 tximportData_1.22.0 tximport_1.22.0
[5] readxl_1.4.0 sleuth_0.30.0 devtools_2.4.3 usethis_2.1.5
loaded via a namespace (and not attached):
[1] bitops_1.0-7 fs_1.5.2 bit64_4.0.5
[4] filelock_1.0.2 RColorBrewer_1.1-3 progress_1.2.2
[7] httr_1.4.3 rprojroot_2.0.3 GenomeInfoDb_1.30.1
[10] tools_4.1.2 utf8_1.2.2 R6_2.5.1
[13] DBI_1.1.2 BiocGenerics_0.40.0 lazyeval_0.2.2
[16] colorspace_2.0-3 rhdf5filters_1.6.0 withr_2.5.0
[19] tidyselect_1.1.2 prettyunits_1.1.1 processx_3.5.3
[22] bit_4.0.4 curl_4.3.2 compiler_4.1.2
[25] cli_3.3.0 Biobase_2.54.0 xml2_1.3.3
[28] desc_1.4.1 scales_1.2.0 readr_2.1.2
[31] callr_3.7.0 rappdirs_0.3.3 stringr_1.4.0
[34] digest_0.6.29 XVector_0.34.0 pkgconfig_2.0.3
[37] sessioninfo_1.2.2 dbplyr_2.1.1 fastmap_1.1.0
[40] rlang_1.0.2 rstudioapi_0.13 RSQLite_2.2.13
[43] generics_0.1.2 vroom_1.5.7 dplyr_1.0.9
[46] RCurl_1.98-1.6 magrittr_2.0.3 GenomeInfoDbData_1.2.7
[49] Rcpp_1.0.8.3 munsell_0.5.0 S4Vectors_0.32.4
[52] Rhdf5lib_1.16.0 fansi_1.0.3 lifecycle_1.0.1
[55] stringi_1.7.6 zlibbioc_1.40.0 brio_1.1.3
[58] rhdf5_2.38.1 pkgbuild_1.3.1 BiocFileCache_2.2.1
[61] grid_4.1.2 blob_1.2.3 parallel_4.1.2
[64] crayon_1.5.1 Biostrings_2.62.0 hms_1.1.1
[67] KEGGREST_1.34.0 ps_1.7.0 pillar_1.7.0
[70] stats4_4.1.2 pkgload_1.2.4 XML_3.99-0.9
[73] glue_1.6.2 data.table_1.14.2 remotes_2.4.2
[76] tzdb_0.3.0 png_0.1-7 vctrs_0.4.1
[79] testthat_3.1.4 cellranger_1.1.0 tidyr_1.2.0
[82] gtable_0.3.0 purrr_0.3.4 assertthat_0.2.1
[85] cachem_1.0.6 ggplot2_3.3.6 tibble_3.1.7
[88] pheatmap_1.0.12 AnnotationDbi_1.56.2 memoise_2.0.1
[91] IRanges_2.28.0 ellipsis_0.3.2
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