Error in metadataFeather(path) : Invalid: Not a feather file

[bunina-lab]

Hello,

I'm getting the error after running the topicsRcisTarget command:

# feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/region_based/hg19-regions-9species.all_regions.mc9nr.regions_vs_motifs.rankings.feather'

pathToFeather <- "/Volumes/AG_Bunina/software_2/cistopic/hg19-regions-9species.all_regions.mc9nr.regions_vs_motifs.rankings.feather" #fast server
#load missing file:
data(list="motifAnnotations_hgnc_v9", package="RcisTarget")
motifAnnotations_hgnc <- motifAnnotations_hgnc_v9

cisTopicObject <- topicsRcisTarget(cisTopicObject, genome='hg19', pathToDb = pathToFeather, reduced_database=FALSE, nesThreshold=3, rocthr=0.005, maxRank=20000, nCores=5)

Loading required package: RcisTarget
Error in metadataFeather(path) : Invalid: Not a feather file

Below is my sessionInfo.

Thanks for looking into it!

`> sessionInfo() R version 4.2.3 (2023-03-15) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS 14.1

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] RcisTarget_1.18.2 rtracklayer_1.58.0 R.utils_2.12.2
[4] R.oo_1.25.0 R.methodsS3_1.8.2 TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0 [7] GenomicFeatures_1.50.4 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[10] org.Hs.eg.db_3.16.0 AnnotationDbi_1.60.2 IRanges_2.32.0
[13] S4Vectors_0.36.2 Biobase_2.58.0 BiocGenerics_0.44.0
[16] cisTopic_0.3.0

loaded via a namespace (and not attached): [1] snow_0.4-4 BiocFileCache_2.6.1 plyr_1.8.9 GSEABase_1.60.0
[5] splines_4.2.3 BiocParallel_1.32.6 feather_0.3.5 usethis_2.2.2
[9] ggplot2_3.4.4 digest_0.6.33 foreach_1.5.2 htmltools_0.5.6.1
[13] float_0.3-1 fansi_1.0.5 lda_1.4.2 magrittr_2.0.3
[17] memoise_2.0.1 remotes_2.4.2.1 Biostrings_2.66.0 annotate_1.76.0
[21] matrixStats_1.0.0 prettyunits_1.2.0 colorspace_2.1-0 blob_1.2.4
[25] rappdirs_0.3.3 xfun_0.40 dplyr_1.1.3 callr_3.7.3
[29] crayon_1.5.2 RCurl_1.98-1.12 graph_1.76.0 survival_3.5-7
[33] iterators_1.0.14 glue_1.6.2 gtable_0.3.4 zlibbioc_1.44.0
[37] XVector_0.38.0 DelayedArray_0.24.0 pkgbuild_1.4.2 mlapi_0.1.1
[41] scales_1.2.1 DBI_1.1.3 miniUI_0.1.1.1 Rcpp_1.0.11
[45] xtable_1.8-4 progress_1.2.2 text2vec_0.6.3 bit_4.0.5
[49] profvis_0.3.8 htmlwidgets_1.6.2 httr_1.4.7 ellipsis_0.3.2
[53] urlchecker_1.0.1 pkgconfig_2.0.3 XML_3.99-0.14 dbplyr_2.4.0
[57] utf8_1.2.3 tidyselect_1.2.0 rlang_1.1.1 later_1.3.1
[61] munsell_0.5.0 tools_4.2.3 cachem_1.0.8 cli_3.6.1
[65] generics_0.1.3 RSQLite_2.3.1 devtools_2.4.5 rsparse_0.5.1
[69] evaluate_0.23 stringr_1.5.0 fastmap_1.1.1 yaml_2.3.7
[73] FigR_0.1.0 processx_3.8.2 RhpcBLASctl_0.23-42 knitr_1.45
[77] bit64_4.0.5 fs_1.6.3 fitdistrplus_1.1-11 lgr_0.4.4
[81] purrr_1.0.2 KEGGREST_1.38.0 sparseMatrixStats_1.10.0 mime_0.12
[85] arrow_13.0.0.1 xml2_1.3.5 biomaRt_2.54.1 compiler_4.2.3
[89] rstudioapi_0.15.0 filelock_1.0.2 curl_5.1.0 png_0.1-8
[93] tibble_3.2.1 stringi_1.7.12 ps_1.7.5 lattice_0.20-45
[97] Matrix_1.5-3 vctrs_0.6.4 pillar_1.9.0 lifecycle_1.0.3
[101] BiocManager_1.30.22 data.table_1.14.8 cowplot_1.1.1 bitops_1.0-7
[105] httpuv_1.6.11 AUCell_1.20.2 R6_2.5.1 BiocIO_1.8.0
[109] promises_1.2.1 sessioninfo_1.2.2 codetools_0.2-19 MASS_7.3-60
[113] assertthat_0.2.1 pkgload_1.3.3 SummarizedExperiment_1.28.0 rjson_0.2.21
[117] GenomicAlignments_1.34.1 Rsamtools_2.14.0 GenomeInfoDbData_1.2.9 parallel_4.2.3
[121] doSNOW_1.0.20 hms_1.1.3 grid_4.2.3 rmarkdown_2.25
[125] DelayedMatrixStats_1.20.0 MatrixGenerics_1.10.0 shiny_1.7.5.1 restfulr_0.0.15 `

[mellyS]

Hello, I am facing the same issue. Did you manage to solve it ?

[Gregjlt]

Hey, same problem here, did you find any solutions ?

[ghuls]

cisTopic is deprecated. Use pycisTopic instead.

cisTopic only supports the old Feather format, which you can find in the https://resources.aertslab.org/cistarget/databases/old/ subdir.

e.g.: https://resources.aertslab.org/cistarget/databases/old/homo_sapiens/hg19/refseq_r45/mc9nr/region_based/hg19-regions-9species.all_regions.mc9nr.feather

# Last 8 bytes for Feather v2 format have "ARROW1":
❯ curl -r -8 'https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/region_based/hg19-regions-9species.all_regions.mc9nr.regions_vs_motifs.rankings.feather' | hexdump -C
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100     8  100     8    0     0    615      0 --:--:-- --:--:-- --:--:--   615
00000000  5f 04 41 52 52 4f 57 31                           |_.ARROW1|
00000008

❯ tail -n 8 'hg19-regions-9species.all_regions.mc9nr.regions_vs_motifs.rankings.feather' | hexdump -C
00000000  5f 04 41 52 52 4f 57 31                           |_.ARROW1|
00000008

# Last 8 bytes for Feather v1 format have "FEA1":
❯ curl -r -8 'https://resources.aertslab.org/cistarget/databases/old/homo_sapiens/hg19/refseq_r45/mc9nr/region_based/hg19-regions-9species.all_regions.mc9nr.feather' | hexdump -C
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100     8  100     8    0     0    347      0 --:--:-- --:--:-- --:--:--   347
00000000  c0 a9 1e 06 46 45 41 31                           |....FEA1|
00000008

❯ tail -n 8 'hg19-regions-9species.all_regions.mc9nr.feather' | hexdump -C
00000000  c0 a9 1e 06 46 45 41 31                           |....FEA1|
00000008