topicsRcisTarget: Error in .column_indexes_feather(x, i)
luzgaral opened this issue · 2 comments
Hi,
When running topicsRcisTarget on the hg38 on liftover to hg19 I get this error.
Error in .column_indexes_feather(x, i) : undefined columns: chr1-reg496, chr1-reg497, chr1-reg498, chr1-reg500, chr1-reg976, chr1-reg977, chr1-reg978, chr1-reg979, chr1-reg980, chr1-reg1117, chr1-reg1119, chr1-reg1120, chr1-reg1121, chr1-reg2014, chr1-reg2016, chr1-reg2017, chr1-reg2018, chr1-reg2310, chr1-reg2312, chr1-reg2314, chr1-reg2315, chr1-reg2316, chr1-reg2317, chr1-reg2318, chr1-reg6260, chr1-reg6261, chr1-reg6262, chr1-reg6467, chr1-reg6468, chr1-reg6618, chr1-reg6619, chr1-reg6620, chr1-reg6621, chr1-reg6622, chr1-reg6623, chr1-reg6624, chr1-reg6634, chr1-reg6635, chr1-reg6637, chr1-reg6638, chr1-reg6639, chr1-reg6641, chr1-reg6642, chr1-reg6643, chr1-reg6644, chr1-reg6645, chr1-reg6891, chr1-reg6892, chr1-reg6893, chr1-reg6972, chr1-reg7710, chr1-reg7711, chr1-reg7712, chr1-reg8470, chr1-reg8776, chr1-reg8778, chr1-reg8779, chr1-reg8967, chr1-reg9123, chr1-reg9125, chr1-reg9127, chr1-reg9128, chr1-reg9609, chr1-reg9783, chr1-reg9784, chr1-reg9785, chr1-reg9787, chr1-reg9788, chr1-reg9789, chr1-reg9790, Calls: topicsRcisTarget ... as_tibble -> [ -> [.feather -> .column_indexes_feather Execution halted
Any guess on why this is happening?
Thank you!
``
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS/LAPACK: /home/jovyan/my-conda-envs/myenvSC/lib/libopenblasp-r0.3.7.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
[2] GenomicFeatures_1.38.0
[3] org.Hs.eg.db_3.10.0
[4] AnnotationDbi_1.48.0
[5] Biobase_2.46.0
[6] rtracklayer_1.46.0
[7] GenomicRanges_1.38.0
[8] GenomeInfoDb_1.22.0
[9] IRanges_2.20.1
[10] S4Vectors_0.24.1
[11] BiocGenerics_0.32.0
[12] R.utils_2.9.2
[13] R.oo_1.23.0
[14] R.methodsS3_1.7.1
[15] cisTopic_0.2.2
loaded via a namespace (and not attached):
[1] bitops_1.0-6 matrixStats_0.55.0
[3] bit64_0.9-7 progress_1.2.2
[5] httr_1.4.1 tools_3.6.1
[7] backports_1.1.5 R6_2.4.1
[9] DBI_1.0.0 npsurv_0.4-0
[11] tidyselect_0.2.5 prettyunits_1.0.2
[13] curl_4.3 bit_1.1-14
[15] compiler_3.6.1 AUCell_1.8.0
[17] graph_1.64.0 RcisTarget_1.6.0
[19] DelayedArray_0.12.0 askpass_1.1
[21] rappdirs_0.3.1 stringr_1.4.0
[23] digest_0.6.23 Rsamtools_2.2.1
[25] XVector_0.26.0 pkgconfig_2.0.3
[27] htmltools_0.4.0 dbplyr_1.4.2
[29] fastmap_1.0.1 rlang_0.4.2
[31] RSQLite_2.1.4 shiny_1.4.0
[33] BiocParallel_1.20.0 dplyr_0.8.3
[35] RCurl_1.95-4.12 magrittr_1.5
[37] feather_0.3.5 GenomeInfoDbData_1.2.2
[39] Matrix_1.2-18 Rcpp_1.0.3
[41] lda_1.4.2 stringi_1.4.3
[43] MASS_7.3-51.4 SummarizedExperiment_1.16.0
[45] zlibbioc_1.32.0 plyr_1.8.5
[47] BiocFileCache_1.10.2 grid_3.6.1
[49] blob_1.2.0 promises_1.1.0
[51] crayon_1.3.4 doSNOW_1.0.18
[53] lattice_0.20-38 Biostrings_2.54.0
[55] splines_3.6.1 annotate_1.64.0
[57] hms_0.5.2 zeallot_0.1.0
[59] pillar_1.4.2 codetools_0.2-16
[61] biomaRt_2.42.0 XML_3.98-1.20
[63] glue_1.3.1 lsei_1.2-0
[65] data.table_1.12.8 vctrs_0.2.0
[67] httpuv_1.5.2 foreach_1.4.4
[69] openssl_1.4.1 purrr_0.3.3
[71] assertthat_0.2.1 mime_0.7
[73] xtable_1.8-4 later_1.0.0
[75] survival_3.1-8 tibble_2.1.3
[77] snow_0.4-3 iterators_1.0.10
[79] GenomicAlignments_1.22.1 memoise_1.1.0
[81] fitdistrplus_1.0-14 GSEABase_1.48.0
``
Hi!
Can you post the code and the output of feather::feather_metadata(pathToFeather)[["dim"]]?
Also to make sure that the database is not corrupt, could you run sha256sum $feather_database and make sure it matches with the one here for that database? Otherwise, you may need to redownload the database.
Cheers!
C
I also meet the same error, did you solved it?