Issue with creating ArrrowFile

[millerkaplanlab]

Attach your log file ArchR-createArrows-3c00321fe031-Date-2023-01-29_Time-08-02-41.log

Describe the bug New issue with creating Arrowfile. I've run multiple datasets and have run into this error.

Error: In sprintf("%s Reading TabixFile %s Percent", prefix, round(100 * : one argument not used by format '%s Reading TabixFile %s Percent'

To Reproduce N/A. I have run the tutorial dataset and other datasets successfully.

Expected behavior Expected to create an Arrowfile

Screenshots N/A

Session Info

sessionInfo() R version 4.2.2 (2022-10-31) Platform: x86_64-apple-darwin17.0 (64-bit)

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

Random number generation: RNG: L'Ecuyer-CMRG Normal: Inversion Sample: Rejection

locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages: [1] stats4 grid stats graphics grDevices utils datasets methods base

other attached packages: [1] Rsamtools_2.14.0 BSgenome.Mmusculus.UCSC.mm10_1.4.3 [3] BSgenome_1.66.2 rtracklayer_1.58.0
[5] Biostrings_2.66.0 XVector_0.38.0
[7] rhdf5_2.42.0 SummarizedExperiment_1.28.0
[9] Biobase_2.58.0 MatrixGenerics_1.10.0
[11] Rcpp_1.0.10 Matrix_1.5-3
[13] GenomicRanges_1.50.2 GenomeInfoDb_1.34.7
[15] IRanges_2.32.0 S4Vectors_0.36.1
[17] BiocGenerics_0.44.0 matrixStats_0.63.0
[19] data.table_1.14.6 stringr_1.5.0
[21] plyr_1.8.8 magrittr_2.0.3
[23] ggplot2_3.4.0 gtable_0.3.1
[25] gtools_3.9.4 gridExtra_2.3
[27] ArchR_1.0.2

loaded via a namespace (and not attached): [1] bitops_1.0-7 fs_1.6.0 usethis_2.1.6
[4] devtools_2.4.5 RColorBrewer_1.1-3 rprojroot_2.0.3
[7] tools_4.2.2 profvis_0.3.7 utf8_1.2.2
[10] R6_2.5.1 DBI_1.1.3 colorspace_2.1-0
[13] rhdf5filters_1.10.0 urlchecker_1.0.1 withr_2.5.0
[16] tidyselect_1.2.0 prettyunits_1.1.1 processx_3.8.0
[19] curl_5.0.0 compiler_4.2.2 cli_3.6.0
[22] Cairo_1.6-0 desc_1.4.2 DelayedArray_0.24.0
[25] labeling_0.4.2 scales_1.2.1 callr_3.7.3
[28] digest_0.6.31 pkgconfig_2.0.3 htmltools_0.5.4
[31] sessioninfo_1.2.2 fastmap_1.1.0 htmlwidgets_1.6.1
[34] rlang_1.0.6 rstudioapi_0.14 shiny_1.7.4
[37] farver_2.1.1 BiocIO_1.8.0 generics_0.1.3
[40] BiocParallel_1.32.5 dplyr_1.0.10 RCurl_1.98-1.10
[43] GenomeInfoDbData_1.2.9 munsell_0.5.0 Rhdf5lib_1.20.0
[46] fansi_1.0.4 lifecycle_1.0.3 yaml_2.3.7
[49] stringi_1.7.12 MASS_7.3-58.1 zlibbioc_1.44.0
[52] pkgbuild_1.4.0 parallel_4.2.2 promises_1.2.0.1
[55] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.20-45
[58] ps_1.7.2 pillar_1.8.1 rjson_0.2.21
[61] codetools_0.2-18 pkgload_1.3.2 XML_3.99-0.13
[64] glue_1.6.2 remotes_2.4.2 BiocManager_1.30.19
[67] vctrs_0.5.2 httpuv_1.6.8 purrr_1.0.1
[70] assertthat_0.2.1 cachem_1.0.6 mime_0.12
[73] xtable_1.8-4 restfulr_0.0.15 later_1.3.0
[76] tibble_3.1.8 pheatmap_1.0.12 GenomicAlignments_1.34.0 [79] memoise_2.0.1 ellipsis_0.3.2

Additional context

[rcorces]

Hi @millerkaplanlab! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
Before we help you, you must respond to the following questions unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. 3. Did you post your log file? If not, add it now. 4. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

[millerkaplanlab]

1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? Yes
2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. No
3. Did you post your log file? Yes
4. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post

[rcorces]

I'm not sure how you are receiving that error but your log file seems to indicate that Arrow file creating completed successfully and my cursory look at your log file didnt show an error.

[millerkaplanlab]

It does appear that the Arrow file is created; however, when I try to import the scRNA data I receive the following error. I have previously run this dataset through the pipeline with no issues, so I am not sure why this is happening.

proj <- addGeneExpressionMatrix(input = proj, seRNA = seRNA, force = TRUE) ArchR logging to : ArchRLogs/ArchR-addGeneExpressionMatrix-4957783b9406-Date-2023-01-30_Time-09-09-31.log If there is an issue, please report to github with logFile! 2023-01-30 09:09:31 : Overlap w/ scATAC = 0 Error in addGeneExpressionMatrix(input = proj, seRNA = seRNA, force = TRUE) : No overlapping cell names found between ArrowFiles and seRNA object! Cell names in ArrowFiles must match colnames in seRNA

ArchR-addGeneExpressionMatrix-4957783b9406-Date-2023-01-30_Time-09-09-31.log

[rcorces]

you must have changed how you named your samples. In your Arrow files for ex the sample is named "E17_SV_N1" and in your gene exp it is named "E17_SVZN1". So the error you received is exactly correct.

[millerkaplanlab]

I was just looking at this and noticed the same. I will try again. Thank you!