runStreme() error

[ivangalvan]

Hi,

I found an error when using the runStreme() function in the following code:

data("example_peaks", package = "memes") dm.genome <- BSgenome.Dmelanogaster.UCSC.dm6::BSgenome.Dmelanogaster.UCSC.dm6 sequences <- example_peaks %>% resize(100, "center") %>% get_sequence(dm.genome) streme_results <- runStreme(sequences, control = "shuffle")

Error: Can't subset columns that don't exist. Column from doesn't exist.

Backtrace:

1. memes::runStreme(sequences, control = "shuffle")
   11. dplyr:::select.data.frame(., -"from")
   12. tidyselect::eval_select(expr(c(...)), .data)
   13. tidyselect:::eval_select_impl(...)
   14. tidyselect:::vars_select_eval(...)
   15. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   16. tidyselect:::eval_c(expr, data_mask, context_mask)
   17. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   18. tidyselect:::walk_data_tree(new, data_mask, context_mask)
   19. tidyselect:::as_indices_sel_impl(...)
   20. tidyselect:::as_indices_impl(x, vars, strict = strict)
   21. tidyselect:::chr_as_locations(x, vars)
   22. vctrs::vec_as_location(x, n = length(vars), names = vars)
   23. vctrs:::stop_subscript_oob(...)
   24. vctrs:::stop_subscript(...)

Would you know what could be the bug? I tried to figure out without success where is the dplyr:::select.data.frame(., -"from") command in your code.

Could you provide an example code to run the runStreme() function properly?

Thank you

[snystrom]

Hey, thanks for reporting the issue & providing a reproducible example, I'll take a look this evening. runStreme has a few odd bugs in that recently cropped up that I need to chase down.

Can you try running it again with:

streme_results <- runStreme(sequences, control = sequences)

Just as a quick check to see if the issue is with the "shuffle" call?

[ivangalvan]

Thank you for your quick reply,

Unfortunately, the same error appears with your command and then the issue seems not to be related with the control argument.

[snystrom]

Great, thanks for trying that out! Swamped w/ work at the moment, but should have some time this evening. Hopefully can patch it quick for you.

[snystrom]

In the mean time, runDreme is probably the best substitute.

[snystrom]

Alternately, you can run the Streme webtool and import the XML results with importStremeXML()

[snystrom]

Hey Iván,

I'm having trouble reproducing this error. Can you post the output of sessionInfo() and the output of check_meme_install()?

Finally, can you try running:

streme_results <- runStreme(sequences, control = "shuffle", outdir = "debug")

Then upload the streme.xml file output from the debug/ directory (created in your R project working directory where you run the command).

Thanks for helping me get to the bottom of this!

[snystrom]

Oh and does:

x <- universalmotif::create_sequences()
runStreme(x)

Also cause the same error?

[ivangalvan]

Hi Spencer,

The runDremeworks well for me, however, I found the same error with your suggestions using the runStreme.

The check_meme_install seems good:

checking main install ✓ /home/igalvan/meme/bin checking util installs ✓ /home/igalvan/meme/bin/dreme ✓ /home/igalvan/meme/bin/ame ✓ /home/igalvan/meme/bin/fimo ✓ /home/igalvan/meme/bin/tomtom ✓ /home/igalvan/meme/bin/meme ✓ /home/igalvan/meme/bin/streme

My session ifno is:

sessionInfo() R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale: [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 LC_COLLATE=es_ES.UTF-8 LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] dplyr_1.0.7 GenomicRanges_1.46.1 GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0 magrittr_2.0.1 memes_1.2.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.7 lattice_0.20-45 tidyr_1.1.4 ps_1.6.0
[5] Rsamtools_2.10.0 Biostrings_2.62.0 ggseqlogo_0.1 rprojroot_2.0.2
[9] utf8_1.2.2 R6_2.5.1 universalmotif_1.12.1 ggplot2_3.3.5
[13] pillar_1.6.4 zlibbioc_1.40.0 rlang_0.4.12 rstudioapi_0.13
[17] R.utils_2.11.0 R.oo_1.24.0 Matrix_1.3-4 BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 [21] desc_1.4.0 BiocParallel_1.28.2 readr_2.1.1 cmdfun_1.0.2
[25] RCurl_1.98-1.5 munsell_0.5.0 DelayedArray_0.20.0 compiler_4.1.2
[29] rtracklayer_1.54.0 pkgconfig_2.0.3 tidyselect_1.1.1 SummarizedExperiment_1.24.0
[33] tibble_3.1.6 GenomeInfoDbData_1.2.7 matrixStats_0.61.0 XML_3.99-0.8
[37] fansi_0.5.0 crayon_1.4.2 tzdb_0.2.0 withr_2.4.3
[41] GenomicAlignments_1.30.0 MASS_7.3-54 bitops_1.0-7 R.methodsS3_1.8.1
[45] grid_4.1.2 gtable_0.3.0 lifecycle_1.0.1 scales_1.1.1
[49] cli_3.1.0 XVector_0.34.0 fs_1.5.1 testthat_3.1.0
[53] xml2_1.3.3 ellipsis_0.3.2 generics_0.1.1 vctrs_0.3.8
[57] rjson_0.2.20 restfulr_0.0.13 tools_4.1.2 BSgenome_1.62.0
[61] Biobase_2.54.0 glue_1.5.1 purrr_0.3.4 hms_1.1.1
[65] MatrixGenerics_1.6.0 processx_3.5.2 pkgload_1.2.4 parallel_4.1.2
[69] yaml_2.2.1 colorspace_2.0-2 BiocManager_1.30.16 BiocIO_1.4.0
[73] usethis_2.1.3

It seems there is in some place of the code the "from" column but data do not have this column. What do you think?

Thank you

[ivangalvan]

Hi again,

I realized that streme generated successfully the outputs in the debug folder and now, I found that the error comes by using the importStremeXML() function.

streme_results = importStremeXML("debug/streme.xml") Error: Can't subset columns that don't exist. x Column from doesn't exist.

rlang::last_error() <error/vctrs_error_subscript_oob> Can't subset columns that don't exist. x Column from doesn't exist. Backtrace:

1. memes::importStremeXML("debug/streme.xml")
   10. dplyr:::select.data.frame(., -"from")
   11. tidyselect::eval_select(expr(c(...)), .data)
   12. tidyselect:::eval_select_impl(...)
   13. tidyselect:::vars_select_eval(...)
   14. tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   15. tidyselect:::eval_c(expr, data_mask, context_mask)
   16. tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
   17. tidyselect:::walk_data_tree(new, data_mask, context_mask)
   18. tidyselect:::as_indices_sel_impl(...)
   19. tidyselect:::as_indices_impl(x, vars, strict = strict)
   20. tidyselect:::chr_as_locations(x, vars)
   21. vctrs::vec_as_location(x, n = length(vars), names = vars)
   22. vctrs:::stop_subscript_oob(...)
   23. vctrs:::stop_subscript(...)

However the importDremeXML() is working fine.

What do you think?

Thank you

[snystrom]

Yeah something is happening at the XML generation step I think where it's leaving out a metadata field called "from" that it usually has. Can you upload the streme.xml file to this issue and I'll take a look at it.

[snystrom]

This could be a bug in STREME or they may have changed the behavior of STREME. Can you also post the version of the meme suite you are using? On the bash terminal streme --version or in R: runStreme(sequences, "shuffle", version = TRUE, silent = FALSE).

[ivangalvan]

Sure, version is 5.4.1.

I can't upload the .xml file or copy here, github does not allow me, sorry.

[snystrom]

Thanks for checking!

Sometimes dragging + dropping the file into the text box works. I'll try something else on my end also.

[snystrom]

Ah, got it! I was a MEME version behind. They've changed STREME behavior. I'll try to add a way to catch this that works for old & current versions. Thanks for reporting, I'll ping when I get the issue resolved.

[ivangalvan]

It sounds good! Thanks!

[snystrom]

This should be fixed now. The changes will propagate to bioc release & devel in a few days. For now, you can install the development version from github with:

remotes::install_github("snystrom/memes")

Thanks so much for reporting the issue, I hope your analysis goes well! And feel free to reopen this issue if the bug persists.

[ivangalvan]

Thank you very much! I confirm that now importStremeXML() is working properly!