`runAme(sequences, control = "shuffle", evalue_report_threshold = 30)` get `FATAL: Template does not contain data section`

[danli349]

Hello:

I run the example codes in the README:

check_meme_install()

checking main install

✔ /home/dan/meme/bin
checking util installs

✔ /home/dan/meme/bin/dreme
✔ /home/dan/meme/bin/ame
✔ /home/dan/meme/bin/fimo
✔ /home/dan/meme/bin/tomtom
✔ /home/dan/meme/bin/meme
✔ /home/dan/meme/bin/streme

sequences

DNAStringSet object of length 10:
     width seq                                              names               
 [1]   200 AGAATGTTATATATTCAAGAGGC...TTAGGTTTCTAGAATAGCCCCG chr3L:14551120-14...
 [2]   200 TGGGCCCATTTTTATCATTTTCC...CCCCCTCACATTTTAATTGTTG chr3L:14625651-14...
 [3]   200 GGGCATACAGTAGAGCATCGTTG...ACAGGCTCTTTACCTAGTGCAA chr3L:14634365-14...
 [4]   200 TCACTCACTGAAAAAAAAACATA...GTACGGTTGCTCCACTTCGATG chr3L:14636806-14...
 [5]   200 ATTTTGCCTGTGTGGTCTCACCT...TTTTCGGGAGTGCAGCCAAAGA chr3L:14638235-14...
 [6]   200 CTGAGTGTATATATGTATATATT...CTCTATCCCCAATATCTTCTTT chr3L:14743361-14...
 [7]   200 TTATATAGCATTGCTCAGAAAAC...TTTGCCGTAGGAGCAAGGGAGA chr3L:14755203-14...
 [8]   200 TCCAATCGGCGTTAAAGCAGTGA...GGTAGGAATAGAATTACTATGT chr3L:14759244-14...
 [9]   200 CATCTCTAGGGTCCGGGTCCGGT...ACAGGCACTTACTCACCAGTGT chr3L:14978542-14...
[10]   200 GCACATTCACACATTGTGTACGT...CTGGCGTTTTTTGCGTTTCAGT chr3L:15104843-15...

# here I set the evalue_report_threshold = 30 to detect motifs in the limited example sequences
# In a real analysis, evalue_report_threshold should be carefully selected
ame_results <- runAme(sequences, control = "shuffle", evalue_report_threshold = 30)
ame_results

Added /home/dan/meme-5.5.5/Databases/motif_databases/FLY/OnTheFly_2014_Drosophila.meme to motif_sources which now has 1 file names.
Motif file name is /home/dan/meme-5.5.5/Databases/motif_databases/FLY/OnTheFly_2014_Drosophila.meme.
Writing results to output directory '/tmp/RtmpfGjF2s/file5e657f9a0350_vs_shuffle'.
E-value threshold for reporting results: 30
Checking alphabets in 1 motif files.
Loading motifs from file '/home/dan/meme-5.5.5/Databases/motif_databases/FLY/OnTheFly_2014_Drosophila.meme'
Loading primary sequences.
Creating control sequences by shuffling input sequences preserving 2-mers.
Not in partition maximization mode. Fixing partition at the number of primary sequences (10).
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
FATAL: Template does not contain data section.



Error: Shell process had non-zero exit status.
Traceback:

1. runAme(sequences, control = "shuffle", evalue_report_threshold = 30)
2. runAme.default(sequences, control = "shuffle", evalue_report_threshold = 30)
3. ps_out %>% process_check_error(help_fun = ~{
 .     ame_help(command)
 . }, user_flags = cmdfun::cmd_help_parse_flags(user_flags) %>% 
 .     grep("shuffle", ., invert = TRUE, value = TRUE), flags_fun = ~{
 .     gsub("-", "_", .x)
 . }, default_help_fun = TRUE)
4. process_check_error(., help_fun = ~{
 .     ame_help(command)
 . }, user_flags = cmdfun::cmd_help_parse_flags(user_flags) %>% 
 .     grep("shuffle", ., invert = TRUE, value = TRUE), flags_fun = ~{
 .     gsub("-", "_", .x)
 . }, default_help_fun = TRUE)
5. usethis::ui_stop("Shell process had non-zero exit status.")

R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3;  LAPACK version 3.9.0

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

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
 [1] universalmotif_1.18.1                 BSgenome.Dmelanogaster.UCSC.dm6_1.4.1
 [3] BSgenome_1.68.0                       rtracklayer_1.60.1                   
 [5] Biostrings_2.68.1                     XVector_0.40.0                       
 [7] GenomicRanges_1.52.1                  GenomeInfoDb_1.36.4                  
 [9] IRanges_2.34.1                        S4Vectors_0.38.2                     
[11] BiocGenerics_0.46.0                   magrittr_2.0.3                       
[13] memes_1.8.0                          

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0            IRdisplay_1.1              
 [3] farver_2.1.1                dplyr_1.1.3                
 [5] R.utils_2.12.2              bitops_1.0-7               
 [7] fastmap_1.1.1               RCurl_1.98-1.12            
 [9] GenomicAlignments_1.36.0    XML_3.99-0.8               
[11] digest_0.6.33               lifecycle_1.0.4            
[13] Cairo_1.6-1                 processx_3.8.2             
[15] compiler_4.3.0              rlang_1.1.2                
[17] tools_4.3.0                 utf8_1.2.4                 
[19] yaml_2.3.7                  data.table_1.14.8          
[21] labeling_0.4.3              S4Arrays_1.0.6             
[23] bit_4.0.5                   splitstackshape_1.4.8      
[25] DelayedArray_0.26.7         xml2_1.3.2                 
[27] repr_1.1.6                  pkgload_1.3.3              
[29] abind_1.4-5                 BiocParallel_1.34.2        
[31] pbdZMQ_0.3-10               withr_2.5.1                
[33] purrr_1.0.2                 desc_1.4.2                 
[35] R.oo_1.25.0                 grid_4.3.0                 
[37] fansi_1.0.5                 MotifDb_1.42.0             
[39] colorspace_2.1-0            ggplot2_3.4.4              
[41] MASS_7.3-60                 scales_1.2.1               
[43] SummarizedExperiment_1.30.2 cli_3.6.1                  
[45] cmdfun_1.0.2                crayon_1.5.2               
[47] generics_0.1.3              tzdb_0.4.0                 
[49] rjson_0.2.21                ggseqlogo_0.1              
[51] zlibbioc_1.46.0             parallel_4.3.0             
[53] restfulr_0.0.15             matrixStats_1.0.0          
[55] base64enc_0.1-3             vctrs_0.6.5                
[57] Matrix_1.6-1.1              jsonlite_1.8.7             
[59] patchwork_1.1.3             hms_1.1.3                  
[61] bit64_4.0.5                 testthat_3.2.0             
[63] tidyr_1.3.0                 glue_1.6.2                 
[65] codetools_0.2-19            ps_1.7.5                   
[67] gtable_0.3.4                BiocIO_1.10.0              
[69] munsell_0.5.0               tibble_3.2.1               
[71] pillar_1.9.0                htmltools_0.5.7            
[73] brio_1.1.3                  IRkernel_1.3.2.9000        
[75] GenomeInfoDbData_1.2.10     R6_2.5.1                   
[77] rprojroot_2.0.3             vroom_1.6.4                
[79] evaluate_0.23               Biobase_2.60.0             
[81] lattice_0.21-9              readr_2.1.4                
[83] R.methodsS3_1.8.2           Rsamtools_2.16.0           
[85] Rcpp_1.0.11                 uuid_1.1-1                 
[87] fs_1.6.3                    MatrixGenerics_1.12.3      
[89] usethis_2.2.2               pkgconfig_2.0.3      

How should I fix this? Thanks

[danli349]

When I run the tutorial
https://snystrom.github.io/memes-manual/articles/integrative_analysis.html
I found this error again:

head(by_binding)

BStringSetList of length 3
[["ectopic"]] chr3L:40482-40581=GGACTGGGGTTGGGTACGAAACGAAATGGAAACATAGCCAAACAC...
[["entopic"]] chr3L:60616-60715=CAGGTGCATCCCGCGACGAGTATTTTTTATATTATTGTTTGGCCG...
[["orphan"]] chr3L:57749-57848=GAAACCTATACCCCGCCGTCGGCCGATTATCACCTTTTCAAGTCTC...

ame_by_binding <- by_binding %>% 
  runAme

Added /tmp/RtmpD0mwb1/file62f8791c7d96.meme to motif_sources which now has 1 file names.
Motif file name is /tmp/RtmpD0mwb1/file62f8791c7d96.meme.
Writing results to output directory '/tmp/RtmpD0mwb1/file62f8206069aa_vs_shuffle'.
E-value threshold for reporting results: 10
Checking alphabets in 1 motif files.
Loading motifs from file '/tmp/RtmpD0mwb1/file62f8791c7d96.meme'
Loading primary sequences.
Creating control sequences by shuffling input sequences preserving 2-mers.
Not in partition maximization mode. Fixing partition at the number of primary sequences (2421).
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
Bad file name.
FATAL: Template does not contain data section.

Error in purrr::map():
ℹ In index: 1.
ℹ With name: ectopic.
Caused by error:
! Shell process had non-zero exit status.
Traceback:

1. by_binding %>% runAme
2. runAme(.)
3. runAme.BStringSetList(.)
4. runAme.list(as.list(input), control, outdir, method, database,
   . meme_path, sequences, silent, ...)
5. purrr::map(input, runAme.default, control = control, outdir = outdir,
   . method = method, database = database, meme_path = meme_path,
   . sequences = sequences, silent = silent, ...)
6. map_("list", .x, .f, ..., .progress = .progress)
7. with_indexed_errors(i = i, names = names, error_call = .purrr_error_call,
   . call_with_cleanup(map_impl, environment(), .type, .progress,
   . n, names, i))
8. withCallingHandlers(expr, error = function(cnd) {
   . if (i == 0L) {
   . }
   . else {
   . message <- c(i = "In index: {i}.")
   . if (!is.null(names) && !is.na(names[[i]]) && names[[i]] !=
   . "") {
   . name <- names[[i]]
   . message <- c(message, i = "With name: {name}.")
   . }
   . else {
   . name <- NULL
   . }
   . cli::cli_abort(message, location = i, name = name, parent = cnd,
   . call = error_call, class = "purrr_error_indexed")
   . }
   . })
9. call_with_cleanup(map_impl, environment(), .type, .progress,
   . n, names, i)
10. .f(.x[[i]], ...)
11. ps_out %>% process_check_error(help_fun = ~{
    . ame_help(command)
    . }, user_flags = cmdfun::cmd_help_parse_flags(user_flags) %>%
    . grep("shuffle", ., invert = TRUE, value = TRUE), flags_fun = ~{
    . gsub("-", "_", .x)
    . }, default_help_fun = TRUE)
12. process_check_error(., help_fun = ~{
    . ame_help(command)
    . }, user_flags = cmdfun::cmd_help_parse_flags(user_flags) %>%
    . grep("shuffle", ., invert = TRUE, value = TRUE), flags_fun = ~{
    . gsub("-", "_", .x)
    . }, default_help_fun = TRUE)
13. usethis::ui_stop("Shell process had non-zero exit status.")
14. stop(cnd)
15. (function (cnd)
    . {
    . if (i == 0L) {
    . }
    . else {
    . message <- c(i = "In index: {i}.")
    . if (!is.null(names) && !is.na(names[[i]]) && names[[i]] !=
    . "") {
    . name <- names[[i]]
    . message <- c(message, i = "With name: {name}.")
    . }
    . else {
    . name <- NULL
    . }
    . cli::cli_abort(message, location = i, name = name, parent = cnd,
    . call = error_call, class = "purrr_error_indexed")
    . }
    . })(structure(list(message = structure("Shell process had non-zero exit status.", class = c("glue",
    . "character"))), class = c("usethis_error", "error", "condition"
    . )))
16. cli::cli_abort(message, location = i, name = name, parent = cnd,
    . call = error_call, class = "purrr_error_indexed")
17. rlang::abort(message, ..., call = call, use_cli_format = TRUE,
    . .frame = .frame)
18. signal_abort(cnd, .file)

[snystrom]

Hi Dan,

Sorry for just now seeing this issue, I was sick the week you reported & this slipped through the cracks!

Would you mind sharing how you installed the meme suite? I believe this error can happen when AME is missing a core file in its install. Perhaps rerun your runAme call using verbose = TRUE and post the resulting log.

I see you are running MEME Suite 5.5.5 which I have not tested myself, so perhaps the developers made a change. I can also take a look at their release notes for any clues.

Another way to test is to attempt to run ame at the commandline and see if it still errors. That may help rule out whether the R code or the install itself is at fault.

Sorry again for the delay.

[QianzhaoJ]

I had same error, only runAme.
I installed Meme using conda and I got same error when I run ame at the commandline. Maybe the version of dependent packages are correct. However, there are so many prerequisite softwares for installing from source, it is diffcult for users. I dont know whether there's an easier solution for this problem.

Qianzhao

[snystrom]

Hi Qianzhao,

Unfortunately, the conda install of the Meme suite is known to be broken. I do not maintain that and haven't looked into fixing it.

Usually these kinds of errors are either because of a missing perl library or a missing system XML library.

A related issue for another set of tools was able to solve by installing some of the html perl modules:
#108 (comment)

You could also try to install from source following the guide here:
https://meme-suite.org/meme/doc/install.html?man_type=web

In particular, note the suggestion to run

cd scripts
perl dependencies.pl

As well as enabling the libxml2 features, and installing that from your system package manager if it is missing. If you are on an HPC system and do not have sudo, you could consider asking your administrator for advice. Perhaps they have the meme suite tools installed as a module, or similar HPC service.

I am sorry to not be of more help. You could reach out to the MEME Suite mailing list (https://groups.google.com/g/meme-suite) if you still have issues installing that are not addressed by their installation guide (note the MEME Suite authors are not affiliated with the {memes} R package, so can't assist there). Long story short, if the MEME Suite works at the commandline, then the R package should work just fine, so if you need to do testing you can always start at the cli to debug issues with the tool install before moving to R-based analysis.