AME failed with input universalmotif list

mikstapes commented 2 years ago

Hi,

I encountered an error running AME and would really appreciate any suggestions. As input, I have GRanges split into a BStringSetList by an mcol, and then run AME on a universalmotif list like so:

pks_by_seq <- resize(pks_mm39, width = 200, fix = 'center') %>% 
    split(mcols(.)$seq_clss) %>% 
    get_sequence(mm39_genome)

jaspar_motifs <- read_jaspar(here("motifs",
                                                  "JASPAR2022_CORE_vertebrates_non-redundant_pfms_jaspar.txt"))

test_ame <- runAme(pks_by_seq, database = jaspar_motifs)

I figured this was quite straightforward, but I can't seem to get the function running and check_meme_install() ran fine. Here's the traceback:

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 (1568).
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(pks_by_seq, database = heart_motifs)
2. runAme.BStringSetList(pks_by_seq, database = jaspar_motifs)
3. runAme.list(as.list(input), control, outdir, method, database, 
 .     meme_path, sequences, silent, ...)
4. purrr::map(input, runAme.default, control = control, outdir = outdir, 
 .     method = method, database = database, meme_path = meme_path, 
 .     sequences = sequences, silent = silent, ...)
5. .f(.x[[i]], ...)
6. 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)
7. 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)
8. usethis::ui_stop("Shell process had non-zero exit status.")

and my session info:

R version 4.1.1 (2021-08-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: MarIuX64 2.0 GNU/Linux

Matrix products: default
BLAS/LAPACK: ~/miniconda3/envs/r4_env/lib/libopenblasp-r0.3.18.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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] BSgenome.Mmusculus.UCSC.mm39_1.4.3 BSgenome_1.62.0                   
 [3] seqPattern_1.26.0                  MotifDb_1.36.0                    
 [5] Biostrings_2.62.0                  XVector_0.34.0                    
 [7] universalmotif_1.12.4              memes_1.2.5                       
 [9] plyranges_1.14.0                   rtracklayer_1.54.0                
[11] GenomicFeatures_1.46.5             AnnotationDbi_1.56.2              
[13] Biobase_2.54.0                     GenomicRanges_1.46.1              
[15] GenomeInfoDb_1.30.1                IRanges_2.28.0                    
[17] S4Vectors_0.32.3                   BiocGenerics_0.40.0               
[19] effsize_0.8.1                      patchwork_1.1.1                   
[21] forcats_0.5.1                      stringr_1.4.0                     
[23] dplyr_1.0.8                        purrr_0.3.4                       
[25] readr_2.1.2                        tidyr_1.2.0                       
[27] tibble_3.1.6                       ggplot2_3.3.5                     
[29] tidyverse_1.3.1                    here_1.0.1                        

loaded via a namespace (and not attached):
  [1] readxl_1.3.1                uuid_1.0-3                 
  [3] backports_1.4.1             BiocFileCache_2.2.1        
  [5] repr_1.1.4                  splines_4.1.1              
  [7] BiocParallel_1.28.3         usethis_2.1.5              
  [9] digest_0.6.29               htmltools_0.5.2            
 [11] fansi_1.0.2                 magrittr_2.0.2             
 [13] memoise_2.0.1               tzdb_0.2.0                 
 [15] modelr_0.1.8                matrixStats_0.61.0         
 [17] R.utils_2.11.0              vroom_1.5.7                
 [19] prettyunits_1.1.1           colorspace_2.0-3           
 [21] blob_1.2.2                  rvest_1.0.2                
 [23] rappdirs_0.3.3              haven_2.4.3                
 [25] crayon_1.5.0                RCurl_1.98-1.6             
 [27] jsonlite_1.8.0              glue_1.6.2                 
 [29] gtable_0.3.0                zlibbioc_1.40.0            
 [31] DelayedArray_0.20.0         scales_1.1.1               
 [33] DBI_1.1.2                   Rcpp_1.0.8.2               
 [35] plotrix_3.8-2               progress_1.2.2             
 [37] bit_4.0.4                   httr_1.4.2                 
 [39] ellipsis_0.3.2              R.methodsS3_1.8.1          
 [41] pkgconfig_2.0.3             XML_3.99-0.9               
 [43] farver_2.1.0                ggseqlogo_0.1              
 [45] dbplyr_2.1.1                utf8_1.2.2                 
 [47] tidyselect_1.1.2            labeling_0.4.2             
 [49] rlang_1.0.2                 munsell_0.5.0              
 [51] cellranger_1.1.0            tools_4.1.1                
 [53] cachem_1.0.6                cli_3.2.0                  
 [55] generics_0.1.2              RSQLite_2.2.10             
 [57] broom_0.7.12                evaluate_0.15              
 [59] fastmap_1.1.0               yaml_2.3.5                 
 [61] processx_3.5.2              bit64_4.0.5                
 [63] fs_1.5.2                    KEGGREST_1.34.0            
 [65] splitstackshape_1.4.8       nlme_3.1-155               
 [67] R.oo_1.24.0                 xml2_1.3.3                 
 [69] biomaRt_2.50.3              brio_1.1.3                 
 [71] compiler_4.1.1              rstudioapi_0.13            
 [73] filelock_1.0.2              curl_4.3.2                 
 [75] png_0.1-7                   testthat_3.1.2             
 [77] reprex_2.0.1                stringi_1.7.6              
 [79] ps_1.6.0                    desc_1.4.1                 
 [81] lattice_0.20-45             IRdisplay_1.1              
 [83] Matrix_1.4-0                vctrs_0.3.8                
 [85] pillar_1.7.0                lifecycle_1.0.1            
 [87] data.table_1.14.2           bitops_1.0-7               
 [89] R6_2.5.1                    BiocIO_1.4.0               
 [91] KernSmooth_2.23-20          MASS_7.3-55                
 [93] assertthat_0.2.1            pkgload_1.2.4              
 [95] SummarizedExperiment_1.24.0 rprojroot_2.0.2            
 [97] rjson_0.2.21                withr_2.5.0                
 [99] GenomicAlignments_1.30.0    Rsamtools_2.10.0           
[101] GenomeInfoDbData_1.2.7      mgcv_1.8-39                
[103] hms_1.1.1                   grid_4.1.1                 
[105] cmdfun_1.0.2                IRkernel_1.3.0.9000        
[107] MatrixGenerics_1.6.0        pbdZMQ_0.3-7               
[109] lubridate_1.8.0             base64enc_0.1-3            
[111] restfulr_0.0.13