danli349
commented
5 months ago 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 %>%
runAmeAdded /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:
- by_binding %>% runAme
- runAme(.)
- runAme.BStringSetList(.)
- runAme.list(as.list(input), control, outdir, method, database, . meme_path, sequences, silent, ...)
- purrr::map(input, runAme.default, control = control, outdir = outdir, . method = method, database = database, meme_path = meme_path, . sequences = sequences, silent = silent, ...)
- map_("list", .x, .f, ..., .progress = .progress)
- with_indexed_errors(i = i, names = names, error_call = .purrr_error_call, . call_with_cleanup(map_impl, environment(), .type, .progress, . n, names, i))
- 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") . } . })
- call_with_cleanup(map_impl, environment(), .type, .progress, . n, names, i)
- .f(.x[[i]], ...)
- 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), flagsfun = ~{ . gsub("-", "", .x) . }, default_help_fun = TRUE)
- process_check_error(., help_fun = ~{ . ame_help(command) . }, user_flags = cmdfun::cmd_help_parse_flags(user_flags) %>% . grep("shuffle", ., invert = TRUE, value = TRUE), flagsfun = ~{ . gsub("-", "", .x) . }, default_help_fun = TRUE)
- usethis::ui_stop("Shell process had non-zero exit status.")
- stop(cnd)
- (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" . )))
- cli::cli_abort(message, location = i, name = name, parent = cnd, . call = error_call, class = "purrr_error_indexed")
- rlang::abort(message, ..., call = call, use_cli_format = TRUE, . .frame = .frame)
- signal_abort(cnd, .file)
snystrom
Hello:
I run the example codes in the
README:How should I fix this? Thanks