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MRCIEU / opengwas-reports

Report module for IEU GWAS pipeline
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error message #27

Open mcgml opened 4 years ago

mcgml commented 4 years ago 
ml18692@ieu-db-interface:/data/igd/ieu-b-2$ cat /data/cromwell-executions/qc/79dd1371-3a19-4ea0-a04e-ba397ff17596/call-report/execution/stderr
Lines   total/split/realigned/skipped:  0/0/0/0
Error: `nm` must be `NULL` or a character vector the same length as `x`
Backtrace:
     █
  1. ├─base::do.call(main, get_args(DOC))
  2. └─(function (input, refdata = NULL, id = NULL, output_dir = NULL, ...
  3.   └─global::read_bcf_file(bcf_file = input, ref_file = refdata)
  4.     └─`%>%`(...)
  5.       ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6.       └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  7.         └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
  8.           └─`_fseq`(`_lhs`)
  9.             └─magrittr::freduce(value, `_function_list`)
 10.               └─function_list[[i]](value)
 11.                 └─rlang::set_names(., col_names)
In addition: Warning message:
In data.table::fread(cmd = cmd, header = FALSE, sep = "\t", na.strings = c("",  :
  File '/tmp/RtmplazMkg/file118365f26' has size 0. Returning a NULL data.table.
Execution halted
explodecomputer commented 4 years ago

thanks @mcgml i think the error might actually be due to the LDSC analysis, will look into it

mcgml commented 4 years ago

I'm taking the report tool offline until this is resolved

explodecomputer commented 4 years ago

this error in the original ldsc branch seems to be causing the issue: https://github.com/bulik/ldsc/issues/214 they seem to be actively working on it so hopefully it will be fixed soon