zuberlab / crispr-mageck-nf Goto Github PK

N E X T F L O W  ~  version 19.01.0
Launching `zuberlab/crispr-mageck-nf` [jovial_engelbart] - revision: 3b2575bbe5 [master]
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$mageck = <value>` with a process selector
[warm up] executor > slurm
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$postprocess = <value>` with a process selector
[74/c8674e] Submitted process > mageck (48hIFNG_d04_HLA_high_vs_NoIFNG_d0)
ERROR ~ Error executing process > 'mageck (48hIFNG_d04_HLA_high_vs_NoIFNG_d0)'

Caused by:
  Process `mageck (48hIFNG_d04_HLA_high_vs_NoIFNG_d0)` terminated with an error exit status (1)

Command executed:

  prefilter_counts.R            counts_mageck_ctrls-grouped.txt                 "pmax(48hIFNG_d04_HLA_high,NoIFNG_d0)"          50 > counts_filtered.txt

  VERSION=$(mageck -v 2>&1 >/dev/null)

  if [ $VERSION = "0.5.5" ]; then

   mageck test                  --output-prefix 48hIFNG_d04_HLA_high_vs_NoIFNG_d0                       --count-table counts_filtered.txt                       --control-id NoIFNG_d0                         --treatment-id 48hIFNG_d04_HLA_high                     --norm-method median                    --adjust-method fdr                     --gene-lfc-method mean                         --normcounts-to-file
  else
   mageck test                  --output-prefix 48hIFNG_d04_HLA_high_vs_NoIFNG_d0                       --count-table counts_filtered.txt                       --control-id NoIFNG_d0                         --treatment-id 48hIFNG_d04_HLA_high                     --norm-method median                    --adjust-method fdr                     --gene-lfc-method mean                         --normcounts-to-file
  fi

Command exit status:
  1

Command output:
  (empty)

Command error:
  .command.stub: line 45: ps: command not found
  .command.stub: line 45: ps: command not found
  .command.stub: line 45: ps: command not found

  Attaching package: ‘dplyr’

  The following objects are masked from ‘package:stats’:

      filter, lag

  The following objects are masked from ‘package:base’:

      intersect, setdiff, setequal, union

  Parsed with column specification:
  cols(
    .default = col_integer(),
    id = col_character(),
    group = col_character()
  )
  See spec(...) for full column specifications.
  Error in parse(text = x) : <text>:1:8: unexpected symbol
  1: pmax(48hIFNG_d04_HLA_high
             ^
  Calls: %>% ... eval_bare -> .Call -> parse_expr -> parse_exprs -> parse
  Execution halted

Work dir:
  /groups/zuber/zubarchive/USERS/Kimon/markus/HLA1_staggered/work/74/c8674eaf6ff6d7d550c57c867ad3d3

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
FAILED