search

transcript / samsa2

SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.
GNU General Public License v3.0
53 stars 36 forks source link

Checkpoint TRIMMO #56

Closed mweberr closed 3 years ago

mweberr commented 3 years ago

Hi,

the first step of TRIMMING is repeated, probably because the checkpoint is not written.

the first checkpoint trimming is created at line 125 master_script.sh printf "TRIMMO\n" >>pipeline/checkpoints

All other checkpoints are written into printf "MERGING\n" >>$INPUT_DIR/checkpoints

Can you please explain shortly what the checkpoint is doing with the debug function ?

checked 

checked() {
  if [[ -n "$DRY_RUN" ]]; then
    debug "DRY RUN: $@"
    logstr "$@"
  else
    debug "Running $@"
    log "$@"
    status=$?
    if [[ $status -ne 0 ]]; then
      echo "'$@' exited with non-zero status $status" >&2
      exit $status
    fi
    debug "Finished running $@"
  fi
}
transcript commented 3 years ago

Hello, thanks for the catch on the TRIMMING not being properly written to the log file! I've corrected this.

For the debugging DRY RUN function, this prints a lot more content out to the log, including the date and time that different components start, which component is running at a time, and also whether any step fails.

I've submitted PR #56 to correct for the trimmomatic step.