---
# System prepended metadata

title: 'BTK Enoplus (putatively E.communis, to be confirmed...)'

---

# BTK Enoplus (putatively E.communis, to be confirmed...)

```

wkdir=/lustre/scratch123/tol/teams/blaxter/users/ek5/SW9/E2
assembly=$wkdir/E2_hifiasm.bp.p_ctg.fa
tolid=neEnoComm
cd $wkdir
mkdir -p $wkdir/btk
#cp assembly & rename
bgzip -c $assembly > btk/${tolid}.fasta.gz

#cp reads & rename
ln -s /lustre/scratch123/tol/teams/blaxter/users/ek5/SW9/E2/E2_hifi_reads.fasta.gz btk/m6e.fasta.gz


cd btk

unset PERL5LIB
unset PYTHONPATH
export LD_LIBRARY_PATH=/software/python-3.7.4/lib/:${LD_LIBRARY_PATH}
export PYTHONPATH=/software/grit/lib/python3_lib:${PYTHONPATH}
export PERL5LIB=/software/grit/projects/vr-runner/modules:${PERL5LIB}

/usr/bin/perl /nfs/team135/yy5/btk_config/run-btkconfig_v264 +loop 30 -b -s neEnoComm -t 'Enoplus communis' -o . -z config_done -r E2_hifiasm.bp.p_ctg.fa #takes time


# Remove some unneccessary BUSCO sets if preferred but keep the ones in basal lineages
vim config.yaml #You can make insert mode by pressing the i key.
#To exit, First, you need to switch to command mode. This can be done by hitting the Esc key. Next, you can type the following commands:
#:q to quit.
#:q! to quit without saving data/file.
#:x save and quit.
#:qa to quit all open files.

mkdir -p /lustre/scratch123/tol/teams/blaxter/btk_runs/data/neEnoComm
#mkdir -p /lustre/scratch123/tol/teams/blaxter/btk_runs/results
cp config.yaml /lustre/scratch123/tol/teams/blaxter/btk_runs/data/neEnoComm
cd /lustre/scratch123/tol/teams/blaxter/btk_runs/data
# Do not copy the script:
#--cp /nfs/team135/yy5/btk_sig/run_pipeline.sh .
# edited memory and working directories
ASSEMBLY=neEnoComm TRANSFER=true bsub < run_pipeline_team301.sh

# This will return a job_id
# The job_id will be btk.$job_id.err
#check progress, pressing double tab to get btk error file name...
less /lustre/scratch123/tol/teams/blaxter/btk_runs/data/btk.992904.err

```
