<commit_before>#!/bin/bash
#
#PBS -N clinomics
#PBS -m e
#
NOW=$(date +"%H%M%S_%m%d%Y")
module load snakemake
wd=analysis_602
cd $wd

export SERPENTINE_HOME=/data/CCRBioinfo/zhujack/projects/serpentine
snakemake --jobname 's.{jobid}.{rulename}' \
  -d $wd \
  -s ../Snakefile \
  --js $SERPENTINE_HOME/jobscript.sh \
  -k -r -p -w 10 \
  -T --rerun-incomplete \
  --stats serpentine_${NOW}.stats \
  -j 3000 --cluster 'qsub -q ccr {params.batch}' \
  >& serpentine_${NOW}.log 

# snakemake -n --forceall --rulegraph | /home/zhujack/bin/dot -Tpng > clinomics_rulegraph.png<commit_msg>Removed some absolute paths from submit.sh<commit_after>#!/bin/bash
#
#PBS -N clinomics
#PBS -m e
#
NOW=$(date +"%H%M%S_%m%d%Y")
module load snakemake
cd $PBS_O_WORKDIR

export SERPENTINE_HOME='.'
snakemake --jobname 's.{jobid}.{rulename}' \
  -d $wd \
  -s ../Snakefile \
  --js $SERPENTINE_HOME/jobscript.sh \
  -k -r -p -w 10 \
  -T --rerun-incomplete \
  --stats serpentine_${NOW}.stats \
  -j 3000 --cluster 'qsub -q ccr {params.batch}' \
  >& serpentine_${NOW}.log 

{'fraction_non_alphanumeric': 0.18578199052132702, 'fraction_numerical': 0.014218009478672985, 'mean_word_length': 3.045977011494253, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 6, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5508097', 'n_tokens_mistral': 496, 'n_tokens_neox': 456, 'n_words': 96}