<commit_before>. ./common.sh

module load gnumap/3.0.2

export GNUMAPS=/home/brentp/src/gnumap/gnumaps
PATH=$PATH:$GNUMAPS/bin:$GNUMAPS/scripts/
export PATH
# taken from gnumap-bs paper
cmd="gnumaps.pl --genome $REF --lib_type wt1 --acc 0.9 --nt_conv bs --num_threads 8 --outdir"

zless $FQ1 > $$.r1.tmp
zless $FQ2 > $$.r2.tmp

rm -f logs/gnumap-$name.err logs/gnumap-$name.out
echo "$cmd results/gnumapbs-$name/ --pair_1 $$.r1.tmp --pair_2 $$.r2.tmp" \
    | bsub -J gnumap-$name \
                 -e logs/gnumap-$name.err \
                 -o logs/gnumap-$name.out -n 8

exit;

rm -f logs/trim-gnumap-$name.err logs/trim-gnumap-$name.out
echo "$cmd results/trim/gnumapbs-$name/ --pair_1 $$.r1.tmp --pair_2 $$.r2.tmp" \
    | bsub -J trim-gnumap-$name \<commit_msg>update gnumap (still not working)<commit_after>. ./common.sh

module load gnumap

#export GNUMAPS=/home/brentp/src/gnumap/gnumaps
#PATH=$PATH:$GNUMAPS/bin:$GNUMAPS/scripts/
#export PATH
# taken from gnumap-bs paper
REF=/misc2/$REF
cmd="gnumaps.pl --genome $REF --lib_type wt1 --acc 0.9 --nt_conv bs --num_threads 8 --outdir"

zless $FQ1 > $$.r1.tmp
zless $FQ2 > $$.r2.tmp

rm -f logs/gnumap-$name.err logs/gnumap-$name.out
echo "$cmd results/gnumapbs-$name/ --pair_1 $$.r1.tmp --pair_2 $$.r2.tmp" \
    | bsub -J gnumap-$name \
                 -R "rusage[mem=42000]" \
                 -e logs/gnumap-$name.err \
                 -o logs/gnumap-$name.out -n 8

exit;

rm -f logs/trim-gnumap-$name.err logs/trim-gnumap-$name.out
echo "$cmd results/trim/gnumapbs-$name/ --pair_1 $$.r1.tmp --pair_2 $$.r2.tmp" \
    | bsub -J trim-gnumap-$name \
{'fraction_non_alphanumeric': 0.18435754189944134, 'fraction_numerical': 0.02669149596523898, 'mean_word_length': 2.5119825708061003, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 7, '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': '885420', 'n_tokens_mistral': 712, 'n_tokens_neox': 678, 'n_words': 141}