<commit_before>#!/bin/bash -eu
#$ -cwd -V
#$ -pe smp 2
#$ -l h_rt=12:00:00
#$ -l h_vmem=6G
#$ -R y
#$ -q all.q,bigmem.q

# <NAME> 2012-2016
# Runs FastQC on the supplied (at command line $1) .fastq or .fastq.gz file.
# Note parallelisation with FastQC is a waste of time as only works with
# multiple input files, and these are submited as diff SoGE jobs.
# Default run time is twelve hours, adjust if need be.

set -o pipefail
hostname
date

source ../GATKsettings.sh

LINE=$(awk "NR==$SGE_TASK_ID" $MASTER_LIST)
set $LINE
SAMP_ID=$1
RG=$2
FILE1=$3
FILE2=$4

B_NAME_F1=$(basename $FILE1)
B_NAME_F2=$(basename $FILE2)

echo "** Variables **"
echo " - BASE_DIR = $BASE_DIR"
echo " - G_NAME = $G_NAME"
echo " - MASTER_LIST = $MASTER_LIST"
echo " - LINE = $LINE"
echo " - SAMP_ID = $SAMP_ID"
echo " - RG = $RG"
echo " - FILE1 = $FILE1"
echo " - FILE2 = $FILE2"
echo " - B_NAME_F1 = $B_NAME_F1"
echo " - B_NAME_F2 = $B_NAME_F2"
echo " - PWD = $PWD"

echo "Copying input $FILE1 and $FILE2 to $TMPDIR/"
/usr/bin/time --verbose cp -v $FILE1 $TMPDIR/
/usr/bin/time --verbose cp -v $FILE2 $TMPDIR/

echo "Running FastQC on $TMPDIR/$FILE1 and $TMPDIR/$FILE2"
/usr/bin/time --verbose $FASTQC -t 2 $TMPDIR/$FILE1 $TMPDIR/$FILE2 --noextract -q -o $PWD -d $TMPDIR

echo "Deleting $TMPDIR/*.gz"
rm $TMPDIR/*.gz

date
echo "END"<commit_msg>Fix for file location<commit_after>#!/bin/bash -eu
#$ -cwd -V
#$ -pe smp 2
#$ -l h_rt=12:00:00
#$ -l h_vmem=6G
#$ -R y
#$ -q all.q,bigmem.q

# <NAME> 2012-2016
# Runs FastQC on the supplied (at command line $1) .fastq or .fastq.gz file.
# Note parallelisation with FastQC is a waste of time as only works with
# multiple input files, and these are submited as diff SoGE jobs.
# Default run time is twelve hours, adjust if need be.

set -o pipefail
hostname
date

source ../GATKsettings.sh

LINE=$(awk "NR==$SGE_TASK_ID" $MASTER_LIST)
set $LINE
SAMP_ID=$1
RG=$2
FILE1=$3
FILE2=$4

B_NAME_F1=$(basename $FILE1)
B_NAME_F2=$(basename $FILE2)

echo "** Variables **"
echo " - BASE_DIR = $BASE_DIR"
echo " - G_NAME = $G_NAME"
echo " - MASTER_LIST = $MASTER_LIST"
echo " - LINE = $LINE"
echo " - SAMP_ID = $SAMP_ID"
echo " - RG = $RG"
echo " - FILE1 = $FILE1"
echo " - FILE2 = $FILE2"
echo " - B_NAME_F1 = $B_NAME_F1"
echo " - B_NAME_F2 = $B_NAME_F2"
echo " - PWD = $<PASSWORD>"

echo "Copying input $FILE1 and $FILE2 to $TMPDIR/"
/usr/bin/time --verbose cp -v $FILE1 $TMPDIR/
/usr/bin/time --verbose cp -v $FILE2 $TMPDIR/

echo "Running FastQC on $TMPDIR/$B_NAME_FILE1 and $TMPDIR/$B_NAME_FILE2"
/usr/bin/time --verbose $FASTQC -t 2 $TMPDIR/$B_NAME_FILE1 $TMPDIR/$B_NAME_FILE2 --noextract -q -o $PWD -d $TMPDIR

echo "Deleting $TMPDIR/*.gz"
rm $TMPDIR/*.gz

date
echo "END"
{'fraction_non_alphanumeric': 0.15830546265328874, 'fraction_numerical': 0.032701597918989224, 'mean_word_length': 3.5938566552901023, 'pattern_counts': {'":': 0, '<': 6, '<?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': '6169532', 'n_tokens_mistral': 1187, 'n_tokens_neox': 1169, 'n_words': 336}