<commit_before>#!/bin/bash
#SBATCH -J s7_baseRecal
#SBATCH -A uoo00053         # Project Account
#SBATCH --time=15:00:00     # Walltime
#SBATCH --mem-per-cpu=31024  # memory/cpu (in MB)
#SBATCH --cpus-per-task=1   # 12 OpenMP Threads
#SBATCH --mail-user=<EMAIL>
#SBATCH --mail-type=ALL
#SBATCH -C sb

# <NAME>
# University of Otago
# 20 Oct 2015

# <NAME>
# University of Otago
# Jun 2016

export OPENBLAS_MAIN_FREE=1

#i=SLURM_ARRAY_TASK_ID
sample=FR07921700
i=$2
#echo slurm jobib = $SLURM_JOBID > $SLURM_SUBMIT_DIR/dirs.txt
#echo slurm submit dir = $SLURM_SUBMIT_DIR >> $SLURM_SUBMIT_DIR/dirs.txt
#echo slurm tmp dir = $TMP_DIR >> $SLURM_SUBMIT_DIR/dirs.txt

#DIR=$SLURM_SUBMIT_DIR
DIR=~/uoo00053/working/
GATK=~/uoo00053/GATK3.6/GenomeAnalysisTK.jar
module load Java/1.8.0_5

DBSNP=~/uoo00053/reference_files/dbsnp_138.b37.vcf.gz
MILLS=~/uoo00053/reference_files/Mills_and_1000G_gold_standard.indels.b37.vcf
INDELS=~/uoo00053/reference_files/1000G_phase1.indels.b37.vcf
REF=~/uoo00053/reference_files/hs37d5/hs37d5.fa

if ! srun java -Xmx30g -jar $GATK \
	-T BaseRecalibrator \
	-R $REF \
	-I ~/uoo00053/working/${sample}_realigned_reads_${i}.bam \
	-o ~/uoo00053/working/${sample}_recal_data${i}.grp \
	-knownSites $DBSNP \
	-knownSites $MILLS \
	-knownSites $INDELS \
	-l INFO \
	-cov ReadGroupCovariate \
	-cov QualityScoreCovariate \
	-cov CycleCovariate \
	-cov ContextCovariate \
	-log ~/uoo00053/working/${sample}_baserecal${i}.log \
	-L ${i} ; then

	echo "base recal on chr $i failed"
	exit 1
fi
sbatch -J s8_applyrecal_chr${i} ~/NeSI_GATK/s8_applyrecal.sl $sample $i<commit_msg>removed .gz from dbsnp need a new file after old one became corrupt<commit_after>#!/bin/bash
#SBATCH -J s7_baseRecal
#SBATCH -A uoo00053         # Project Account
#SBATCH --time=15:00:00     # Walltime
#SBATCH --mem-per-cpu=31024  # memory/cpu (in MB)
#SBATCH --cpus-per-task=1   # 12 OpenMP Threads
#SBATCH --mail-user=<EMAIL>
#SBATCH --mail-type=ALL
#SBATCH -C sb

# <NAME>
# University of Otago
# 20 Oct 2015

# <NAME>
# University of Otago
# Jun 2016

export OPENBLAS_MAIN_FREE=1

#i=SLURM_ARRAY_TASK_ID
sample=FR07921700
i=$1
#echo slurm jobib = $SLURM_JOBID > $SLURM_SUBMIT_DIR/dirs.txt
#echo slurm submit dir = $SLURM_SUBMIT_DIR >> $SLURM_SUBMIT_DIR/dirs.txt
#echo slurm tmp dir = $TMP_DIR >> $SLURM_SUBMIT_DIR/dirs.txt

#DIR=$SLURM_SUBMIT_DIR
DIR=~/uoo00053/working/
GATK=~/uoo00053/GATK3.6/GenomeAnalysisTK.jar
module load Java/1.8.0_5

DBSNP=~/uoo00053/reference_files/dbsnp_138.b37.vcf
MILLS=~/uoo00053/reference_files/Mills_and_1000G_gold_standard.indels.b37.vcf
INDELS=~/uoo00053/reference_files/1000G_phase1.indels.b37.vcf
REF=~/uoo00053/reference_files/hs37d5/hs37d5.fa

if ! srun java -Xmx30g -jar $GATK \
	-T BaseRecalibrator \
	-R $REF \
	-I ~/uoo00053/working/${sample}_realigned_reads_${i}.bam \
	-o ~/uoo00053/working/${sample}_recal_data${i}.grp \
	-knownSites $DBSNP \
	-knownSites $MILLS \
	-knownSites $INDELS \
	-l INFO \
	-cov ReadGroupCovariate \
	-cov QualityScoreCovariate \
	-cov CycleCovariate \
	-cov ContextCovariate \
	-log ~/uoo00053/working/${sample}_baserecal${i}.log \
	-L ${i} ; then

	echo "base recal on chr $i failed"
	exit 1
fi
sbatch -J s8_applyrecal_chr${i} ~/NeSI_GATK/s8_applyrecal.sl $sample $i
{'fraction_non_alphanumeric': 0.1384853168469861, 'fraction_numerical': 0.07418856259659969, 'mean_word_length': 4.22778675282714, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 19, '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': '4284662', 'n_tokens_mistral': 1630, 'n_tokens_neox': 1462, 'n_words': 261}