module load swset/2018.05
module load gcc/7.3.0
module load usearch/10.0.240
module load perl-text-levenshtein-xs
perl //project/microbiome/data_queue/seq/5CM/rawdata/parse_count.pl 5CMDemux.csv 5CM_S1_L001_R1_001.fastq 5CM_S1_L001_R2_001.fastq M01247
./run_splitFastq_fwd.sh
./run_splitFastq_rev.sh
./run_aggregate.sh
salloc --account=microbiome -t 0-05:00
module load swset/2018.05 gcc/7.3.0 usearch/10.0.240 perl-txt-levenshtein-xs
mkdir -p /gscratch/grandol1/5CM/rawdata
cd /gscratch/grandol1/5CM/rawdata
unpigz --to-stdout /project/microbiome/data_queue/seq/5CM/rawdata/5CM_S1_L001_R1_001.fastq | split -l 13000000 -d --suffix-length=3 --additional-suffix=.fastq - 5CM_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/5CM/rawdata/5CM_S1_L001_R2_001.fastq | split -l 13000000 -d --suffix-length=3 --additional-suffix=.fastq - 5CM_R2_
cd /project/microbiome/data_queue/seq/5CM/rawdata
perl //project/microbiome/data_queue/seq/5CM/rawdata/run_parse_count_onSplitInput.pl 5CMDemux.csv
./run_splitFastq_fwd.sh
./run_splitFastq_rev.sh
./run_aggregate.sh