1st Attempt:
cat ./*_R1_001.fastq > 5RM1_R1.fastq
cat ./*_R2_001.fastq > 5RM1_R2.fastq
gzip 5RM1_R1.fastq
gzip 5RM1_R2.fastq
mkdir -p /gscratch/grandol1/loc_ad2/rawdata
cd /gscratch/grandol1/loc_ad2/rawdata
unpigz --to-stdout /project/microbiome/data_queue/seq/loc_ad2/rawdata/5RM1_R1.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - 5RM1_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/loc_ad2/rawdata/5RM1_R2.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - 5RM1_R2_
//project/microbiome/data_queue/seq/loc_ad2/rawdata/run_parse_count_onSplitInput.pl
cd /project/microbiome/data_queue/seq/loc_ad2/rawdata
./run_splitFastq_fwd.sh
./run_splitFastq_rev.sh
./run_aggregate.sh
cd /project/microbiome/data_queue/seq/loc_ad1/rawdata/sample_fastq/16S/loc_ad2
rename $'\r' '' *
cd /project/microbiome/data_queue/seq/loc_ad2/tfmergedreads
./run_slurm_mergereads.pl
cd /project/microbiome/data_queue/seq/loc_ad2/otu
./run_slurm_mkotu.pl