/project/microbiome/data_queue/seq/LowReadII/rawdata
salloc --account=microbiome -t 0-06:00
mkdir -p /gscratch/grandol1/LowReadII/rawdata
cd /gscratch/grandol1/LowReadII/rawdata
unpigz --to-stdout /project/microbiome/data_queue/seq/LowReadII/rawdata/Low-Read-II_S1_L001_R1_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - LowReadII_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/LowReadII/rawdata/Low-Read-II_S1_L001_R2_001.fastq | split -l 1000000 -d --suffix-length=3 --additional-suffix=.fastq - LowReadII_R2_
//project/microbiome/data_queue/seq/LowReadII/rawdata/run_parse_count_onSplitInput.pl
cd /project/microbiome/data_queue/seq/LowReadII/rawdata
./run_splitFastq_fwd.sh
./run_splitFastq_rev.sh
./run_aggregate.sh
cd /project/microbiome/data_queue/seq/LowReadII/tfmergedreads
./run_slurm_mergereads.pl
cd /project/microbiome/data_queue/seq/LowReadII/otu
./run_slurm_mkotu.pl
vsearch -sintax OTUFILE -db REFERENCEDATABASE -tabbedout OUTPUT -sintax_cutoff 0.8 -strand both -threads 32
salloc --account=microbiome -t 0-02:00 --mem=500G
module load swset/2018.05 gcc/7.3.0
module load vsearch/2.15.1
vsearch --sintax zotus.fa --db /project/microbiome/users/grandol1/ref_db/gg_16s_13.5.fa -tabbedout LRII.sintax -sintax_cutoff 0.8
Output:
Reading file /project/microbiome/users/grandol1/ref_db/gg_16s_13.5.fa 100%
1769520677 nt in 1262986 seqs, min 1111, max 2368, avg 1401
Counting k-mers 100%
Creating k-mer index 100%
Classifying sequences 100%
Classified 4038 of 4042 sequences (99.90%)