/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
Assign taxonomy
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%)
Convert into useful form:
awk -F "\t" '{OFS=","} NR==1 {print "OTU_ID","SEQS","SIZE","DOMAIN","KINGDOM","PHYLUM","CLASS","ORDER","FAMILY","GENUS","SPECIES"} {gsub(";", ","); gsub("centroid=", ""); gsub("seqs=", ""); gsub("size=", ""); match($4, /d:[^,]+/, d); match($4, /k:[^,]+/, k); match($4, /p:[^,]+/, p); match($4, /c:[^,]+/, c); match($4, /o:[^,]+/, o); match($4, /f:[^,]+/, f); match($4, /g:[^,]+/, g); match($4, /s:[^,]+/, s); print $1, d[0]=="" ? "NA" : d[0], k[0]=="" ? "NA" : k[0], p[0]=="" ? "NA" : p[0], c[0]=="" ? "NA" : c[0], o[0]=="" ? "NA" : o[0], f[0]=="" ? "NA" : f[0], g[0]=="" ? "NA" : g[0], s[0]=="" ? "NA" : s[0] }' LRII.sintax > LRIItaxonomy.csv