...
In /project/microbiome/data_queue/seq/*/coligoIS or /project/microbiome/data/seq/*/coligoISD, there are 16S and ITS directories for all projects. These contain a file named coligoISDtable.txt with counts of the coligos and the ISD found in the trimmed forward reads, per sample. The file run_slurm_mkcoligoISDtable.pl has the code that passes over all of the projects and uses vsearch for making the table.
Repeat All above steps for ITS with noted changes
Add protected or 16S as appropriate to creations from last run through:
mv 16S protected16S
This will avoid needless double processing while keeping everything together as typical
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mkdir -p /gscratch/grandol1/ReRun3/rawdata
cd /gscratch/grandol1/ReRun3/rawdata
unpigz --to-stdout /project/microbiome/data_queue/seq/ReRun3/rawdata/ReRun3_ITS_S1_R1_001.fastq.gz | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - ReRun3_R1_ ;
unpigz --to-stdout /project/microbiome/data_queue/seq/ReRun3/rawdata/ReRun3_ITS_S1_R2_001.fastq.gz | split -l 16000000 -d --suffix-length=3 --additional-suffix=.fastq - ReRun3_R2_ |