runQiime.qsub

#!/bin/bash

#PBS -r n
#PBS -l walltime=180:00:00
#PBS -m bea
#PBS -M theajobreports@gmail.com

# need Xming to make plots


mappingFile=/home.westgrid/thea/CHILD/compare16S/data/stuart/mappingFileStuart_R1.txt
workDir=/home.westgrid/thea/CHILD/compare16S/qiime/myOldProtocol/R1noQC
referenceDB=/home.westgrid/thea/databases/qiime/greenGenes/gg_13_8_otus/rep_set/97_otus.fasta
paramFile=/home.westgrid/thea/CHILD/compare16S/qiime/myOldProtocol/qiimeParams.txt

echo "prog started at: `date`"

cd $workDir

# Pre-processing
echo "Check mapping file"
rm -rf mapping_output ; validate_mapping_file.py -m $mappingFile -o $workDir/mapping_output -v
mappingFile=$workDir/mapping_output/*_corrected.txt

echo "Make links to input sequences"
inputDir="$workDir/inputReads"
mkdir $inputDir
cd $inputDir
grep -v "^#" $mappingFile | cut -f 4 | sed 's/^/ln -s /' | sed 's/$/ ./' > makeLinkCmds.sh
bash makeLinkCmds.sh
cd $workDir

echo "Prepare amplicon sequences"
add_qiime_labels.py -i $inputDir -m $mappingFile -c InputFileName -n 1 -o $workDir/combinedInput

# otus
echo "Cluster sequences"
pick_open_reference_otus.py -o $workDir/otus -i $workDir/combinedInput/combined_seqs.fna -p $paramFile

cd otus
ln -s otu_table_mc2_w_tax_no_pynast_failures.biom otu_table.biom
cd ..

echo "Summarize biom file"
biom summarize-table -i $workDir/otus/otu_table.biom -o $workDir/otus/otu_table_summary.txt

echo "Make JSON version of biom file for phyloseq"
biom convert -i $workDir/otus/otu_table.biom -o $workDir/otus/otu_table_json.biom --table-type="OTU table" --to-json

echo "prog finished at: `date`"
echo "prog finished with error code: $?"