File: step3_sam2marker.sh

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metaphlan2 2.6.0%2Bds-2
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#!/bin/bash
mkdir -p consensus_markers
cwd=$(pwd -P)
export PATH=${cwd}/../strainphlan_src:${PATH}
python ../strainphlan_src/sample2markers.py --ifn_samples sams/*.sam.bz2 --input_type sam --output_dir consensus_markers --nprocs 10 &> consensus_markers/log.txt