CBW IMPACTT Metagenome sequence data analysis with MMSeqs2 and JarrVis

conda activate functional
cd workspace/metagenome_workshop
mkdir mmseqs_U90_out

parallel -j 1 'mmseqs createdb {} mmseqs_U90_out/mmseqs-{/.}queryDB' ::: cat_reads/*

#parallel -j 1 'mmseqs search mmseqs_U90_out/mmseqs-{/.}queryDB ~/CourseData/MIC_data/metagenome_data/MMSeqs2_db/mmseqsUniref90DB mmseqs_U90_out/mmseqs-{/.}resultDB tmp --db-load-mode 3 --threads 4 --max-seqs 25 -s 1 -a -e 1e-5 > /dev/null 2>&1' ::: cat_reads/*
#parallel -j 1 'mmseqs convertalis mmseqs_U90_out/mmseqs-{/.}queryDB MMSeqs2_db/mmseqsUniref90DB mmseqs_U90_out/mmseqs-{/.}resultDB mmseqs_U90_out/mmseqs-{/.}-s1.m8 --db-load-mode 2 > /dev/null 2>&1' ::: cat_reads/*
mkdir mmseqs_m8_files
ln -s ~/CourseData/MIC_data/metagenome_data/mmseqs_U90_out/*.m8 mmseqs_m8_files/

mkdir mmseqs_U90_out_tophit
cp -r ~/CourseData/MIC_data/metagenome_data/Functional_Helper_Scripts/ .
python Functional_Helper_Scripts/pick_uniref_top_hit.py --unirefm8Dir mmseqs_m8_files --output_path mmseqs_U90_out_tophit

cp ~/CourseData/MIC_data/metagenome_data/multi-sample-outfiles-w-m8.txt .
ln -s ~/CourseData/MIC_data/metagenome_data/MMSeqs2_db/*.pbz2 .

#python Functional_Helper_Scripts/parse_TaxonomyFunction.py --multisample multi-sample-outfiles-w-m8.txt --outputf Workshop_strat_matrix_RPKM.txt --stratified Y --map2EC Y
ln -s ~/CourseData/MIC_data/metagenome_data/Workshop_strat_matrix_RPKM.txt .
python add_descriptions.py