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| # cml template | ||
| # install ---- | ||
| chmod a+x install.sh | ||
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| time ./install.sh src/ bins/ | ||
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| # working directory ---- | ||
| cp="/working_dir" | ||
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| # Step 1 ---- | ||
| time ./bins/Step1_preparation \ | ||
| -i $cp"/dir_input_annotated/" \ | ||
| -o $cp"/test_op/Step1_pre_res.txt" | ||
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| # Step 2 ---- | ||
| time ./bins/Step2_simple_derep \ | ||
| -i $cp"/test_op/Step1_pre_res.txt" \ | ||
| -o $cp"/test_op/dereped" \ | ||
| -u 16 | ||
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| # Step 3 ---- | ||
| time ./bins/Step3_seq_concat \ | ||
| -i $cp"/test_op/dereped/" \ | ||
| -c $cp"/test_op/cated.fasta" | ||
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| # Step4 ---- | ||
| time ./bins/Step4_pre_cluster \ | ||
| -i $cp"/test_op/cated.fasta" \ | ||
| -d $cp"/test_op/dereped_cated.fasta" \ | ||
| -n $cp"/test_op/nr_genomes" \ | ||
| -l $cp"/test_op/seq_len.txt" \ | ||
| -p $cp"/test_op/pre_cluster.txt" \ | ||
| -u 16 | ||
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| # Step 5 ---- | ||
| time python3 ./bins/Step5_makeblastdb.py \ | ||
| -c makeblastdb \ | ||
| -i $cp"/test_op/nr_genomes" \ | ||
| -o $cp"/test_op/dbs" \ | ||
| -u 16 \ | ||
| -t nucl | ||
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| time python3 ./bins/Step5_reciprocal_blast.py \ | ||
| -c blastn \ | ||
| -i $cp"/test_op/dereped_cated.fasta" \ | ||
| -d $cp"/test_op/dbs" \ | ||
| -o $cp"/test_op/blast_op" \ | ||
| -e 1e-5 \ | ||
| -u 14 \ | ||
| -m off | ||
|
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| # Step 6 ---- | ||
| time ./bins/Step6_query_binning \ | ||
| -i $cp"/test_op/blast_op" \ | ||
| -o $cp"/test_op/query_binning" \ | ||
| -u 16 \ | ||
| -L 64 \ | ||
| -k off | ||
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| # Step 7 ---- | ||
| time ./bins/Step7_filter_n_bin \ | ||
| -i $cp"/test_op/query_binning" \ | ||
| -o $cp"/test_op/bin_op" \ | ||
| -s $cp"/test_op/seq_len.txt" \ | ||
| -p $cp"/test_op/pre_cluster.txt" \ | ||
| -L 48 -r 0.3 -u 16 -k off | ||
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| # Step 8 ---- | ||
| time ./bins/Step8_RBF \ | ||
| -i $cp"/test_op/bin_op" \ | ||
| -o $cp"/test_op/RBB_op" \ | ||
| -u 16 -L 32 -k off | ||
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| # Step 9 ---- | ||
| time ./bins/Step9_SLC \ | ||
| -i $cp"/test_op/RBB_op" \ | ||
| -o $cp"/test_op/SLC_1" \ | ||
| -u 16 \ | ||
| -S 1 | ||
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| time ./bins/Step9_SLC \ | ||
| -i $cp"/test_op/SLC_1" \ | ||
| -o $cp"/test_op/SLC_final" \ | ||
| -p $cp"/test_op/pre_cluster.txt" \ | ||
| -u 16 \ | ||
| -S all | ||
|
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| # Step 10, 200 genomes participates analysis ---- | ||
| time ./bins/Step10_write_clusters \ | ||
| -i $cp"/test_op/SLC_final/0.txt" \ | ||
| -o $cp"/test_op/write_fasta" \ | ||
| -f $cp"/test_op/cated.fasta" \ | ||
| -c 200 \ | ||
| -t strict,surplus,accessory \ | ||
| -u 16 |