From 16f2f4d0ff2028766752e2b5580b339c856b9469 Mon Sep 17 00:00:00 2001 From: Yu Wan Date: Sat, 24 Nov 2018 22:30:02 +1100 Subject: [PATCH] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 0c039cb..efb69c6 100644 --- a/README.md +++ b/README.md @@ -111,7 +111,7 @@ This is a special case of calling the best alleles for a panel of seven genes gi An example command is: ``` -python screener\_slurm.py --walltime '0-1:0:0' --outdir mlst --script screener.py --assemblies assemblies/*.fasta --gene_db mlst_db.fasta --prefix test --suffix ".fasta" --report_all_consensus --mlst > mlst.log +python screener_slurm.py --walltime '0-1:0:0' --outdir mlst --script screener.py --assemblies assemblies/*.fasta --gene_db mlst_db.fasta --prefix test --suffix ".fasta" --report_all_consensus --mlst > mlst.log ``` ### 3. Screening for all valid alleles per gene @@ -127,7 +127,7 @@ python screener.py --gene_db ARGannot_r2.fasta --prefix demo1 --suffix '_spades. A parallel version for a large number of assemblies ``` -python screener\_slurm.py --script screener.py --algorithm megablast --walltime "0-0:30:0" --memory 1024 --partition project1 --bundle_name_prefix test --bundle_size 16 --outdir genes --assemblies data/assemblies/*.fasta --prefix demo2 --suffix '_spades.fasta' --gene_db ARGannot_r2.fasta --other_args "--incl_alt --max_overlapping_nt 0 --report_all_consensus" > gene_screen.log +python screener_slurm.py --script screener.py --algorithm megablast --walltime "0-0:30:0" --memory 1024 --partition project1 --bundle_name_prefix test --bundle_size 16 --outdir genes --assemblies data/assemblies/*.fasta --prefix demo2 --suffix '_spades.fasta' --gene_db ARGannot_r2.fasta --other_args "--incl_alt --max_overlapping_nt 0 --report_all_consensus" > gene_screen.log ``` **Example output table**