From 219089f941e6163d60ce83f45b685cf398b9f2d1 Mon Sep 17 00:00:00 2001
From: Jingchao Zhang <jzhang30@unl.edu>
Date: Fri, 19 Apr 2019 15:55:59 +0000
Subject: [PATCH] Update running_blast_alignment.md
---
.../alignment_tools/blast/running_blast_alignment.md | 2 ++
1 file changed, 2 insertions(+)
diff --git a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
index 6423e3f0..a3b03c7a 100644
--- a/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
+++ b/content/guides/running_applications/bioinformatics_tools/alignment_tools/blast/running_blast_alignment.md
@@ -56,6 +56,7 @@ If you want to create and use a BLAST database that is not mentioned above, chec
Basic SLURM example of nucleotide BLAST run against the non-redundant **nt** BLAST database with `8 CPUs` is provided below. When running BLAST alignment, it is recommended to first copy the query and database files to the **/scratch/** directory of the worker node. Moreover, the BLAST output is also saved in this directory (**/scratch/blastn_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
{{% notice info %}}
**Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+**This example will first copy your database to faster local storage called “scratch”. This can greatly improve performance!**
{{% /notice %}}
{{% panel header="`blastn_alignment.submit`"%}}
@@ -95,6 +96,7 @@ The default BLAST output is in pairwise format. However, BLAST’s parameter **-
Basic SLURM example of protein BLAST run against the non-redundant **nr **BLAST database with tabular output format and `8 CPUs` is shown below. Similarly as before, the query and database files are copied to the **/scratch/** directory. The BLAST output is also saved in this directory (**/scratch/blastx_output.alignments**). After BLAST finishes, the output file is copied from the worker node to your current work directory.
{{% notice info %}}
**Please note that the worker nodes can not write to the */home/* directories and therefore you need to run your job from your */work/* directory.**
+**This example will first copy your database to faster local storage called “scratch”. This can greatly improve performance!**
{{% /notice %}}
{{% panel header="`blastx_alignment.submit`"%}}
--
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