<p>Your link with those command line options is 1 year old.  Looks like that version of bwa is 6 years old.  You probably should update.</p>

CC BY-SA 4.0
2020-10-12T05:17:58.757Z
2020-10-12T05:17:58.757Z
swbarnes2
<p>I'm trying to run bwa on HiC data. This is the command I'm giving:</p>
<pre><code>bwa mem -5SP -T0 -t4 -R '@RG\tID:\tSM:\tLB:\tPL:ILLUMINA\tPU:none' REFERENCE.fa PAIR1.fq PAIR2.fq
</code></pre>
<p>and here's the error message:</p>
<pre><code>mem: illegal option -- 5
</code></pre>
<p>Supposedly, the 5SP option is for HiC data (<a href="https://phasegenomics.github.io/2019/09/19/hic-alignment-and-qc.html" rel="nofollow noreferrer">cite</a>), but my BWA isn't recognizing it. Anybody have any ideas? My initial thought is to update BWA to the newest version, but I don't want to mess with our replicatibility since I am new to the lab and don't want to be updating software when I don't need to. The server is a Mac Pro and bwa version is 0.7.12-r1039. Thanks.</p>

CC BY-SA 4.0
2020-10-12T09:29:34.497Z
You can use `conda` to install and test the desired version of `bwa` to test. This will not interfere with whatever version installed on the server.
haci
<bwa><hi-c>
BWA doesn't recognize HiC options
# BWA doesn't recognize HiC options

(Asked by: username_0 on 2020-10-12)

I'm trying to run bwa on HiC data. This is the command I'm giving:
bwa mem -5SP -T0 -t4 -R '@RG\tID:\tSM:\tLB:\tPL:ILLUMINA\tPU:none' REFERENCE.fa PAIR1.fq PAIR2.fq

and here's the error message:
mem: illegal option -- 5

Supposedly, the 5SP option is for HiC data (cite), but my BWA isn't recognizing it. Anybody have any ideas? My initial thought is to update BWA to the newest version, but I don't want to mess with our replicatibility since I am new to the lab and don't want to be updating software when I don't need to. The server is a Mac Pro and bwa version is 0.7.12-r1039. Thanks.

**Tags:** bwa, hi-c
> **Comments:**
> **username_1**: You can use `conda` to install and test the desired version of `bwa` to test. This will not interfere with whatever version installed on the server.  

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## 1 answers

### Answer by username_2 on 2020-10-12. Score: 3

Your link with those command line options is 1 year old. Looks like that version of bwa is 6 years old. You probably should update.


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