<p>Hi,</p>

<p>I&#39;m having trouble removing duplicates using Picard tools on SOLiD data. I get a regex not matching error.</p>

<p>The reads have the following names:</p>

<pre>
22_758_632_F3

604_1497_576

124_1189_1519_F5

358_1875_702_F5-DNA</pre>

<p>And I don&#39;t think Picard tools is able to pick these read names with its default regex.</p>

<p>I tried to change the default regex. This time it does not throw an error, but it takes too long and times out (out of memory). I suspect I&#39;m not giving the right regex. Here is my command:</p>

<pre>
java -jar $PICARD_TOOLS_HOME/MarkDuplicates.jar I=$FILE O=$BAMs/MarkDuplicates/$SAMPLE.MD.bam M=$BAMs/MarkDuplicates/$SAMPLE.metrics READ_NAME_REGEX=&quot;([0-9]+)_([0-9]+)_([0-9]+).*&quot;</pre>

<p>Any help is appreciated. Thanks!</p>

<p>I was able to fix the issue, by adding -<code>Xmx16g</code> and increasing the RAM size. Apparently the RAM was not sufficient.</p>
