<div dir="ltr">What is the output of `ls kak.group*.pe.fa.gz`?<br><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jan 8, 2014 at 4:42 PM, Yiseul Kim <span dir="ltr"><<a href="mailto:kimyise2@msu.edu" target="_blank">kimyise2@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">I already reflected the change of naming scheme… Sorry that I did not mention this earlier.<div class="gmail_extra">
<br clear="all"><div><div dir="ltr"><div><span style="color:rgb(102,102,102);font-size:small">Regards,</span><br>
</div><div><font color="#666666">Yiseul</font></div></div></div><div><div class="h5">
<br><br><div class="gmail_quote">On Wed, Jan 8, 2014 at 4:36 PM, Michael R. Crusoe <span dir="ltr"><<a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Okay, then you need to modify the fourth line of your script to reflect the change you made to the naming scheme:<div><br></div><div>" if [ -e ${groupid}.pe.fa.gz ]; then"<div><div><br></div>
</div>
<div class="gmail_extra"><div><div><br><div class="gmail_quote">On Wed, Jan 8, 2014 at 4:15 PM, Yiseul Kim <span dir="ltr"><<a href="mailto:kimyise2@msu.edu" target="_blank">kimyise2@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">Yes, velvet assembly files are named in that way except "fa" instead of "<span>fq</span>" not to get confused as the files are <span>fasta</span> format. I am around the campus and can stop by your office if you mind emails back and forth. Thanks for your help!<br>
<div class="gmail_extra"><br clear="all"><div><div dir="ltr"><div><span style="color:rgb(102,102,102);font-size:small">Regards,</span><br></div><div><font color="#666666"><span>Yiseul</span></font></div></div>
</div><div><div>
<br><br><div class="gmail_quote">On Wed, Jan 8, 2014 at 3:54 PM, Michael R. Crusoe <span dir="ltr"><<a href="mailto:mcrusoe@msu.edu" target="_blank"><span>mcrusoe</span>@<span>msu</span>.<span>edu</span></a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><br><div class="gmail_quote">
<div>On Sat, Jan 4, 2014 at 10:26 AM, Yiseul Kim <span dir="ltr"><<a href="mailto:kimyise2@msu.edu" target="_blank">kimyise2@msu.edu</a>></span> wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi Michael,<div><br></div><div>
<div>I am sorry for my late reply. Thanks for your help again!</div>
<div><br></div><div>Yes, assemstats3.py worked.</div><div><br></div><div>I am running all of this in a directory named assembly created on HPCC.</div>
<div><br></div><div>When I ran the command you asked, the output says "cat: grouplist.txt: No such file or directory".</div></div></div></blockquote><div><br></div><div><br></div><div>Are your velvet assembly files named in the format "kak.groupNNNN.pe.fq.gz" where NNNN is a four digit number between 0 and 1,000 inclusive?<br>
</div><div><div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div class="gmail_extra">
<br clear="all"><div><div dir="ltr"><div><span style="color:rgb(102,102,102);font-size:small">Regards,</span><br>
</div><div><font color="#666666">Yiseul</font></div></div></div><div><div>
<br><br><div class="gmail_quote">On Fri, Jan 3, 2014 at 6:05 PM, Michael R. Crusoe <span dir="ltr"><<a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">Does the invocation of assemstats3.py work?<div><br></div><div>This is being run in <span style="line-height:15px;color:rgb(102,102,102)">/</span><span style="color:rgb(51,51,51);line-height:15px">mnt</span><span style="line-height:15px;color:rgb(102,102,102)">/</span><span style="color:rgb(51,51,51);line-height:15px">assembly, yes?</span></div>
<div><span style="color:rgb(51,51,51);line-height:15px"><br></span></div><div><font color="#333333"><span style="line-height:15px">What is the output of this command?</span></font></div><div><font color="#333333"><span style="line-height:15px"><br>
</span></font></div><div>for group in $(cat grouplist.txt); do echo '$group.*velvet.*.d/contigs.fa'; ls $group.*velvet.*.d/contigs.fa; done</div></div><div><div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Fri, Jan 3, 2014 at 5:11 PM, Yiseul Kim <span dir="ltr"><<a href="mailto:kimyise2@msu.edu" target="_blank">kimyise2@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Thanks for your help in advance!<div><br></div>
<div>Basically, I am following the Kalamazoo metagenomic assembly protocol with my viral metagenomic dataset. In the assembly step, the protocol runs dataset with three different assemblers but I wanted to test only with the velvet. I am not an expert on writing a script and trying to modify the one below only for velvet output by deleting the part underlined. When I ran it, the error message says "too few arguments". Could you help me with modifying the script only from one assembler? Please let me know if I am not making myself clear.</div>
<div><br></div><div><pre style="padding:5px;background-color:rgb(238,255,204);color:rgb(51,51,51);line-height:15px;border-top-width:1px;border-bottom-width:1px;border-style:solid none;border-top-color:rgb(170,204,153);border-bottom-color:rgb(170,204,153)">
for i in {0..1000};
do
groupid=$(printf kak.group%04d $i);
if [ -e ${groupid}.pe.fq.gz ]; then
echo $groupid
fi
done > grouplist.txt
for group in $(cat grouplist.txt)
do
python /usr/local/share/khmer/sandbox/calc-best-assembly.py -q $group.{*velvet.*.d/contigs.fa<u>,*idba.d/scaffold.fa,*spades.d/contigs.fasta</u>} -o $group.best.fa
done > best-assemblies.txt
python /usr/local/share/khmer/sandbox/multi-rename.py testasm *.best.fa > final-assembly.fa</pre></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><div><span style="color:rgb(102,102,102);font-size:small">Regards,</span><br>
</div><div><font color="#666666">Yiseul</font></div></div></div><div><div>
<br><br><div class="gmail_quote">On Fri, Jan 3, 2014 at 4:57 PM, Michael R. Crusoe <span dir="ltr"><<a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">Please :-)</div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jan 3, 2014 at 4:40 PM, Yiseul Kim <span dir="ltr"><<a href="mailto:kimyise2@msu.edu" target="_blank">kimyise2@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi Michael,<div><br></div><div>Can I ask one more question for you?</div>
</div><div class="gmail_extra">
<br clear="all"><div><div dir="ltr"><div><span style="color:rgb(102,102,102);font-size:small">Regards,</span><br>
</div><div><font color="#666666">Yiseul</font></div></div></div><div><div>
<br><br><div class="gmail_quote">On Fri, Jan 3, 2014 at 4:16 PM, Michael R. Crusoe <span dir="ltr"><<a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">You are welcome!</div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Jan 3, 2014 at 4:14 PM, Yiseul Kim <span dir="ltr"><<a href="mailto:kimyise2@msu.edu" target="_blank">kimyise2@msu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Thanks!</div><div class="gmail_extra"><br clear="all">
<div><div dir="ltr"><div><span style="color:rgb(102,102,102);font-size:small">Regards,</span><br>
</div><div><font color="#666666">Yiseul</font></div></div>
</div><div><div>
<br><br><div class="gmail_quote">On Fri, Jan 3, 2014 at 4:11 PM, Michael R. Crusoe <span dir="ltr"><<a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div dir="ltr">It is in the protocols-v0.8.3 branch of khmer:<div><br></div><div><a href="https://github.com/ged-lab/khmer/blob/protocols-v0.8.3/sandbox/calc-best-assembly.py" target="_blank">https://github.com/ged-lab/khmer/blob/protocols-v0.8.3/sandbox/calc-best-assembly.py</a><br>
</div><div><br></div><div>Install instructions are at: <a href="https://khmer-protocols.readthedocs.org/en/v0.8.3/metagenomics/1-quality.html#install-software" target="_blank">https://khmer-protocols.readthedocs.org/en/v0.8.3/metagenomics/1-quality.html#install-software</a></div>
<div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On Fri, Jan 3, 2014 at 4:07 PM, Yiseul Kim <span dir="ltr"><<a href="mailto:kimyise2@msu.edu" target="_blank">kimyise2@msu.edu</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div>
<div dir="ltr"><div>Hello,</div><div><br></div><div>Could someone help me with finding the location of <b>calc-best-assembly.py</b>? The newly released metagenomic assembly protocol (<a href="https://khmer-protocols.readthedocs.org/en/v0.8.3/metagenomics/4-assemble.html" target="_blank">https://khmer-protocols.readthedocs.org/en/v0.8.3/metagenomics/4-assemble.html</a>) says it is located under /khmer/sandbox but I am not able to find it. Any help would be appreciated.</div>
<br clear="all"><div><div dir="ltr"><div><span style="color:rgb(102,102,102);font-size:small">Regards,</span><br></div><div><font color="#666666">Yiseul</font></div></div></div></div></div></div></blockquote></div></div>
</div></blockquote></div></div></div></div></blockquote></div></div></div></div></blockquote></div></div></div></div></blockquote></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div>
</div></div></blockquote></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div><div><br></div></div></div><div>-- <br><div dir="ltr"><font face="courier new, monospace">Michael R. Crusoe: Software Engineer and Bioinformatician <a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a><br>
@ the Genomics, Evolution, and Development lab; Michigan State University<br><a href="http://ged.msu.edu/" target="_blank">http://ged.msu.edu/</a> <a href="http://orcid.org/0000-0002-2961-9670" target="_blank">http://orcid.org/0000-0002-2961-9670</a> <a href="http://twitter.com/biocrusoe" target="_blank">@biocrusoe</a></font><br>
</div>
</div></div></div></div>
</blockquote></div><br></div></div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><font face="courier new, monospace">Michael R. Crusoe: Software Engineer and Bioinformatician <a href="mailto:mcrusoe@msu.edu" target="_blank">mcrusoe@msu.edu</a><br>
@ the Genomics, Evolution, and Development lab; Michigan State University<br><a href="http://ged.msu.edu/" target="_blank">http://ged.msu.edu/</a> <a href="http://orcid.org/0000-0002-2961-9670" target="_blank">http://orcid.org/0000-0002-2961-9670</a> <a href="http://twitter.com/biocrusoe" target="_blank">@biocrusoe</a></font><br>
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</div></div>