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Seattle Oneeechan | 24 May 2013 19:55
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BWA errors

Hi,

 

Two related issues:

 

We tried to run BWA for Illumina on two groomed files (fastqsanger)  and got the following error message. 

 

24: Map with BWA for Illumina on data 6 and data 5: mapped reads

error

An error occurred with this dataset: BWA Version: 0.5.9-r16 The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln]

 

 

We have done this many times before on the public server.  However, this is a new local instance and we just uploaded the files for “hg19 indexed for bwa” (from the TopHat website) which put it into the pull down menu.

 

Along those same lines.  I thought that a .fa file put into history, could be used and would be indexed automatically in bowtie and bwa (maybe tophat as well, haven’t used that one yet).  With bowtie, having the WholeGenomeFasta file from the UCSC seems to work, but not with bwa.

 

Does anybody know if it should work with bwa as well?

 

Any help is much appreciated.

 

Thank you,

 

<div>
<p class="MsoNormal"><span>Hi,</span></p>
<p class="MsoNormal"><span>&nbsp;</span></p>
<p class="MsoNormal"><span>Two related issues:</span></p>
<p class="MsoNormal"><span>&nbsp;</span></p>
<p class="MsoNormal"><span>We tried to run BWA for Illumina on two groomed files (fastqsanger)&nbsp; and got the following error message.&nbsp; </span></p>

<p class="MsoNormal"><span><span>&nbsp;</span></span></p>

<p class="MsoNormal"><span>24: Map with BWA for Illumina on data 6 and data 5: mapped reads</span><span></span></p>

<p class="MsoNormal"><span>error</span></p>
<p class="MsoNormal"><span>An error occurred with this dataset: BWA Version: 0.5.9-r16 The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: max_diff = 5 [bwa_aln] 124bp reads: max_diff = 6 [bwa_aln]</span></p>

<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal"><span>We have done this many times before on the public server.&nbsp; However, this is a new local instance and we just uploaded the files for &ldquo;hg19 indexed for bwa&rdquo; (from the TopHat website) which put it into the pull down menu.</span></p>

<p class="MsoNormal"><span>&nbsp;</span></p>
<p class="MsoNormal"><span>Along those same lines.&nbsp; I thought that a .fa file put into history, could be used and would be indexed automatically in bowtie and bwa (maybe tophat as well, haven&rsquo;t used that one yet).&nbsp; With bowtie, having the WholeGenomeFasta file from the UCSC seems to work, but not with bwa.</span></p>

<p class="MsoNormal"><span>&nbsp;</span></p>
<p class="MsoNormal"><span>Does anybody know if it should work with bwa as well?</span></p>

<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Any help is much appreciated.</p>
<p class="MsoNormal">&nbsp;</p>
<p class="MsoNormal">Thank you,</p>
<p class="MsoNormal">&nbsp;</p>
</div>
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Eduardo Fox | 24 May 2013 16:31
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Unable to use FASTQ tool on Main over several days

Please, I have been unable to use any of the tools under FASTQ Tools
for the last 4 days. I keep getting an error message with codes, for
instance GURU MEDITATION: #376b73ae417d41f3a7c2088770e13b8f.

Is this part of the platform down for some reason?

Best wishes and thanks,

E. Fox
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Nikolay N. | 24 May 2013 18:23
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obsolete cuffdiff version in main.g2.bx.psu.edu

Hi,

I noticed that the version of cuffdiff used in main.g2.bx.psu.edu is really obsolete (0.0.5) whereas the most recent version is 2.1.1.

Is there a chance that a more up-to-date version will be ever installed on the main galaxy instance?

many thanks,
Nikolay
<div><div dir="ltr">
<div>
<div>
<div>
<div>Hi,<br><br>
</div>I noticed that the version of cuffdiff used in <a href="http://main.g2.bx.psu.edu">main.g2.bx.psu.edu</a> is really obsolete (0.0.5) whereas the most recent version is 2.1.1.<br><br>
</div>Is there a chance that a more up-to-date version will be ever installed on the main galaxy instance?<br><br>
</div>many thanks,<br>
</div>Nikolay<br>
</div></div>
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Sun, Wenping [USA] | 24 May 2013 15:59

Question on megablast databases

Dear galaxy members,

 

I have a question on the databases used in megablast module from galaxy. There are four db options to blast against with -

1.      htgs 28-Jan-2013

2.      nt 28-Jan-2013

3.      wgs 28-Jan-2013

4.      phiX174

Is there any further information to guide which database would be appropriate to use? In addition, how to find the genome information contained in each database?

 

Many thanks,

Kathryn

<div>
<div class="WordSection1">
<p class="MsoNormal"><span>Dear galaxy members,<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>I have a question on the databases used in megablast module from galaxy. There are four db options to blast against with -<p></p></span></p>
<p class="MsoListParagraph">
<span><span>1.<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><span>htgs 28-Jan-2013<p></p></span></p>
<p class="MsoListParagraph">
<span><span>2.<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><span>nt 28-Jan-2013<p></p></span></p>
<p class="MsoListParagraph">
<span><span>3.<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><span>wgs 28-Jan-2013<p></p></span></p>
<p class="MsoListParagraph">
<span><span>4.<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span></span></span><span>phiX174<p></p></span></p>
<p class="MsoNormal"><span>Is there any further information to guide which database would be appropriate to use? In addition, how to find the genome information contained in each database?<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span>Many thanks,<p></p></span></p>
<p class="MsoNormal"><span>Kathryn<p></p></span></p>
</div>
</div>
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Marc DELOGER | 24 May 2013 14:17
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Problem to download mercurial egg

Hello,

I tried to download several times the several egg on these following mirrors but the download is always blocked near 50%...I asked several different people and they all have the same problem :

http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg

http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg

Thank you in advance,

Marc DELOGER 
<div>
    Hello,<br><br>
    I tried to download several times the several egg on these following
    mirrors but the download is always blocked near 50%...I asked
    several different people and they all have the same problem :<br><br><a href="http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg" target="_blank">http://eggs.g2.bx.psu.edu/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg</a><br><br><a href="http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg" target="_blank">http://eggs.galaxyproject.org/mercurial/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg</a><br><br>
    Thank you in advance,<br><br>
    Marc DELOGER
  </div>
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Ianiri, Giuseppe | 21 May 2013 01:10
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(no subject)

Hi, 
I have worked so far on the free web-based version of Galaxy; now I have installed Bio-Linux 7, and there is Galaxy in there as well. However, I cannot access to my data (stored on the web version of Galaxy) using Galaxy on Bio Linux. If it is possible, does anyone know how to do it?
Thanks,

Giuseppe Ianiri

<div>
<div>Hi,&nbsp;
<div>I have worked so far on the free&nbsp;<span>web-based version of Galaxy; now I have installed Bio-Linux 7, and there is Galaxy in there as well. However, I cannot access to my data (stored on the web version of Galaxy) using Galaxy
 on Bio Linux. If it is possible, does anyone know how to do it?</span>
</div>
<div><span>Thanks,</span></div>
<div><span><br></span></div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNoSpacing"></p>
<p class="MsoNoSpacing"></p>
<p class="MsoNoSpacing"><span>Giuseppe Ianiri</span></p>
<p></p>
<p></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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Colaneri, Alejandro Cesar | 20 May 2013 23:38
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changing parameters in tophat

I want to run tophat with the parameter  "--no-novel-juncs genome"
Where do I find the options to add this parameter?

Dr. Alejandro Colaneri

Departments of Biology

University of North Carolina at Chapel Hill

310 Coker Hall, CB# 3280

120 South Road

Chapel Hill, NC 27599-3280

Tel: 919-962-2273

fax: 919- 962-1625

<div>
<div>
<div>
<div>I want to run tophat with the parameter &nbsp;"--no-novel-juncs genome"</div>
<div>Where do I find the options to add this parameter?</div>
<div>
<div>
<p class="MsoNormal">
<span class="Apple-style-span"></span></p>
<p class="MsoNormal"><span class="Apple-style-span"></span></p>
<p class="MsoNormal"></p>
<p class="MsoNormal">
<span>Dr. Alejandro Colaneri</span><span><p></p></span></p>

<p class="MsoNormal">
<span>Departments of Biology</span><span><p></p></span></p>
<p class="MsoNormal">
<span>University of North Carolina at Chapel Hill<p></p></span></p>
<p class="MsoNormal">
<span>310 Coker Hall, CB# 3280<p></p></span></p>
<p class="MsoNormal">
<span>120 South Road<p></p></span></p>
<p class="MsoNormal">
<span>Chapel Hill, NC 27599-3280<p></p></span></p>
<p class="MsoNormal">
<span>Tel: 919-962-2273<p></p></span></p>
<p class="MsoNormal"><span>fax: 919- 962-1625</span><span><p></p></span></p>

<p></p>

<p></p>

<p>
</p>
</div>
</div>
</div>
</div>
</div>
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Nikolay N. | 17 May 2013 23:26
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failed Tophat processing steps

Hi,

I submitted a sample for Tophat processing on the main Galaxy instance and it seems to me that that the processing of that sample has failed. The corresponding sections in the history are in red (see attached screenshot). 

How can I find out what has happened? I don't see any error message. 

Shall I simple re-submit these processing steps hoping that next time they won't fail?

many thanks,

Nikolay
<div><div dir="ltr">Hi,<div><br></div>
<div>I submitted a sample for Tophat processing on the main Galaxy instance and it seems to me that that the processing of that sample has failed. The corresponding sections in the history are in red (see attached screenshot).&nbsp;</div>
<div><br></div>
<div>How can I find out what has happened? I don't see any error message.&nbsp;</div>
<div><br></div>
<div>Shall I simple re-submit these processing steps hoping that next time they won't fail?</div>
<div><br></div>
<div>many thanks,</div>
<div><br></div>
<div>Nikolay</div>
</div></div>
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Michael Axtell | 17 May 2013 18:18
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User -> Custom Builds fail on public server

Hello.  For the last several days the Custom Builds dialog has failed
on the public server (main.g2.bx.psu.edu).  Specifically, User ->
Custom Builds returns the 'Internal Server Error' message, and other
paths to the custom builds tools similarly have been failing for me.
Advice?

Thanks!
Mike

--
Michael J. Axtell, Ph.D.
Associate Professor
Dept. of Biology
Penn State University
http://axtell-lab-psu.weebly.com
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Nikolay N. | 17 May 2013 15:01
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receiving an email when a processing step finishes

Hi,

I am using the main galaxy instance and have submitted several processing steps that seem to have been scheduled for execution. Is there a way to get an email notification when such a processing step finishes?

many thanks,
Nick
<div><div dir="ltr">Hi,<div><br></div>
<div>I am using the main galaxy instance and have submitted several processing steps that seem to have been scheduled for execution. Is there a way to get an email notification when such a processing step finishes? </div>
<div><br></div>
<div>many thanks,</div>
<div>Nick</div>
</div></div>
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Els Willems | 17 May 2013 11:11
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Raw counts from Galaxy

Dear all,

 

I would like to analyse some RNA-Seq I obtained in the chicken. I am implemented the Tophat-Cufflinks pipeline in Galaxy, but I would like to obtain a raw count of the number of mappings per transcript. I have not found a way to do this in Galaxy, is this possible? Thank you very much.

 

Regards, Els

 

---
Ir. Els Willems
KU Leuven
Department of Biosystems
Division Livestock - Nutrition - Quality
Laboratory of Livestock Physiology
Kasteelpark Arenberg 30 bus 2456
B - 3001 Heverlee
T (+32) 016 32 17 29
F (+32) 016 32 19 94
<div>
<div>
<div>
<p>Dear all,</p>
<p>&nbsp;</p>
<p>I would like to analyse some RNA-Seq I obtained in the chicken. I am implemented the Tophat-Cufflinks pipeline in Galaxy, but I would like to obtain a raw count of the number of mappings per transcript. I have not found a way to do this in Galaxy, is this
 possible? Thank you very much.</p>
<p>&nbsp;</p>
<p>Regards, Els</p>
<p>&nbsp;</p>
<div>
<div>---</div>
<div>Ir. Els Willems</div>
<div>KU Leuven</div>
<div>Department of Biosystems</div>
<div>Division Livestock - Nutrition - Quality</div>
<div>Laboratory of Livestock Physiology</div>
<div>Kasteelpark Arenberg 30 bus 2456</div>
<div>B - 3001 Heverlee</div>
<div>T (+32) 016 32 17 29</div>
<div>F (+32) 016 32 19 94</div>
</div>
</div>
</div>
</div>
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