Praveen Raj Somarajan | 1 Mar 09:30 2012

Error in DepthOfCoverage (GATK) tool

Hello,

 

I'm facing an issue with "Depth Of Coverage" tool when it runs on refGene and target BED file. The error message is:

 

File "cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py", line 402, in respond

NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics'

 

I noticed that the issue is only when the "Advanced GATK options" is enabled to set target BED file.

 

The commandline runs perfectly with the input files, but galaxy fails due to this error. Can anyone suggest what's the issue?

 

Best,

 

Raj


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OCIMUMBIO SOLUTIONS (P) LTD
<div>
<div class="Section1">
<p class="MsoNormal">Hello,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">I'm facing an issue with "Depth Of Coverage" tool when it runs on refGene and target BED file. The error message is:<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal"><span>File "cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py", line 402, in respond<p></p></span></p>
<p class="MsoNormal"><span>NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics'<p></p></span></p>
<p class="MsoNormal"><span><p>&nbsp;</p></span></p>
<p class="MsoNormal">I noticed that the issue is only when the "Advanced GATK options" is enabled to set target BED file.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">The commandline runs perfectly with the input files, but galaxy fails due to this error. Can anyone suggest what's the issue?<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">Best,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">Raj<p></p></p>
</div>
<br>This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message.
 Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk,
 but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment.<br>
<table><tr><td bgcolor="#ffffff">The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system.<br><br>
OCIMUMBIO SOLUTIONS (P) LTD<br>
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Noa Sher | 1 Mar 10:48 2012
Picon

Quality trimming of sequences before RNA-Seq

Hi

I am looking at various options of quality trimming sequences for RNA Seq analysis

I know I can chop off a certain number of bases off the 3' or 5' ends of the reads.

Is it possible to use a sliding window to chop reads to different lengths, leaving everything above quality score 20 (for example) or would this be inadvisable as the differing lengths of reads would skew the downstream FPKM analysis?

Thanks

noa

<div>
    <p>Hi</p>
    <p>I am looking at various options of quality trimming sequences for
      RNA Seq analysis</p>
    <p>I know I can chop off a certain number of bases off the 3' or 5'
      ends of the reads.</p>
    <p>Is it possible to use a sliding window to chop reads to different
      lengths, leaving everything above quality score 20 (for example)
      or would this be inadvisable as the differing lengths of reads
      would skew the downstream FPKM analysis?</p>
    <p>Thanks</p>
    <p>noa<br></p>
  </div>
Bomba Dam | 1 Mar 11:19 2012
Picon

Re: Quality trimming of sequences before RNA-Seq

Dear Noa,

I also feel the same. So I think it would be better to use these three steps

remove sequencing artifacts

then trim the sequences by from the 5' end or if needed from the 3'end also (2-5 bases, depending on your sequence quality)

finally filter the sequences by quality (I used the default parameters). Although it removed 15% of the sequences but I feel confident with the high quality data.

Any better suggestion will be appreciated.

CHeers,

Bomba

On Thu, Mar 1, 2012 at 10:48 AM, Noa Sher <noa.sher-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Hi

I am looking at various options of quality trimming sequences for RNA Seq analysis

I know I can chop off a certain number of bases off the 3' or 5' ends of the reads.

Is it possible to use a sliding window to chop reads to different lengths, leaving everything above quality score 20 (for example) or would this be inadvisable as the differing lengths of reads would skew the downstream FPKM analysis?

Thanks

noa


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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--
Dr. BOMBA DAM
Alexander von Humboldt Postdoctoral Research Fellow
Max-Planck-Institut für terrestrische Mikrobiologie
Karl-von-Frisch-Straße 10
D-35043 Marburg, Germany
E mail: bomba.dam-QidqKpz2+uDjtQW52tizGYQuADTiUCJX@public.gmane.org
PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 (ROOM)

Assistant Professor of Microbiology
Department of Botany, Institute of Science
Visva-Bharati (A Central University)
Santiniketan, West Bengal 731235, India.
E mail: bumba_micro-islk/lqeCKIVNiuSxAKqjzEVjDUJwPlv@public.gmane.org, bumba_micro-QOiod4cnrWAN+BqQ9rBEUg@public.gmane.org;     



<div>
<p>Dear Noa,<br><br>I also feel the same. So I think it would be better to use these three steps<br><br>remove sequencing artifacts<br><br>then trim the sequences by from the 5' end or if needed from the 3'end also (2-5 bases, depending on your sequence quality)<br><br>finally filter the sequences by quality (I used the default parameters). Although it removed 15% of the sequences but I feel confident with the high quality data.<br><br>Any better suggestion will be appreciated.<br><br>
CHeers,<br><br>Bomba<br><br></p>
<div class="gmail_quote">On Thu, Mar 1, 2012 at 10:48 AM, Noa Sher <span dir="ltr">&lt;<a href="mailto:noa.sher <at> gmail.com">noa.sher@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">

    

  <div bgcolor="#FFFFFF" text="#000000">
    <p>Hi</p>
    <p>I am looking at various options of quality trimming sequences for
      RNA Seq analysis</p>
    <p>I know I can chop off a certain number of bases off the 3' or 5'
      ends of the reads.</p>
    <p>Is it possible to use a sliding window to chop reads to different
      lengths, leaving everything above quality score 20 (for example)
      or would this be inadvisable as the differing lengths of reads
      would skew the downstream FPKM analysis?</p>
    <p>Thanks</p>
<span class="HOEnZb">
    <p>noa<br></p>
  </span>
</div>

<br>___________________________________________________________<br>
The Galaxy User list should be used for the discussion of<br>
Galaxy analysis and other features on the public server<br>
at <a href="http://usegalaxy.org" target="_blank">usegalaxy.org</a>. &nbsp;Please keep all replies on the list by<br>
using "reply all" in your mail client. &nbsp;For discussion of<br>
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use the Galaxy Development list:<br><br>
 &nbsp;<a href="http://lists.bx.psu.edu/listinfo/galaxy-dev" target="_blank">http://lists.bx.psu.edu/listinfo/galaxy-dev</a><br><br>
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</blockquote>
</div>
<br><br clear="all"><br>-- <br>Dr. BOMBA DAM<br>Alexander von Humboldt Postdoctoral Research Fellow <br>Max-Planck-Institut f&uuml;r terrestrische Mikrobiologie<br>
Karl-von-Frisch-Stra&szlig;e 10<br>D-35043 Marburg, Germany<br>E mail: <a href="mailto:bomba.dam@...">bomba.dam@...</a><br>PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 (ROOM) <br><br>Assistant Professor of Microbiology <br>Department of Botany, Institute of Science<br>Visva-Bharati (A Central University)<br>Santiniketan, West Bengal 731235, India. <br>E mail: <a href="mailto:bumba_micro <at> visva-bhatari.ac.in">bumba_micro@...</a>, <a href="mailto:bumba_micro <at> rediffmail.com">bumba_micro@...</a>;&nbsp; &nbsp; &nbsp; <br><br><br><br>
</div>
Noa Sher | 1 Mar 11:22 2012
Picon

Filtering reads on wrong strand before FPKM scoring on cufflinks

Hi

I am running sequencing data from a directional RNASeq protocol on bowtie (it is a bacterial genome) and then cuffdiff or cufflinks.

I occasionally see a few reads that align to the wrong direction (opposite strand). Is there any way to filter these out before I do my FPKM analysis?

Thanks

Noa

<div>
    <p>Hi</p>
    <p>I am running sequencing data from a directional RNASeq protocol
      on bowtie (it is a bacterial genome) and then cuffdiff or
      cufflinks.</p>
    <p>I occasionally see a few reads that align to the wrong direction
      (opposite strand). Is there any way to filter these out before I
      do my FPKM analysis?</p>
    <p>Thanks</p>
    <p>Noa<br></p>
  </div>
Bomba Dam | 1 Mar 11:52 2012
Picon

Re: Filtering reads on wrong strand before FPKM scoring on cufflinks

Dear Noa,

Bowtie in --best mode eliminates strand bias by forcing Bowtie to select one strand or the other with a probability that is proportional to the number of best sites on the strand.


try with this mode. I am also trying to do the same. If you find any good alternative for the whole process please let me know.

Bomba

On Thu, Mar 1, 2012 at 11:22 AM, Noa Sher <noa.sher-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Hi

I am running sequencing data from a directional RNASeq protocol on bowtie (it is a bacterial genome) and then cuffdiff or cufflinks.

I occasionally see a few reads that align to the wrong direction (opposite strand). Is there any way to filter these out before I do my FPKM analysis?

Thanks

Noa


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/



--
Dr. BOMBA DAM
Alexander von Humboldt Postdoctoral Research Fellow
Max-Planck-Institut für terrestrische Mikrobiologie
Karl-von-Frisch-Straße 10
D-35043 Marburg, Germany
E mail: bomba.dam-QidqKpz2+uDjtQW52tizGYQuADTiUCJX@public.gmane.org
PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 (ROOM)

Assistant Professor of Microbiology
Department of Botany, Institute of Science
Visva-Bharati (A Central University)
Santiniketan, West Bengal 731235, India.
E mail: bumba_micro-islk/lqeCKIVNiuSxAKqjzEVjDUJwPlv@public.gmane.org, bumba_micro-QOiod4cnrWAN+BqQ9rBEUg@public.gmane.org;     



<div>
<p>Dear Noa,<br><br></p>
<p class="MsoNormal"><span>Bowtie in </span><a href="http://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-best"><span>--best</span></a><span> mode eliminates strand bias by forcing Bowtie to select one
strand or the other with a probability that is proportional to the number of
best sites on the strand.</span></p>

<br>try with this mode. I am also trying to do the same. If you find any good alternative for the whole process please let me know.<br><br>Bomba<br><br><div class="gmail_quote">On Thu, Mar 1, 2012 at 11:22 AM, Noa Sher <span dir="ltr">&lt;<a href="mailto:noa.sher@...">noa.sher@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">

    

  <div bgcolor="#FFFFFF" text="#000000">
    <p>Hi</p>
    <p>I am running sequencing data from a directional RNASeq protocol
      on bowtie (it is a bacterial genome) and then cuffdiff or
      cufflinks.</p>
    <p>I occasionally see a few reads that align to the wrong direction
      (opposite strand). Is there any way to filter these out before I
      do my FPKM analysis?</p>
    <p>Thanks</p>
<span class="HOEnZb">
    <p>Noa<br></p>
  </span>
</div>

<br>___________________________________________________________<br>
The Galaxy User list should be used for the discussion of<br>
Galaxy analysis and other features on the public server<br>
at <a href="http://usegalaxy.org" target="_blank">usegalaxy.org</a>. &nbsp;Please keep all replies on the list by<br>
using "reply all" in your mail client. &nbsp;For discussion of<br>
local Galaxy instances and the Galaxy source code, please<br>
use the Galaxy Development list:<br><br>
 &nbsp;<a href="http://lists.bx.psu.edu/listinfo/galaxy-dev" target="_blank">http://lists.bx.psu.edu/listinfo/galaxy-dev</a><br><br>
To manage your subscriptions to this and other Galaxy lists,<br>
please use the interface at:<br><br>
 &nbsp;<a href="http://lists.bx.psu.edu/" target="_blank">http://lists.bx.psu.edu/</a><br>
</blockquote>
</div>
<br><br clear="all"><br>-- <br>Dr. BOMBA DAM<br>Alexander von Humboldt Postdoctoral Research Fellow <br>Max-Planck-Institut f&uuml;r terrestrische Mikrobiologie<br>
Karl-von-Frisch-Stra&szlig;e 10<br>D-35043 Marburg, Germany<br>E mail: <a href="mailto:bomba.dam@...">bomba.dam@...</a><br>PHONE: +49 176 321 321 75 (Mobile); +49 6421 178 721 (LAB); +49 6421 2828516 (ROOM) <br><br>Assistant Professor of Microbiology <br>Department of Botany, Institute of Science<br>Visva-Bharati (A Central University)<br>Santiniketan, West Bengal 731235, India. <br>E mail: <a href="mailto:bumba_micro <at> visva-bhatari.ac.in">bumba_micro@...</a>, <a href="mailto:bumba_micro <at> rediffmail.com">bumba_micro@...</a>;&nbsp; &nbsp; &nbsp; <br><br><br><br>
</div>
Montoya, Vincent | 1 Mar 02:32 2012
Picon

Metagenomics

Hello 
I am a relatively new user on Galaxy and I had a question regarding "Fetching Taxonomic Information".  It is
great that I can retrieve all of the hits for each sequence, but I cannot seem to find an option to also
provide how accurate of a match it is to the given taxon.  For instance, a percentage match.  I can access this
information in the original file and programmatically retrieve it but, it would be nice if it came in one
package so that I can avoide those false hits that have a low percentage match.  Can you please provide me
with instructions on how to best to retrieve this information (hopefully in a single file)?
Thank you
Vincent
Waldron, Michael H | 1 Mar 14:49 2012
Picon

Getting errors trying to enable samtools_mpileup

I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12.

I am trying to enable use of Mpileup for SAM Tools, and have added the entry for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup Galaxy, the link for Mpileup does not appear in the Tools pane, and I see the following errors from the Galaxy startup:

galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path: samtools/samtools_mpileup.xml
Traceback (most recent call last):
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 212, in load_tool_tag_set
    tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 305, in load_tool
    return ToolClass( config_file, root, self.app, guid=guid )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 531, in __init__
    self.parse( root, guid=guid )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 641, in parse
    self.parse_inputs( root )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 723, in parse_inputs
    display, inputs = self.parse_input_page( page, enctypes )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 922, in parse_input_page
    inputs = self.parse_input_elem( input_elem, enctypes )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 989, in parse_input_elem
    case.inputs = self.parse_input_elem( case_elem, enctypes, context )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 945, in parse_input_elem
    group.inputs = self.parse_input_elem( elem, enctypes, context )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1015, in parse_input_elem
    param = self.parse_param_elem( elem, enctypes, context )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1027, in parse_param_elem
    param = ToolParameter.build( self, input_elem )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 176, in build
    return parameter_types[param_type]( tool, param )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 1330, in __init__
    ToolParameter.__init__( self, tool, elem )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 43, in __init__
    self.validators.append( validation.Validator.from_element( self, elem ) )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 23, in from_element
    return validator_types[type].from_element( param, elem )
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 279, in from_element
    tool_data_table = param.tool.app.tool_data_tables[ table_name ]
  File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py", line 21, in __getitem__
    return self.data_tables.__getitem__( key )
KeyError: 'sam_fa_indexes'

Can someone tell me what is wrong here? Am I missing something in the database?

Thanks,

Mike Waldron

<div>
<div>I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12.<br><br>
I am trying to enable use of Mpileup for SAM Tools, and have added the entry for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup Galaxy, the link for Mpileup does not appear in the Tools pane, and I see the following errors from the
 Galaxy startup:<br><br>
galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path: samtools/samtools_mpileup.xml<br>
Traceback (most recent call last):<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 212, in load_tool_tag_set<br>
&nbsp;&nbsp;&nbsp; tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 305, in load_tool<br>
&nbsp;&nbsp;&nbsp; return ToolClass( config_file, root, self.app, guid=guid )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 531, in __init__<br>
&nbsp;&nbsp;&nbsp; self.parse( root, guid=guid )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 641, in parse<br>
&nbsp;&nbsp;&nbsp; self.parse_inputs( root )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 723, in parse_inputs<br>
&nbsp;&nbsp;&nbsp; display, inputs = self.parse_input_page( page, enctypes )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 922, in parse_input_page<br>
&nbsp;&nbsp;&nbsp; inputs = self.parse_input_elem( input_elem, enctypes )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 989, in parse_input_elem<br>
&nbsp;&nbsp;&nbsp; case.inputs = self.parse_input_elem( case_elem, enctypes, context )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 945, in parse_input_elem<br>
&nbsp;&nbsp;&nbsp; group.inputs = self.parse_input_elem( elem, enctypes, context )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1015, in parse_input_elem<br>
&nbsp;&nbsp;&nbsp; param = self.parse_param_elem( elem, enctypes, context )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1027, in parse_param_elem<br>
&nbsp;&nbsp;&nbsp; param = ToolParameter.build( self, input_elem )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 176, in build<br>
&nbsp;&nbsp;&nbsp; return parameter_types[param_type]( tool, param )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 1330, in __init__<br>
&nbsp;&nbsp;&nbsp; ToolParameter.__init__( self, tool, elem )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 43, in __init__<br>
&nbsp;&nbsp;&nbsp; self.validators.append( validation.Validator.from_element( self, elem ) )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 23, in from_element<br>
&nbsp;&nbsp;&nbsp; return validator_types[type].from_element( param, elem )<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 279, in from_element<br>
&nbsp;&nbsp;&nbsp; tool_data_table = param.tool.app.tool_data_tables[ table_name ]<br>
&nbsp; File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py", line 21, in __getitem__<br>
&nbsp;&nbsp;&nbsp; return self.data_tables.__getitem__( key )<br>
KeyError: 'sam_fa_indexes'<br><br>
Can someone tell me what is wrong here? Am I missing something in the database?<br><br>
Thanks,<br><div>
<br><div class="BodyFragment">
<div class="PlainText">Mike Waldron<br><br>
</div>
</div>
</div>
</div>
</div>
Jennifer Jackson | 1 Mar 15:20 2012
Picon

Getting errors trying to enable samtools_mpileup

Hello Mike,

I am going to move your question over to the galaxy-dev@... 
mailing list, which is for the discussion of local instance questions.

Some things to double check:

SAMTools is already set up correctly, with indexes?
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
-> see "SAM Tools installation"

If you are still running pile-up, note that two versions of SAMTools are 
required:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies

Including some reorganization to accommodate both versions, as explained 
in this wiki:
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies

Hopefully this helps,

Best,

Jen
Galaxy team

On 3/1/12 5:49 AM, Waldron, Michael H wrote:
> I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12.
>
> I am trying to enable use of Mpileup for SAM Tools, and have added the
> entry for the samtools_mpileup.xml file in tool_conf.xml. However, when
> I startup Galaxy, the link for Mpileup does not appear in the Tools
> pane, and I see the following errors from the Galaxy startup:
>
> galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path:
> samtools/samtools_mpileup.xml
> Traceback (most recent call last):
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 212, in load_tool_tag_set
> tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 305, in load_tool
> return ToolClass( config_file, root, self.app, guid=guid )
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 531, in __init__
> self.parse( root, guid=guid )
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 641, in parse
> self.parse_inputs( root )
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 723, in parse_inputs
> display, inputs = self.parse_input_page( page, enctypes )
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 922, in parse_input_page
> inputs = self.parse_input_elem( input_elem, enctypes )
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 989, in parse_input_elem
> case.inputs = self.parse_input_elem( case_elem, enctypes, context )
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 945, in parse_input_elem
> group.inputs = self.parse_input_elem( elem, enctypes, context )
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 1015, in parse_input_elem
> param = self.parse_param_elem( elem, enctypes, context )
> File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 1027, in parse_param_elem
> param = ToolParameter.build( self, input_elem )
> File
> "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
> line 176, in build
> return parameter_types[param_type]( tool, param )
> File
> "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
> line 1330, in __init__
> ToolParameter.__init__( self, tool, elem )
> File
> "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
> line 43, in __init__
> self.validators.append( validation.Validator.from_element( self, elem ) )
> File
> "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py",
> line 23, in from_element
> return validator_types[type].from_element( param, elem )
> File
> "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py",
> line 279, in from_element
> tool_data_table = param.tool.app.tool_data_tables[ table_name ]
> File
> "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py",
> line 21, in __getitem__
> return self.data_tables.__getitem__( key )
> KeyError: 'sam_fa_indexes'
>
> Can someone tell me what is wrong here? Am I missing something in the
> database?
>
> Thanks,
>
> Mike Waldron
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
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> use the Galaxy Development list:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/

--

-- 
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
Scott Tighe | 1 Mar 15:27 2012
Picon

Re: Metagenomics

Vincent

Great question!!!  And a follow up for me, is how to purge the conserved sequences. Presently the current data set I have from "Fetch" is likely to be 99% composed of incorrect taxon just because of conserved sequence. So, how do you select just unique sequences (ie  those that do not have more then... say 5 hits above 99%). Any advice would be nice.

Our bioinformatic person said there was a way to do it thru blast X.

Scott


Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999-6666
On 2/29/2012 8:32 PM, Montoya, Vincent wrote:
Hello I am a relatively new user on Galaxy and I had a question regarding "Fetching Taxonomic Information". It is great that I can retrieve all of the hits for each sequence, but I cannot seem to find an option to also provide how accurate of a match it is to the given taxon. For instance, a percentage match. I can access this information in the original file and programmatically retrieve it but, it would be nice if it came in one package so that I can avoide those false hits that have a low percentage match. Can you please provide me with instructions on how to best to retrieve this information (hopefully in a single file)? Thank you Vincent ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
<div>
    Vincent<br><br>
      Great question!!!&nbsp; And a follow up for me, is how to purge the
      conserved sequences. Presently the current data set I have from
      "Fetch" is likely to be 99% composed of incorrect taxon just
      because of conserved sequence. So, how do you select just unique
      sequences (ie&nbsp; those that do not have more then... say 5 hits
      above 99%). Any advice would be nice.<br><br>
      Our bioinformatic person said there was a way to do it thru blast
      X. <br><br>
      Scott<br><br><br>
    Scott Tighe
Advanced Genome Technology Lab
Vermont Cancer Center at the University of Vermont
149 Beaumont Avenue
Health Science Research Bd RM 305
Burlington Vermont USA 05405
lab  802-656-AGTC (2482)
cell 802-999-6666

    <br>
    On 2/29/2012 8:32 PM, Montoya, Vincent wrote:
    <blockquote cite="mid:1617305365F4C54CA9638049D94D01200102B398E7A6@..." type="cite">
      Hello 
I am a relatively new user on Galaxy and I had a question regarding "Fetching Taxonomic Information".  It is great that I can retrieve all of the hits for each sequence, but I cannot seem to find an option to also provide how accurate of a match it is to the given taxon.  For instance, a percentage match.  I can access this information in the original file and programmatically retrieve it but, it would be nice if it came in one package so that I can avoide those false hits that have a low percentage match.  Can you please provide me with instructions on how to best to retrieve this information (hopefully in a single file)?
Thank you
Vincent
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  <a class="moz-txt-link-freetext" href="http://lists.bx.psu.edu/listinfo/galaxy-dev">http://lists.bx.psu.edu/listinfo/galaxy-dev</a>

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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    </blockquote>
  </div>
Peter Cock | 1 Mar 15:31 2012

Re: [galaxy-bugs] GI errors in the megablast table of results ?

Hello all,

Did this issue get resolved?

If Sandrine was right about there being an off by one error in GI number in
the BLAST tabular output, it could be a bug in 'legacy' blastall command.

I say 'legacy' BLAST because that's what Galay's NGS 'megablast' tool
is using internally (as opposed to the the NCBI's replacement BLAST+).

Peter

On Wed, Jan 25, 2012 at 3:14 PM, Guru Ananda <guru@...> wrote:
> Dear Sandrine,
>
> Thanks for pointing out this issue.
> The BLAST databases we have on Galaxy are from last year, while those on
> NCBI website are the latest (Jan 2012). As pointed out on NCBI website
> (http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html), it appears that each
> time any change is made to a sequence/database, GI numbers change as well.
> This is perhaps why you're observing discrepancies in GI numbers and lengths
> between megablast outputs on Galaxy and NCBI. I'm currently in the process
> of downloading the latest BLAST databases from NCBI, and I'll let you know
> when they're available for use on Galaxy.
>
> Thanks for your patience,
> Guru
> Galaxy team.
>
>
> On Wed, Nov 9, 2011 at 8:03 AM, Sandrine Hughes
> <Sandrine.Hughes@...> wrote:
>>
>> Dear all,
>>
>> I’m not sure where I need to send my email so I apologize if I’m wrong.
>>
>> I have a trouble with the Megablast program available in NGS Mapping and I
>> hope that you can help. Indeed, I think that there might be a problem with
>> the table given in output, and notably a shift between the GI numbers and
>> the parameters associated.
>>
>> Here are the details:
>>
>> I. First, what I have done :
>>     I used the program to identify the species that I have in a mix of
>> sequences by using the following options:
>>             Database nt 27-Jun-2011
>>             Word size 16
>>             Identity 90.0
>>             Cutoff 0.001
>>             Filter out low complexity regions Yes
>>     I run the analyses twice and obtained exactly the same results (I used
>> the online version of Galaxy, not a local one).
>>
>> II. Second, I analysed the data obtained for one of my sequence (1-202).
>> The following lines are the beginning of the table that I obtained after the
>> megablast and two lines with troubles:
>>
>>  1-202   312182292       484     99.33   150     1       0       1
>>       150     1       150     2e-75   289.0
>>  1-202   312182201       476     99.33   150     1       0       1
>>       150     1       150     2e-75   289.0
>>  1-202   308228725       928     99.33   150     1       0       1
>>       150     19      168     2e-75   289.0
>>  1-202   308228711       938     99.33   150     1       0       1
>>       150     22      171     2e-75   289.0
>>  1-202   308197083       459     99.33   150     1       0       1
>>       150     10      159     2e-75   289.0
>>  1-202   300392378       920     99.33   150     1       0       1
>>       150     10      159     2e-75   289.0
>>  1-202   300392376       918     99.33   150     1       0       1
>>       150     9       158     2e-75   289.0
>>  1-202   300392375       922     99.33   150     1       0       1
>>       150     11      160     2e-75   289.0
>>  1-202   300392374       931     99.33   150     1       0       1
>>       150     21      170     2e-75   289.0
>>  1-202   300392373       909     99.33   150     1       0       1
>>       150     21      170     2e-75   289.0
>>  1-202   300392371       1172    99.33   150     1       0       1
>>       150     9       158     2e-75   289.0
>> ...
>> 1-202   179366399       151762  98.67   150     2       0       1
>>       150     46880   47029   6e-73   281.0
>> 1-202   58617849        511     98.67   150     2       0       1
>>       150     21      170     6e-73   281.0
>>
>>
>> III. Third, what I’ve noticed:
>>     My first trouble was that among all the species identified, two were
>> very different from the expected ones (2 last lines). So I decided to search
>> if that could be possible for that sequence and performed independently a
>> megablast on the NCBI with similar options. I was not able to find these two
>> species in the results.
>>     So, I decided to check the hits identified in the table above and
>> identified a second trouble. In the table, the second column give the GI of
>> the database hit and the third column give the length of the database hit.
>> However, when I manually checked in NCBI the length of the GI, this one was
>> incorrect. Indeed, for the GI 312182292, the length should be 580 and not
>> 484.
>>     By checking different lines, I noticed that the length that is given
>> for a GI corresponds to the length of the GI-1. As you can see in the above
>> table, some GI are consecutive (300392376, 300392375,...). When checking the
>> length of 300392376 in NCBI, I should have 920. But when I checked
>> 300392375, I found 918. And this was true for the following lines :
>> 300392374 give normally 922 and 300392373 give 931... My conclusion at that
>> point was that there was a shift of –1 between the GI and the other
>> parameters of the line (indeed the parameters for the remaining columns are
>> in agreement with the length of the GI-1). However, that’s not always
>> true.... For some GI given in the table (for example, the two last lines),
>> if we check the parameters of the GI-1, the parameters are completely
>> different... So, I suppose that there is a trouble in the GI sorting during
>> the megablast but I’m not able to clearly define the problem.
>>
>> IV. Fourth, confirmed with an other dataset
>>     In order to be sure that the problem was not linked to my data or my
>> process, I asked a colleague to do a megablast on independent data. The
>>  conclusions were similar to mine : a shift in the GI given in the table and
>> the parameters associated, that most of the time but not always, correspond
>> to GI-1.
>>
>> Can you confirm that there is a problem with the output of the megablast
>> available in Galaxy ? If yes, do you think you can fix it ?
>>
>> Many thanks for your help,
>>
>> Best regards,
>>
>> Sandrine
>
>
>
>
> --
> Graduate student, Bioinformatics and Genomics
> Makova lab/Galaxy team
> Penn State University
> 505 Wartik lab
> University Park PA 16802
> guru@...
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>  http://lists.bx.psu.edu/


Gmane