Hi Fabrice,
I work on C. elegans too, and I have found that you need to have the same ce 
genome database for all steps; otherwise, some tools won't work later in your 
workflow.  With some help from the Galaxy staff, I discovered that there is a 
version of ce10 in the CloudMap shared information on the Galaxy server.  You 
can find it under "CloudMap ot266 proof of principle dataset".  I found it 
works well to copy this file into your history.   When I used GATK tools, it 
requests the location of your genome datafile:  locally cached versus history.  
If you choose history, it always finds the ce10 version that you put there.  
Not sure this will help with SAM to BAM conversion, but ce10 is a more up to 
date version of the database anyway.  And the CloudMap version is sorted in a 
way that is "GATK-friendly", which was necessary for my application.
Hope this helps,

Sam Politz

-----Original Message-----
From: galaxy-user-boun...@lists.bx.psu.edu 
[mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Fabrice BESNARD
Sent: Monday, July 29, 2013 9:58 AM
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Problem with SAM-to-BAM conversion

Hello,

I am trying to map Illumina paired-ends reads from the nematode Caenorhabditis 
briggsae.

Here are the steps of my history:
1)I uploaded and groomed two .fq files corresponding to paired-end reads.
In the attributes, I choose the cb4 database.
2)I mapped them using BWA (BWA Version: 0.5.9-r16 BWA run on paired-end data). 
However, I used the cb3 database here, since the cb4 was not available.
3)I filtered the output SAM file for mapped reads (galaxy tool version 1.0.0). 
cb3 is still said to be the reference database in the filtered SAM I got as 
output.
4) Then I tried to convert the SAM into BAM. Here it failed.
When I chose the parameters of this tool, what I had for the 1st option "Choose 
the source for the reference list" is either:
-from the history
-locally cached
I chose locally cached.

Then, when running the tool, and I had this message error:
"20: SAM-to-BAM on data 16: converted BAM error An error occurred with this 
dataset: Samtools Version: 0.1.18 (r982:295) No sequences are available for 
build (cb3), request them by reporting this error."

As recommended, I report you now this error !

I found a similar problem in the Galaxy_user mailing list... But I did not get 
how the problem was solved !
http://user.list.galaxyproject.org/SAM-to-BAM-conversion-problem-td4135498.html
I tried to change the attributes of the SAM and filtered-SAM files to cb4, but 
it did not work.

Note also that in the error report, the version is said to be 0.1.18.
But when I click on the SAM-to-BAM tool, the header of the page says:
SAM-to-BAM (version 1.1.2). I don't know if this matters or not.

Could you please help me fixing this issue ?
Many thanks !
--
Fabrice Besnard
Institute of Biology of the Ecole Normale Supérieure (IBENS)
46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: 
Room 817.
mail: fbesn...@biologie.ens.fr
Tel: +33-1-44-32-39-44

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___________________________________________________________
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

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