Hello,

Thank you Sam for your answer. Unfortunately, it still doesn't work.
I tried to create new histories with all the datasets having the same
reference database in their attributes/options, with no success. I even
tried the two reference genomes available as option of the BWA (cb3full &
cb3Canonical), but neither worked: the SAM-to-BM conversion always stopped
with the same error message.

So I would be very grateful to anyone having another idea to fix this issue !

One possibility I see would be to download the reference genome in my
history. Except the fact that it takes a lot of memory space, does anyone
think it is a bad idea ?
If not, from where can I get the reference genome of C. briggsae (last
assembly cb4)?
In wormbase, there are various files available, but I don't know which one
to pick:
ftp://ftp.wormbase.org/pub/wormbase/species/c_briggsae/sequence/genomic/

Thanks for help and advice,

Fabrice


> Oh sorry, you are using Cb datatase, so embarrassing.  Sorry!  But the
> same approach is good, use the same database for all steps, and try to
> find a way to put it in your history.
> Best,
> Sam
>
> -----Original Message-----
> From: galaxy-user-boun...@lists.bx.psu.edu
> [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Politz, Samuel
> M.
> Sent: Monday, July 29, 2013 10:20 AM
> To: fbesn...@biologie.ens.fr; galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Problem with SAM-to-BAM conversion
>
> 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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> replies on the list by using "reply all" in your mail client.  For
> discussion of local Galaxy instances and the Galaxy source code, please
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-- 
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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use the Galaxy Development list:

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To manage your subscriptions to this and other Galaxy lists,
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