Re: [galaxy-user] Help with sam to bam (Zachary A Lewis)
Hi Zach, Would you have time to send this in as a bug report so that we can take a closer look? Format problems are likely the issue, but this can be double checked. To report as a bug, click on the green bug icon in the error dataset's box in your history. If your Galaxy account uses a different email, just note that in the comments so the two questions can be linked. Thanks! Jen Galaxy team On 9/14/11 11:01 AM, Pandey, Ashutosh wrote: Message: 1 Date: Tue, 13 Sep 2011 18:32:43 + From: Zachary A Lewiszle...@uga.edu To: galaxy-user@lists.bx.psu.edugalaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Help with sam to bam Message-ID:ae8e036c-cbd3-46f9-b5a4-0615cd806...@uga.edu Content-Type: text/plain; charset=us-ascii Hi, I was wondering if someone could help me with an error message I'm getting after performing a sam to bam conversion in galaxy. I've used Bowtie to map sequence reads to a custom fasta file corresponding to one chromosome in my organism. The mapping seems to work fine, but when I attempt a sam to bam conversion, I receive the folowing error message: An error occurred running this job: Samtools Version: 0.1.12 (r862) Error creating indexes from reference (/galaxy/main_database/files/002/977/dataset_2977193.dat), [fai_build_core] line length exceeds 65535 in sequence 'LGVII'. Segmentation fault Any help would be appreciated. Thanks, Zack Hi Zack, I got a similar problem but I am not sure if you have the same problem. My problem was due to use of different chromosome symbol by reference fasta file and the SAM file. May be you are using chr2 in SAM file and 2 in reference file or vice-versa. Converting chromosome symbol would be easy for reference fasta file. Thanks -Ash ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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/
[galaxy-user] Fwd: Help with sam to bam
Hi Zach, You should reply to all so people dont keep working on your questions. Glad to help. Austin -- Forwarded message -- From: Zachary A Lewis zle...@uga.edu Date: Tue, Sep 13, 2011 at 3:10 PM Subject: Re: [galaxy-user] Help with sam to bam To: Austin Paul austi...@usc.edu Thanks Austin! That did the trick. Zack On Sep 13, 2011, at 4:47 PM, Austin Paul wrote: You could try fasta width formatter on your reference fasta. This has helped me in the past when I received a similar error. On Tue, Sep 13, 2011 at 11:32 AM, Zachary A Lewis zle...@uga.edu wrote: Hi, I was wondering if someone could help me with an error message I'm getting after performing a sam to bam conversion in galaxy. I've used Bowtie to map sequence reads to a custom fasta file corresponding to one chromosome in my organism. The mapping seems to work fine, but when I attempt a sam to bam conversion, I receive the folowing error message: An error occurred running this job: *Samtools Version: 0.1.12 (r862)* *Error creating indexes from reference (/galaxy/main_database/files/002/977/dataset_2977193.dat), [fai_build_core] line length exceeds 65535 in sequence 'LGVII'. Segmentation fault* * * Any help would be appreciated. Thanks, Zack ___ 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/ ___ 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/
Re: [galaxy-user] Fwd: Help with sam to bam
Thanks Austin, good suggestions all around. The question came through again, so I didn't realize this was completely solved. Glad this was just a format issue! Take care, Jen Galaxy team On 9/14/11 4:54 PM, Austin Paul wrote: Hi Zach, You should reply to all so people dont keep working on your questions. Glad to help. Austin -- Forwarded message -- From: *Zachary A Lewis* zle...@uga.edu mailto:zle...@uga.edu Date: Tue, Sep 13, 2011 at 3:10 PM Subject: Re: [galaxy-user] Help with sam to bam To: Austin Paul austi...@usc.edu mailto:austi...@usc.edu Thanks Austin! That did the trick. Zack On Sep 13, 2011, at 4:47 PM, Austin Paul wrote: You could try fasta width formatter on your reference fasta. This has helped me in the past when I received a similar error. On Tue, Sep 13, 2011 at 11:32 AM, Zachary A Lewis zle...@uga.edu mailto:zle...@uga.edu wrote: Hi, I was wondering if someone could help me with an error message I'm getting after performing a sam to bam conversion in galaxy. I've used Bowtie to map sequence reads to a custom fasta file corresponding to one chromosome in my organism. The mapping seems to work fine, but when I attempt a sam to bam conversion, I receive the folowing error message: An error occurred running this job: /Samtools Version: 0.1.12 (r862)/ /Error creating indexes from reference (/galaxy/main_database/files/002/977/dataset_2977193.dat), [fai_build_core] line length exceeds 65535 in sequence 'LGVII'. Segmentation fault/ / / Any help would be appreciated. Thanks, Zack ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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/
Re: [galaxy-user] Upload of most recent genome data for Apis mellifera onto Galaxy and/or NCSC web sites?
Hi Diana, As Anton mentioned, we can add this genome to our working list. A check-in with UCSC about their plans for an update seems appropriate and that will be part of our prioritization of this genome. Meanwhile, the fastest way for you to start working with this genome right away is to load it into your history as a custom reference genome. Simply upload the fasta version via FTP and most tools will function just as if the genome was native to Galaxy. You can even create your own custom browser for the genome using the GTB (Galaxy Track Browser). The GTB is undergoing active development right now, so you will notice new features over the near-term. Currently, visualization for custom genomes is based on coordinates only, but adding in the reference genome back-bone sequence itself is a priority and will be added in soon. Any data mapped to the reference genome can be visualized and there is feedback between the browser and your working histories. Please see: http://galaxyproject.org/wiki/Learn/Visualization Thanks for using Galaxy! Best, Jen Galaxy team On 9/12/11 10:51 AM, Anton Nekrutenko wrote: Diana: It is best to direct such requests to galaxy-u...@bx.psu.edu mailto:galaxy-u...@bx.psu.edu mailing list, which I am doing. Adding this genome should be possible, but will take us some time. Thanks, anton Anton Nekrutenko http://galaxyproject.org On Sep 12, 2011, at 1:23 PM, Diana Cox-Foster wrote: Hi, Anton--- I am currently doing a NGS project and want to compare the sequencing data to the Apis mellifera genome. Unfortunately, the genomes on Galaxy and the UCSC website are quite outdated. I am planning to do another sequencing project that would also benefit from having the newest version as well. ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support ___ 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/
[galaxy-user] Merging of illumina paired end files
I have 3 illumina paired end reads of exome capture of the sample. I want to assemble these reads to genome using tools available in Galaxy (BWA etc). My concern is the amount of data that I can analyzed and when these reads should be merged. The total size of data is +30Gb. Thanks, Arun ___ 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/
