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 Lewis To: "galaxy-user@lists.bx.psu.edu" Subject: [galaxy-user] Help with sam to bam Message-ID: 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] Help with sam to bam (Zachary A Lewis)
Message: 1 Date: Tue, 13 Sep 2011 18:32:43 + From: Zachary A Lewis To: "galaxy-user@lists.bx.psu.edu" Subject: [galaxy-user] Help with sam to bam Message-ID: 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/
Re: [galaxy-user] Help with sam to bam
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 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/
[galaxy-user] Help with sam to bam
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/
