[galaxy-user] Error in annotation tools
Hello, I'm using Nebula and when I try to use the annotation tools (genomic annotation and gene annotation in NGS annotation menu) I got always this error despite of the bed file that I use: An error occurred running this job:Unable to run this job due to a cluster error Could you indicate me how to solve this? Regards, Gema From: Jennifer Jackson j...@bx.psu.edu Date: Wednesday, May 8, 2013 5:36 AM To: Elwood Linney ellin...@gmail.com Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] problems with Tophat Hello Elwood, The public Main Galaxy server was very busy this weekend this likely contributed to the problems you were having with loaded and possibly with job execution. First, be sure that you are loading with FTP and confirming that loading is successful with a client during this time. This also permits interrupted loads can be restarted as necessary. http://wiki.galaxyproject.org/FTPUpload For the Tophat job, there were some known job failures related to load. I would restart the job and see if a new run resolves the issue. If the problem is persistent, please submit the new error as a bug report and we can take a closer look. Be sure to leave all inputs and both Tophat runs active (undeleted) if you submit a bug report, as a history is often very helpful/necessary when diagnosing a problem. Sorry that you were having problems, but hopefully these can be resolved quickly. Best, Jen Galaxy team On 5/7/13 6:34 AM, Elwood Linney wrote: Hello, I have successfully used the public server for processing RNAseq data but I have run into some problems this weekend. And this weekend there were various times when I would get a message that Galaxy was not available. Specifically, I received some new 50bp single-ended RNAseq data and proceeded to process it through the public server as I have done successfully before. I concatenated it the subfiles into one fastq file, transferred it to Galaxy, groomed it just to be safe, looked at its quality and did not have to trim it and then I passed it on to Tophat. [all in the same manner that had worked for me before] It consisted of 4, approximately 15gb files. While i was moving these files individuallly into the Tophat stage this weekend there were interruptions in the availability of Galaxy. I waited during the weekend, one set of the 4 Tophat files for one of the 4 datasets was processed but then 1 file that I had processed during the interruption turned out to have errors, so I deleted it and re-entered it, another set was processing overnight and then it turned out to have errors. So thinking that maybe 3 of the 4 sets for some reason had problems, I deleted them, re entered them. One was going overnight and into the day and this morning it had errors. Since i am not sure how to read these errors, I am at a loss as to what is happening, particularly since one of my files was successfully processed through Tophat. This is the readout for one of the 4 Tophat files that were in error. Any advice on this would be welcome since I hope to soon have a 64gb ram computer with 12 cores to transfer Galaxy to. 43: Tophat for Illumina on data 8: accepted_hits error An error occurred with this dataset: TopHat v1.4.0 tophat -p 8 /galaxy/data/danRer7/bowtie_index/danRer7 /galaxy/main_pool/pool7/files/006/143/dataset_6143636.dat Exception in thread Thread-1: Traceback (most recent call last): File /usr/global/python/2.6.5/lib/python2.6/threading.py, l Sincerely, Elwood Linney Duke University Medical Center ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/ To
[galaxy-user] FW: Error in annotation tools
I edit: Actually I can´t do anything in nebula server, even upload data, I got the cluster error all the time From: Gema Sanz Santos ge2sa...@gmail.com Date: Thursday, May 9, 2013 1:14 PM To: Jennifer Jackson j...@bx.psu.edu Cc: galaxy-u...@bx.psu.edu Subject: Error in annotation tools Hello, I'm using Nebula and when I try to use the annotation tools (genomic annotation and gene annotation in NGS annotation menu) I got always this error despite of the bed file that I use: An error occurred running this job:Unable to run this job due to a cluster error Could you indicate me how to solve this? Regards, Gema ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Filter Fastq
Hi, We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run? Richard ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Filter Fastq
On Thu, May 9, 2013 at 12:27 PM, Casey,Richard richard.ca...@colostate.edu wrote: Hi, We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run? Which FASTQ filtering tool exactly are you referring too? The one called Filter FASTQ reads by quality score and length in the left hand column, tool ID fastq_filter? How big were the input files? Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] nebula problem
Hello, I'm using Nebula and when I try to use the annotation tools (genomic annotation and gene annotation in NGS annotation menu) I got always this error despite of the bed file that I use: An error occurred running this job:Unable to run this job due to a cluster error I also got this error message for everything that I try, even upload data sets (which I can not upload anymore) Could you indicate me how to solve this? Regards, Gema ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] How to analyze the Encode RNA-seq data from UCSC genome browser with Galazy
Dear Sir/Madam, I am new at Galaxy. I need to define if a set loci ( about 700) is transcribed, i.e. these loci overlap with those reported in the Encode RNA-seq data. The track contains several tables, can you please suggest me how to proceed? do I need to download all the tables from UCSC table browser and then upload/send them to Galaxy? Is there a way to refer only to the Encode RNA-seq track without downloading the whole table set? I have the coordinates of each one of my loci, from those I can obtain the sequences. I intended to use the Public Galaxy Main Instance. Thank you, Marco Santagostino -- Marco Santagostino, PhD Laboratorio di Biologia Molecolare e Cellulare Dipartimento di Biologia e Biotecnologie, University of Pavia Ferrata street, 9 - 27100 Pavia, Italy Tel.: +39 0382 985540 Fax: +39 0382 528496 e-mail: marco.santagost...@unipv.it ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Filter Fastq
Hi Richard, The public Main Galaxy server has been very busy lately. To let you know, the size of the job will not determine when a job will start, only the time it was started/queued with respect to other user's jobs also queued and in less common circumstances the specific type of job (that requires a particular cluster node type - this was not the case for your job). How long a job executes (will be in the yellow running state) is related to the size of the inputs, the type of job, and parameters. I see that these have now failed with a cluster error - please re-run the failed jobs one more time. If you continue to have problems, please submit one of the error datasets as a bug report, leaving all inputs/outputs undeleted. http://wiki.galaxyproject.org/Support#Reporting_tool_errors Very sorry that this was causing confusion. And thanks Peter for the help! Jen Galaxy team On 5/9/13 4:27 AM, Casey,Richard wrote: Hi, We have two Filter FASTQ jobs running on the Galaxy public server. Both jobs have been running for more than four days. This seems like an excessive amount of runtime. Do Filter FASTQ jobs normally take this long to run? Richard ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] nebula problem
Hi Gema, This is the support email for the public Main Galaxy instance at usegalaxy.org (https://main.g2.bx.psu.edu/). To get help with this other public Galaxy instance, it would be best to contact them directly for help. http://wiki.galaxyproject.org/PublicGalaxyServers They have two troubleshooting contacts listed at their welcome page here: http://nebula.curie.fr/ Good luck, Jen Galaxy team On 5/9/13 8:38 AM, Gema Sanz Santos wrote: Hello, I'm using Nebula and when I try to use the annotation tools (genomic annotation and gene annotation in NGS annotation menu) I got always this error despite of the bed file that I use: An error occurred running this job:/Unable to run this job due to a cluster error/ / / I also got this error message for everything that I try, even upload data sets (which I can not upload anymore) Could you indicate me how to solve this? Regards, Gema ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] How to analyze the Encode RNA-seq data from UCSC genome browser with Galazy
Hi Marco, Each RNA-seq study in the ENCODE project may have variable coverage, but if the goal is to identify overlapping regions with gene annotations targeted by the ENCODE project, the GENCODE Genes track is most likely the one you are looking for. Review the contents of the track at the ENCODE hub at UCSC by going to their web site http://genome.ucsc.edu, clicking into Genomes, the target genome (hg19?), then scroll down to the track group Gene and Gene Predictions. Click on the track Gencode genes to read about how it is constructed, what the content options are, and how these relate to ENCODE builds. You can follow more links in the description to the subtracks (for example, in hg19, Version 14 is the most current), and describe schema will take you into the Table Browser where the actual format of the data table can be reviewed. Tools - Table Browser will bring you to a form where the table can be extracted and sent to Galaxy, it is the same form found in Galaxy under Get data - UCSC Main. If you start this browser process while still logged into Galaxy from the history you want to import the data in to, you can extract directly from here, making sure that Galaxy is checked (it will be by default) next to the output format: BED section of the form. Or, you can simply explore, and once you know what tracks/tables you are interested in, go through the Galaxy tool Get data - UCSC Main. You may know this already, but the core hub for ENCODE is at: http://genome.ucsc.edu/ENCODE/index.html Basic examples that show how to extract data from UCSC and use coordinate overlap comparison tools can be found at: https://main.g2.bx.psu.edu/u/aun1/p/galaxy101 https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 (protocol 1) More screencasts/tutorials are at: http://wiki.galaxyproject.org/Learn/Screencasts https://main.g2.bx.psu.edu/page/list_published Hopefully this helps, Jen Galaxy team On 5/9/13 11:01 AM, Santagostino Marco wrote: Dear Sir/Madam, I am new at Galaxy. I need to define if a set loci ( about 700) is transcribed, i.e. these loci overlap with those reported in the Encode RNA-seq data. The track contains several tables, can you please suggest me how to proceed? do I need to download all the tables from UCSC table browser and then upload/send them to Galaxy? Is there a way to refer only to the Encode RNA-seq track without downloading the whole table set? I have the coordinates of each one of my loci, from those I can obtain the sequences. I intended to use the Public Galaxy Main Instance. Thank you, Marco Santagostino -- Marco Santagostino, PhD Laboratorio di Biologia Molecolare e Cellulare Dipartimento di Biologia e Biotecnologie, University of Pavia Ferrata street, 9 - 27100 Pavia, Italy Tel.: +39 0382 985540 Fax: +39 0382 528496 e-mail: marco.santagost...@unipv.it mailto:marco.santagost...@unipv.it ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
