Re: [galaxy-user] Galaxy error
Hello, Thanks for your response. I can almost never get anything done on the public instance of Galaxy. It can take an entire day to even load a.bed file. When I was encountering the error I was on the Broad Instance. Marco, I tried following the instructions above to ensure that genome was available but got lost. Is there a way to link this with the Broad Instance so I can use this tool? Thanks, Toni On Tue, Jul 23, 2013 at 7:48 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Toni, Bjoern is correct - if you are using a local Galaxy that does not have this reference genome available, it needs to be added. The Extract DNA tool requires a .2bit version of the genome available and the alignseq.loc file configured. More is here, section LASTZ and EXTRACT Genomic DNA: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup The builds.txt file would need to be intact and the genome assigned for this specific error to come up, but in general when adding new reference genomes, that file also needs to be adjusted. Instructions are on this wiki page, along with rsync instructions if you would like to get/model your data after ours: http://wiki.galaxyproject.org/Admin/Data%20Integration The public Main server and the cloud AMI both have this build available. So, if you are using the public server, and this error came up, the issue is likely related to a temporary, earlier issue with job dispatching. Processing load at this time is extremely high as this resolves - so a re-run may not be successful immediately, but do try again in a few hours or even tomorrow morning. Our apologies for any confusion this may have caused, Jen Galaxy team On 7/23/13 9:24 AM, Toni Delorey wrote: Hello, I'm trying to convert a .bed file to a FASTA file. I get the following error when I do. An error occurred with this dataset: *No sequences are available for 'sacCer2', request them by reporting this error.* I'm not sure what the issue is? Thanks, Toni -- Toni Marie Delorey Regev Lab, 6175-OO The Broad Institute of MIT and Harvard 7 Cambridge Center Cambridge, MA 02141 Email: delo...@broadinstitute.org Phone: 617-714-8225 ___ 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 Traininghttp://galaxyproject.org -- Toni Marie Delorey Regev Lab, 6175-OO The Broad Institute of MIT and Harvard 7 Cambridge Center Cambridge, MA 02141 Email: delo...@broadinstitute.org Phone: 617-714-8225 ___ 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] Galaxy error
Toni, As a quick work-around until set up natively, you may be able to use the Extract DNA tool with a custom reference genome: http://wiki.galaxyproject.org/Support#Custom_reference_genome See the example in: Tools on the Main server, should work on any Galaxy set up as a production server In short, you load a fasta version of the genome into your history and use it with tools. UCSC is the source for sacCer2, in the downloads area: http://genome.ucsc.edu Most, but not all, core tools from the Galaxy team have a custom genome support option on the form. When they don't, there is a reason (likely not practical from a indexing/memory usage perspective). Tools developed by the community set their own priority for this support. Best, Jen Galaxy team On 7/25/13 9:19 AM, Toni Delorey wrote: Hello, Thanks for your response. I can almost never get anything done on the public instance of Galaxy. It can take an entire day to even load a.bed file. When I was encountering the error I was on the Broad Instance. Marco, I tried following the instructions above to ensure that genome was available but got lost. Is there a way to link this with the Broad Instance so I can use this tool? Thanks, Toni On Tue, Jul 23, 2013 at 7:48 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Toni, Bjoern is correct - if you are using a local Galaxy that does not have this reference genome available, it needs to be added. The Extract DNA tool requires a .2bit version of the genome available and the alignseq.loc file configured. More is here, section LASTZ and EXTRACT Genomic DNA: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup The builds.txt file would need to be intact and the genome assigned for this specific error to come up, but in general when adding new reference genomes, that file also needs to be adjusted. Instructions are on this wiki page, along with rsync instructions if you would like to get/model your data after ours: http://wiki.galaxyproject.org/Admin/Data%20Integration The public Main server and the cloud AMI both have this build available. So, if you are using the public server, and this error came up, the issue is likely related to a temporary, earlier issue with job dispatching. Processing load at this time is extremely high as this resolves - so a re-run may not be successful immediately, but do try again in a few hours or even tomorrow morning. Our apologies for any confusion this may have caused, Jen Galaxy team On 7/23/13 9:24 AM, Toni Delorey wrote: Hello, I'm trying to convert a .bed file to a FASTA file. I get the following error when I do. An error occurred with this dataset: /No sequences are available for 'sacCer2', request them by reporting this error./ I'm not sure what the issue is? Thanks, Toni -- Toni Marie Delorey Regev Lab, 6175-OO The Broad Institute of MIT and Harvard 7 Cambridge Center Cambridge, MA 02141 Email: delo...@broadinstitute.org mailto:delo...@broadinstitute.org Phone: 617-714-8225 tel:617-714-8225 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.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/ 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 -- Toni Marie Delorey Regev Lab, 6175-OO The Broad Institute of MIT and Harvard 7 Cambridge Center Cambridge, MA 02141 Email: delo...@broadinstitute.org mailto:delo...@broadinstitute.org Phone: 617-714-8225 -- 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] Galaxy error
Hi Toni, to convert a bed file to a fasta file you need the genomic sequence. You can specify a genome-build for every bed file in your history. You probably don't have a genome build specified or its specified as sacCer2. sacCer2 is not configured I would guess, so no genome is available. Try to install a genome for your organism and set the bed file to this genome-build. Cheers, Bjoern Hello, I'm trying to convert a .bed file to a FASTA file. I get the following error when I do. An error occurred with this dataset: No sequences are available for 'sacCer2', request them by reporting this error. I'm not sure what the issue is? Thanks, Toni -- Toni Marie Delorey Regev Lab, 6175-OO The Broad Institute of MIT and Harvard 7 Cambridge Center Cambridge, MA 02141 Email: delo...@broadinstitute.org Phone: 617-714-8225 ___ 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/ ___ 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] Galaxy error
Hi Toni, Bjoern is correct - if you are using a local Galaxy that does not have this reference genome available, it needs to be added. The Extract DNA tool requires a .2bit version of the genome available and the alignseq.loc file configured. More is here, section LASTZ and EXTRACT Genomic DNA: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup The builds.txt file would need to be intact and the genome assigned for this specific error to come up, but in general when adding new reference genomes, that file also needs to be adjusted. Instructions are on this wiki page, along with rsync instructions if you would like to get/model your data after ours: http://wiki.galaxyproject.org/Admin/Data%20Integration The public Main server and the cloud AMI both have this build available. So, if you are using the public server, and this error came up, the issue is likely related to a temporary, earlier issue with job dispatching. Processing load at this time is extremely high as this resolves - so a re-run may not be successful immediately, but do try again in a few hours or even tomorrow morning. Our apologies for any confusion this may have caused, Jen Galaxy team On 7/23/13 9:24 AM, Toni Delorey wrote: Hello, I'm trying to convert a .bed file to a FASTA file. I get the following error when I do. An error occurred with this dataset: /No sequences are available for 'sacCer2', request them by reporting this error./ I'm not sure what the issue is? Thanks, Toni -- Toni Marie Delorey Regev Lab, 6175-OO The Broad Institute of MIT and Harvard 7 Cambridge Center Cambridge, MA 02141 Email: delo...@broadinstitute.org mailto:delo...@broadinstitute.org Phone: 617-714-8225 ___ 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] Galaxy Error
Hello Delong ZHOU, On 6/7/13 8:23 AM, Delong, Zhou wrote: Hello, I'm using the main galaxy server to analyse some data and then I got this messege: An error occurred while getting updates from the server. Please contact a Galaxy administrator if the problem persists. This message indicates that the server is busy. Usually waiting a few minutes and trying again is the solution. If the message still comes up, then wait a bit longer between attempts - the server is still busy. I was uploading data from my computer since yesterday morning and it seems to take forever to accomplish. After one of my reads is uploaded I used the groomer tool on this dataset and then I got this messege. I tried the reflesh bottom on the right pannal severial times and I got the same messege each time. You can access to my history here: https://main.g2.bx.psu.edu/u/zhoud/h/knockdown I see that the 'Fastq Groomer is running now on the one fully loaded dataset now, which is good. Besides, is it possible to show the grade of progress of uploading? If you switch to using FTP, upload progress can be tracked through a client. http://wiki.galaxyproject.org/FTPUpload General upload help: http://wiki.galaxyproject.org/Support#Trouble_loading_data Best, Jen Galaxy team Thanks, Delong ZHOU ___ 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] Galaxy error: can't fine fasta file
Hello Kenneth, Are you using BLAST+ in a local install or cloud instance? The problem may be that the query dataset needs to have the datatype assigned as fasta. To do this, click on the pencil icon for the dataset to reach the Edit Attributes form. Then either scroll down to (or click on the tab for) the attribute Datatype and change to fasta and save. [The UI is undergoing some changes, so you may or may not have the new tabs style form in your instance yet). The best mailing list going forward for local/cloud support is galaxy-...@bx.psu.edu. http://wiki.g2.bx.psu.edu/Mailing%20Lists Take care and please let us know if your question has been misunderstood, Jen Galaxy team On 9/17/12 8:52 AM, Kenneth R. Auerbach wrote: Hello, I'm new to Galaxy. When I read in a fasta file to Galaxy and then try to use it (in a blast search) as the query sequence, I get the error message below, although the uploaded fasta file is present in the history. Can anyone tell me what the problem could be? Is there some other step I need to do? Thank you. Error that appears under nucleotide query sequence: - History does not include a dataset of the required format / build - ___ 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://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/
Re: [galaxy-user] Galaxy error: can't fine fasta file
Hi Kenneth, Yes, target databases require indexes and *.loc file set-up. Please see this wiki for details. For Genbank data such as NR, FTP the pre-built indexes and use those (generating them with formatdb is not necessary). http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup See the second section, 'Tips for Installing Tools - 'Megablast installation', then down in the wiki again under 'Megablast' for more detail. The same indexes can be used for BLAST+ (both now are based on BLAST+). The location of the data can be where you have it - it seems like Galaxy is looking in the right place for it (it does not go under a genome like the other indexes on the wiki). Also, make sure the data is uncompressed before you use it. And be sure to point to the data into the blastdb.loc file (this appears to be done already based on your error message, but double check). Hopefully this helps, Jen Galaxy team On 9/17/12 10:11 AM, Kenneth R. Auerbach wrote: Hi Jennifer, Thank you for that info. I have another question, when I submit my job I get this error: - An error occurred running this job: BLAST Database error: No alias or index file found for protein database [/9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr] in search path [/9720/galaxyprod/galaxy-dist/database/job_working_directory/1560::] Return error code 2 from command: blast -- I checked and the 'nr' database file is there in that path and it has read permissions for everyone. It's in a directory called 'nr-newstyle' with only its archive file (.gz). There are no other files. Should there also be 'alias' or 'index' files as well? Are other files needed besides 'nr'? Thank you. On Mon, 2012-09-17 at 09:29 -0700, Jennifer Jackson wrote: Hello Kenneth, Are you using BLAST+ in a local install or cloud instance? The problem may be that the query dataset needs to have the datatype assigned as fasta. To do this, click on the pencil icon for the dataset to reach the Edit Attributes form. Then either scroll down to (or click on the tab for) the attribute Datatype and change to fasta and save. [The UI is undergoing some changes, so you may or may not have the new tabs style form in your instance yet). The best mailing list going forward for local/cloud support is galaxy-...@bx.psu.edu. http://wiki.g2.bx.psu.edu/Mailing%20Lists Take care and please let us know if your question has been misunderstood, Jen Galaxy team On 9/17/12 8:52 AM, Kenneth R. Auerbach wrote: Hello, I'm new to Galaxy. When I read in a fasta file to Galaxy and then try to use it (in a blast search) as the query sequence, I get the error message below, although the uploaded fasta file is present in the history. Can anyone tell me what the problem could be? Is there some other step I need to do? Thank you. Error that appears under nucleotide query sequence: - History does not include a dataset of the required format / build - ___ 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://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/
Re: [galaxy-user] Galaxy error: can't fine fasta file
Hi Kenneth, It is likely that the path is wrong in the .loc file. It has to point to the actual files, not just the directory. Inside here /9720/genome_references/ncbi/nr-protein-db is where all the nr.* files are? In that case, the path should be /9720/genome_references/ncbi/nr-protein-db/nr You will want to open the .loc file in a text editor that allows you to view the whitespace, too, to double check that the columns are single tab separated and that there are no extra spaces before or after the data in any individual column. The middle column can contain internal spaces, but those should be the only spaces in any row. You also do not want any trailing blank/empty lines in the file. And yes, restart the server. A checklist is at the top of the wiki to help: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Best, Jen Galaxy team On 9/17/12 12:46 PM, Kenneth R. Auerbach wrote: Hi Jennifer, I changed the path of the nr files in the .loc file to the following: nr NCBI NR (non -redundant) /9720/genome_references/ncbi/nr-protein-db This is the directory that has all those many nr files (index files, etc) But I still get the same error where the old path is still referenced. Does the galaxy server need to be restarted for the new .loc file to go into effect? Thank you. Ken. On Mon, 2012-09-17 at 10:42 -0700, Jennifer Jackson wrote: Hi Kenneth, Yes, target databases require indexes and *.loc file set-up. Please see this wiki for details. For Genbank data such as NR, FTP the pre-built indexes and use those (generating them with formatdb is not necessary). http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup See the second section, 'Tips for Installing Tools - 'Megablast installation', then down in the wiki again under 'Megablast' for more detail. The same indexes can be used for BLAST+ (both now are based on BLAST+). The location of the data can be where you have it - it seems like Galaxy is looking in the right place for it (it does not go under a genome like the other indexes on the wiki). Also, make sure the data is uncompressed before you use it. And be sure to point to the data into the blastdb.loc file (this appears to be done already based on your error message, but double check). Hopefully this helps, Jen Galaxy team On 9/17/12 10:11 AM, Kenneth R. Auerbach wrote: Hi Jennifer, Thank you for that info. I have another question, when I submit my job I get this error: - An error occurred running this job: BLAST Database error: No alias or index file found for protein database [/9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr] in search path [/9720/galaxyprod/galaxy-dist/database/job_working_directory/1560::] Return error code 2 from command: blast -- I checked and the 'nr' database file is there in that path and it has read permissions for everyone. It's in a directory called 'nr-newstyle' with only its archive file (.gz). There are no other files. Should there also be 'alias' or 'index' files as well? Are other files needed besides 'nr'? Thank you. On Mon, 2012-09-17 at 09:29 -0700, Jennifer Jackson wrote: Hello Kenneth, Are you using BLAST+ in a local install or cloud instance? The problem may be that the query dataset needs to have the datatype assigned as fasta. To do this, click on the pencil icon for the dataset to reach the Edit Attributes form. Then either scroll down to (or click on the tab for) the attribute Datatype and change to fasta and save. [The UI is undergoing some changes, so you may or may not have the new tabs style form in your instance yet). The best mailing list going forward for local/cloud support is galaxy-...@bx.psu.edu. http://wiki.g2.bx.psu.edu/Mailing%20Lists Take care and please let us know if your question has been misunderstood, Jen Galaxy team On 9/17/12 8:52 AM, Kenneth R. Auerbach wrote: Hello, I'm new to Galaxy. When I read in a fasta file to Galaxy and then try to use it (in a blast search) as the query sequence, I get the error message below, although the uploaded fasta file is present in the history. Can anyone tell me what the problem could be? Is there some other step I need to do? Thank you. Error that appears under nucleotide query sequence: - History does not include a dataset of the required format / build - ___ 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://galaxyproject.org ___ The
