[galaxy-user] Galaxy error: can't fine fasta file
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/
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
