Re: [galaxy-user] (no subject)
Hi Maria, This message indicates that an error occurred on the cluster node processing the job. Normally these are not linked to inputs or tools and the general solution is to re-run the job. Please give this a try today - it is possible the error was linked to recent transient server issues. If you continue to have problems after the re-run today, please submit a bug report from the error dataset, leaving inputs and outputs undeleted: http://wiki.galaxyproject.org/Support#Reporting_tool_errors Best, Jen Galaxy team On 9/11/13 12:38 PM, Maria Hoffman wrote: Hello, I am fairly new to galaxy and I am trying to use bowtie2 to map my reads against a custom genome (specifically a ribosomal RNA fasta file). I have formatted the file as suggested in the Galaxywiki ect and I am still getting the following message: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. Any help would me much appreciated! Maria ___ 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 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] Data sources don't load in Firefox
Hi Carrie, We are aware of this new issue with the Firefox 23.0.1 update. Using an alternate browser is recommended to avoid the problem with direct https->http connections, as several of Galaxy's "Get Data" tools/sources are impacted. Our team is reviewing solutions at a priority. Hopefully this helps to confirm the issue, and our apologies for the current inconvenience, Jen Galaxy team On 9/11/13 8:01 AM, Ganote, Carrie L wrote: Hi List, I'm trying to go through Galaxy 101, and the first step is halting me (UCSC Main table browser does nothing on click). I'm giving a presentation on how to use Galaxy, but the data sources do not load when using Firefox. The tool click registers, because the history pane is minimized, but the URL is not invoked (no activity from browser). I went through my FF settings to see if I'm doing anything to block iframe loads. The funny thing is, though UCSC and BX don't load, but Biomart does - likely because it is not in an iframe but gets loaded as its own window. If I open in a new tab, it's fine. These things load on Chrome, IE and Safari. A lot of my users use Firefox, however. I appreciate any insight into this. Sincerely, Carrie Ganote ___ 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 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/
[galaxy-user] error message from Filezilla
Hi, I am getting the following error from the server : Command:USER genebus...@googlemail.com Response:331 Password required for genebus...@googlemail.com Command:PASS *** Response:530 Sorry, the maximum number of clients (3) for this user are already connected. Error:Critical error Error:Could not connect to server. Can you please help. warm regards, Amit. ___ 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] Data sources don't load in Firefox
Hi List, I'm trying to go through Galaxy 101, and the first step is halting me (UCSC Main table browser does nothing on click). I'm giving a presentation on how to use Galaxy, but the data sources do not load when using Firefox. The tool click registers, because the history pane is minimized, but the URL is not invoked (no activity from browser). I went through my FF settings to see if I'm doing anything to block iframe loads. The funny thing is, though UCSC and BX don't load, but Biomart does - likely because it is not in an iframe but gets loaded as its own window. If I open in a new tab, it's fine. These things load on Chrome, IE and Safari. A lot of my users use Firefox, however. I appreciate any insight into this. Sincerely, Carrie Ganote ___ 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] Questions about MEME & Sequence logo generator
Hi, Has the MEME module been taken out of the main galaxy server? Assuming it'll be back, what's roughly a recommended number of sequences to feed into MEME? It has a limit on the sequences that it can digest but I don't know what it is. Likewise, what's this limit for the Sequence Logo Generator? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ___ 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] (no subject)
Hello, I am fairly new to galaxy and I am trying to use bowtie2 to map my reads against a custom genome (specifically a ribosomal RNA fasta file). I have formatted the file as suggested in the Galaxywiki ect and I am still getting the following message: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. Any help would me much appreciated! Maria ___ 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] FASTQ joiner
Lilach: This tool works on unaligned reads in fastq format before they are mapped. It is useful for merging mates together into a single read for QC processing, filtering, and trimming. Thanks! anton On Wed, Sep 11, 2013 at 4:34 AM, lilach noy wrote: > Hi all, > > Has anyone used FASTQ joiner with a file containing multi-mapped reads? > I'm pretty sure i have reads mapped to several locations and i don't know > what this tool does with it? will it locate the right map according to the > paired read? will it use the first read location and ignore the rest or > maybe it will exclude all multi-mapped reads prior to paring? > > Regards, > Lilach > > ___ > 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] cannot download data to Galaxy
On Sep 11, 2013, at 9:56 AM, Elwood Linney wrote: > > Hello, > My connection with Galaxy online shutoff last night while I was transferring > data to it. When I tried to connect again with Fetch this morning I was not > allowed and a message like "Sorry the maximum number of clients for this user > are already connected." > > I have had what appears to be the bad habit of not logging off to Galaxy. I > am working on the same data sets with three different computers, I only have > one login to Galaxy, so yes, I was logged in on 3 different computers. When > I logged off of them, and tried to transfer data, I still got the same > message. > > I realize people might be trying to get around the 250gb limit by having > multiple logins--I am not one of them, I am the only user on the three > computers I am using. If not logging off when I leave the computer is a > problem to Galaxy, I will religiously log off each time I am not using the > computer (the computers are in three different rooms in my lab and my lab > consists of just me and a tech--I am the only one who knows the computer > login for both the computers and for Galaxy). > > If I have created a problem by being "lazy", I apologize, but I have grown > dependent upon using Galaxy online and some new data just came in. Hi Elwood, This is not due to staying logged in to the web interface, I believe it's a bug in the FTP server that we're using. I've restarted the server, could you let us know if you're still getting the maximum clients message if you try to connect? --nate > > Sincerely, > > Elwood Linney > Professor of Molecular Genetics and Microbiology > 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/ ___ 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] error message from Filezilla
On Sep 11, 2013, at 7:48 AM, Amit Pande wrote: > Hi, > > I am getting the following error from the server : > Command:USER genebus...@googlemail.com > Response:331 Password required for genebus...@googlemail.com > Command:PASS *** > Response:530 Sorry, the maximum number of clients (3) for this user are > already connected. > Error:Critical error > Error:Could not connect to server. > > Can you please help. Hi Amit, Please give it a try now, I've restarted the FTP server (I believe this is due to a bug in the server). --nate > > warm regards, > Amit. > ___ > 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/
[galaxy-user] cannot download data to Galaxy
Hello, My connection with Galaxy online shutoff last night while I was transferring data to it. When I tried to connect again with Fetch this morning I was not allowed and a message like "Sorry the maximum number of clients for this user are already connected." I have had what appears to be the bad habit of not logging off to Galaxy. I am working on the same data sets with three different computers, I only have one login to Galaxy, so yes, I was logged in on 3 different computers. When I logged off of them, and tried to transfer data, I still got the same message. I realize people might be trying to get around the 250gb limit by having multiple logins--I am not one of them, I am the only user on the three computers I am using. If not logging off when I leave the computer is a problem to Galaxy, I will religiously log off each time I am not using the computer (the computers are in three different rooms in my lab and my lab consists of just me and a tech--I am the only one who knows the computer login for both the computers and for Galaxy). If I have created a problem by being "lazy", I apologize, but I have grown dependent upon using Galaxy online and some new data just came in. Sincerely, Elwood Linney Professor of Molecular Genetics and Microbiology 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/
[galaxy-user] GATK error Argument with name 'T' isn't defined
Aloha. I am using GATK in Galaxy for the first time, on a local Galaxy server, and when I try to run Count Covariates I get the error: ERROR stack trace org.broadinstitute.sting.commandline.InvalidArgumentException: Argument with name 'T' isn't defined. at org.broadinstitute.s I have looked at the GATK Count Covariates command line, and it looks to me like the argument with name 'T' is not a place where I need to input a file, but is where the Count Covariates software information goes. I get this same error when trying to run Realigner Target Creator. I wondered if this might be something that could be simply fixed by reinstalling the wrappers for GATK, or something along those lines? Thank you! ___ 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] extension of read length
Dear all, I am working on an MNAse-Seq experiment with 50bp single end reads. To identify nucleosome positions, I read that one needs to extend the single reads to approximately the length of nucleosome protected DNA, being approximately 150bp. Is there a way in Galaxy to extend 50bp reads to 150bp length, lets say from a .BAM file with mapped reads? Of course any other comment on this topic is much appreciated! Thank you very much, Tobias -- Tobias Hohenauer, PhD GCNA, Disease Mechanism Research Core RIKEN Brain Science Institute 2-1 Hirosawa, Wako-shi 351-0198 Japan ___ 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] FASTQ joiner
Hi all, Has anyone used FASTQ joiner with a file containing multi-mapped reads? I'm pretty sure i have reads mapped to several locations and i don't know what this tool does with it? will it locate the right map according to the paired read? will it use the first read location and ignore the rest or maybe it will exclude all multi-mapped reads prior to paring? Regards, Lilach ___ 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/
