Re: [galaxy-user] Error message
Hello Heller, The server errors were a transient issue. Our apologies for the confusion. I can see that your jobs are now processing. This wiki section explains in more detail about how to interpret interface cues to determine job status: https://wiki.galaxyproject.org/Support#Dataset_status_and_how_jobs_execute Best, Jen Galaxy team On 3/4/14 5:17 AM, Heller Gerwin wrote: Hello! I use Galaxy to convert unaligned .bam files (RNA-seq) to fastq files. That works! Then i want to align the fastq files using TopHat2 or Tophat, but the analysis does not start since yesterday. However, I received the following error message several times since yesterday: Details user usernamenull quota_percent30 total_disk_usage81718693796 nice_total_disk_usage76.1 GB emailgerwin.hel...@meduniwien.ac.at Thanks for help!! With kind regards, Gerwin Heller -- 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] 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/
Re: [galaxy-user] error message running Cufflinks on local galaxy
Hi Davide, Is this the same job as you can on the public Galaxy Main instance (same inputs/settings)? If so, let's review that one once the bug report comes in and see if the there is a data issue we can trace back to as one of the first steps (GTF file or other). Jeremy might also have more information (know what this error code is). We will be get back to you soon, Jen Galaxy team On 2/1/13 7:27 AM, Davide Degli Esposti wrote: Dear Jen, I have downloaded Galaxy on my computer. When trying to run cufflinks locally I have this error message: 8: Cufflinks on data 3 and data 2: gene expression error An error occurred running this job:/Could not determine Cufflinks version cufflinks -q --no-update-check -I 30 -F 0.05 -j 0.15 -p 4 -G /Users/davidedegliesposti/galaxy-dist/database/files/000/dataset_2.dat -N Error running cufflinks. return code = 127 /bin/sh: cufflinks: command/ / / / / May this be due to an error of installation? Thank you for your help Davide / / --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel.+33 4 72738036 Fax.+33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France / This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use. / ___ 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 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/
Re: [galaxy-user] Error message on local install
Hi Chris, It sounds like the file is too large for your set up and there is a memory problem. There are a few options: 1 - If you really want to try to use your desktop computer, break the large file into smaller files before running the tools, then merge together data from the same barcode together once split away from the rest. This may get tedious depending on how many barcodes you are working with, but possible. Just double check that the tool you are running makes sense to run on the partial datasets you are providing as input (most of the tools you list will run on any partial dataset). I would suggest running some tests to see if these are small enough to work with in your environment before you invest too much in this strategy (you may find that you run into resource issues again in later steps, like mapping). 2 - Run Galaxy on a different local computer, one with more memory. 3 - Run Galaxy on a cloud instance with sufficient memory. http://usegalaxy.org/cloud Going forward, the galaxy-...@bx.psu.edu mailing list would be a good choice for local/cloud install questions: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Best, Jen Galaxy team On 10/10/12 3:28 PM, Chris Merrikh wrote: Hi, I'm trying to solve an issue I'm having with my local installation of Galaxy (installed on my own computer, rather than on a server). I'm using data in the form of fastq files from an Illumina Hi-seq and I want Galaxy to parse the bar coded sequences out into individual files for me. I've been using the public server in the past, and I'm able to use the Groomer, Joiner, Reverse-Complement, Trimmer, and Barcode Splitter tools just fine. Now I'm trying to do the same thing locally on the same files. Both the large file (38 GB) and a smaller file consisting of the first 10k lines will upload just fine. However, I can only get the Groomer to work on the small file. When I use it on the large file I get an error: "Error executing tool: maximum recursion depth exceeded while calling a Python object." Any help on this would be greatly appreciated! - Chris M. ___ 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] Error message on local install
Hi Chris, Are you able to share a copy of the offending file? Perhaps by uploading to the public Galaxy server, possibly trying the Grooming step there, and then sharing the history with me or by using the bug report option on the Grooming step if it fails? If not, you could look at the output created (the error dataset) and use e.g. tail to find out the last few fastq blocks that were successfully processed or wc -l to find out the number of lines written, and then use grep -C or a combination of head/tail to look at the original file and see if anything is amiss. Thanks for using Galaxy, Dan On Oct 10, 2012, at 6:28 PM, Chris Merrikh wrote: > Hi, I'm trying to solve an issue I'm having with my local installation of > Galaxy (installed on my own computer, rather than on a server). I'm using > data in the form of fastq files from an Illumina Hi-seq and I want Galaxy to > parse the bar coded sequences out into individual files for me. I've been > using the public server in the past, and I'm able to use the Groomer, Joiner, > Reverse-Complement, Trimmer, and Barcode Splitter tools just fine. Now I'm > trying to do the same thing locally on the same files. Both the large file > (38 GB) and a smaller file consisting of the first 10k lines will upload just > fine. However, I can only get the Groomer to work on the small file. When I > use it on the large file I get an error: "Error executing tool: maximum > recursion depth exceeded while calling a Python object." > > Any help on this would be greatly appreciated! > > - Chris M. > ___ > 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/
