[galaxy-user] An error in reporting a tool error...
Hello all I am working with the LefSe module. Over the last two days, I am gettimg a recurring error in the Plot LefSe result step. LefSe analysis itself is performed OK (I can see the the results in a text browser) but when I want to plot them - I get a red error message. When I do plot differential features , I get a zip file but its empty. The plot one feature function DOES work; but since my datasets have hundreds of species, its quite difficult to find the relevant features one by one manually. The worst thing is, when I try to report this error - by pressing the bug icon in the red failed toolbox - i get this message: Mail is not configured for this galaxy instance So I CAN'T even report the error! Help, anyone? ___ 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] An error in reporting a tool error...
Hi Leah, It sounds like you are using the Galaxy instance run by the Huttenhower Lab at Harvard? At this link? http://huttenhower.org/galaxy/ If so, then at the bottom of the home page is a link you can use to contact the lab members about issues with the instance. (They probably have the default bug report email turned off as a preference). Hopefully this puts you in contact with the right folks who can help, Jen Galaxy team On 7/9/12 4:38 AM, leah reshef wrote: Hello all I am working with the LefSe module. Over the last two days, I am gettimg a recurring error in the Plot LefSe result step. LefSe analysis itself is performed OK (I can see the the results in a text browser) but when I want to plot them - I get a red error message. When I do plot differential features , I get a zip file but its empty. The plot one feature function DOES work; but since my datasets have hundreds of species, its quite difficult to find the relevant features one by one manually. The worst thing is, when I try to report this error - by pressing the bug icon in the red failed toolbox - i get this message: Mail is not configured for this galaxy instance So I CAN'T even report the error! Help, anyone? ___ 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] Indexing files everytime - Performance Issue
Hi Raj, The GATK tool wrappers are still in Beta and are currently under redesign. Since this question is about a local install, it is probably better for the galaxy-...@bx.psu.edu mailing list. When you write in (new thread, please), could you please clarify a bit more? Do you need help with installing native indexes for GATK? Or do you want to re-use indexes generated after a custom genome/other inputs are used (not a current feature, but maybe you want feedback from other developers)? Thanks! Jen Galaxy team On 7/3/12 11:53 PM, Praveen Raj Somarajan wrote: All, It is noticed that Galaxy/GATK indexes reference fasta dbSNP file everytime when it runs. Re-indexing takes time (~10min), hence it affects overall run time when it use for multiple times. However, this could be avoided by reusing the available index. Here is the snapshot of the log: INFO 11:43:57,365 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-21-g30b937d, Compiled 2012/02/01 19:01:14 INFO 11:43:57,365 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 11:43:57,365 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki INFO 11:43:57,366 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa INFO 11:43:57,367 HelpFormatter - - INFO 11:43:57,429 GenomeAnalysisEngine - Strictness is STRICT INFO 11:43:57,432 ReferenceDataSource - Index file /tmp/tmp-gatk-6jlUfH/gatk_input.fasta.fai does not exist. Trying to create it now. PROGRESS UPDATE: file is 15 percent complete PROGRESS UPDATE: file is 28 percent complete PROGRESS UPDATE: file is 91 percent complete INFO 11:45:32,231 ReferenceDataSource - Dict file /tmp/tmp-gatk-6jlUfH/gatk_input.dict does not exist. Trying to create it now. INFO 11:45:54,262 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 11:45:54,280 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02 INFO 11:45:54,304 RMDTrackBuilder - Creating Tribble index in memory for file /tmp/tmp-gatk-6jlUfH/input_dbsnp_0.vcf INFO 11:48:05,910 RMDTrackBuilder - Writing Tribble index to disk for file /tmp/tmp-gatk-6jlUfH/input_dbsnp_0.vcf.idx Do we have any option/alternate in Galaxy to avoid this re-indexing at /tmp, as I have already built the index for reference and dbSNP. Look forward to any suggestions. Thanks, Raj This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD ___ 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/
[galaxy-user] job is waiting to run forever
Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). Any job I submitted today is labeled as Job is waiting to run forever. Could you please let me know the possible reasons? Sincerely, Enuka ___ 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] job is waiting to run forever
Hello Eunuka, A job that is grey in color means that it is queued. A job that is yellow is running - and actual run time can vary. Generally, jobs will begin to run (move from grey to yellow) within a short time period or if the public instance is very busy, within 24hrs. I found three jobs that appear to be yours in the job queue, which means that they are in line to be run (the account is from a slightly different email address). It is important that these are left queued and not restarted, or your jobs will be moved back to the end of the queue. If your work is urgent, a local or cloud instance is recommended: http://getgalaxy.org Best, Jen Galaxy team On 7/9/12 1:17 AM, Yehoshua Enuka wrote: Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). Any job I submitted today is labeled as Job is waiting to run forever. Could you please let me know the possible reasons? Sincerely, Enuka ___ 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] job is waiting to run forever
I brought up this issue previously, I guess Galaxy team please look into it your user base is expending the jobs never get fisnished. Fisrt problem of data uplaod and then running jobs. I never had problem but having lot of problem sfrom last 3-4 months so started using other tools too. Thanks On Mon, Jul 9, 2012 at 1:17 AM, Yehoshua Enuka y.s.en...@gmail.com wrote: Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). Any job I submitted today is labeled as Job is waiting to run forever. Could you please let me know the possible reasons? Sincerely, Enuka ___ 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/
