May 2013 - galaxy-user - lists.galaxyproject.org

FW: Error in annotation tools
by Gema Sanz Santos 09 May '13

09 May '13

I edit: Actually I can´t do anything in nebula server, even upload data, I got the cluster error all the time From: Gema Sanz Santos <ge2sasag(a)gmail.com> Date: Thursday, May 9, 2013 1:14 PM To: Jennifer Jackson <jen(a)bx.psu.edu> Cc: <galaxy-user(a)bx.psu.edu> Subject: Error in annotation tools Hello, I'm using Nebula and when I try to use the annotation tools (genomic annotation and gene annotation in NGS annotation menu) I got always this error despite of the bed file that I use: An error occurred running this job:Unable to run this job due to a cluster error Could you indicate me how to solve this? Regards, Gema

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problems with Tophat
by Elwood Linney 09 May '13

09 May '13

Hello, I have successfully used the public server for processing RNAseq data but I have run into some problems this weekend. And this weekend there were various times when I would get a message that Galaxy was not available. Specifically, I received some new 50bp single-ended RNAseq data and proceeded to process it through the public server as I have done successfully before. I concatenated it the subfiles into one fastq file, transferred it to Galaxy, groomed it just to be safe, looked at its quality and did not have to trim it and then I passed it on to Tophat. [all in the same manner that had worked for me before] It consisted of 4, approximately 15gb files. While i was moving these files individuallly into the Tophat stage this weekend there were interruptions in the availability of Galaxy. I waited during the weekend, one set of the 4 Tophat files for one of the 4 datasets was processed but then 1 file that I had processed during the interruption turned out to have errors, so I deleted it and re-entered it, another set was processing overnight and then it turned out to have errors. So thinking that maybe 3 of the 4 sets for some reason had problems, I deleted them, re entered them. One was going overnight and into the day and this morning it had errors. Since i am not sure how to read these errors, I am at a loss as to what is happening, particularly since one of my files was successfully processed through Tophat. This is the readout for one of the 4 Tophat files that were in error. Any advice on this would be welcome since I hope to soon have a 64gb ram computer with 12 cores to transfer Galaxy to. 43: Tophat for Illumina on data 8: accepted_hits error An error occurred with this dataset: *TopHat v1.4.0 tophat -p 8 /galaxy/data/danRer7/bowtie_index/danRer7 /galaxy/main_pool/pool7/files/006/143/dataset_6143636.dat Exception in thread Thread-1: Traceback (most recent call last): File "/usr/global/python/2.6.5/lib/python2.6/threading.py", l* Sincerely, Elwood Linney Duke University Medical Center

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Workflow not running
by Lanelle Oni Edwards 08 May '13

08 May '13

Hello, My name is Lanelle Edwards. I am having a problem executing my workflow. I am getting the following error message: Internal Server Error Galaxy was unable to successfully complete your request An error occurred. This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem. The error has been logged to our team. If you want to contact us about this error, please reference the following GURU MEDITATION: #749a5592dc9c42c59ddae1aa9e649fc1 I would really appreciate some assistance on this. Thank You, Lanelle Edwards

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Support for other Genomes in SNPeff
by Diego Borges-Rivera 08 May '13

08 May '13

Hello, My name is Diego and am currently trying to use SNPeff to annotate some variants called from RNA-seq data. I wanted to use SNPeff to annotate human variants but unfortunately the genome is not hosted (only C. Elegans is up there). The genomes I need are specifically: hg19 hg_g1k_v37 --Thank you very much. --Diego

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Error in Tophat
by lilach noy 07 May '13

07 May '13

I have ran Tophat v1.4.0 and it is marked red and has an error " long_spanning_reads". What does this mean? what should i do? Thank you, Lilach

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Downloading files via FTP
by lilach noy 07 May '13

07 May '13

Is it possible? If so, how? Thank you, Lilach

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purging deleted histories
by Suzie Hight 06 May '13

06 May '13

Hello, Is there a way to purge deleted histories which I initially did not "permanently delete"? I just deleted several histories in an effort to free up more disk space, but I see no way to purge them now that they no longer show up in the list. Thanks, Suzie ________________________________ UT Southwestern Medical Center The future of medicine, today.

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server error query
by shreya ghosh 06 May '13

06 May '13

I am using the LEfSe tool on galaxy ( http://huttenhower.sph.harvard.edu/galaxy/root) The upload data step is fine, the next step is format data for LEfSe. When am attempting to carry out this step I am getting the below mentioned error message. Server ErrorAn error occurred. See the error logs for more information. (Turn debug on to display exception reports here) I was wondering if I can get some help regarding how to fix this issue. Thanks, Shreya

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May 2013 Galaxy Update
by Dave Clements 06 May '13

06 May '13

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trimming illumina reads from 3' without considering quality score
by Mathew Bunj 01 May '13

01 May '13

Is it possible to trim certain number of bases from 3' end with taking into consideration quality of reads. To explain it further, I want to remove 10bases from 3 ' end of all reads and keep first forty. Thanks

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