- galaxy-user - lists.galaxyproject.org

metadata error when using megablast
by Elaine Youngman 20 Feb '14

20 Feb '14

Hello, I am attempting to megablast a FASTA file containing ~45,000 records of 100nt each against the nt database using the Galaxy web interface. I am using a Galaxy-generated FASTA file produced from a groomed FASTQ file using the 'FASTQ to tabular' and 'Tabular to FASTA' tools. When I try to use this as input for the Megablast tool, I get the "Required metadata values are missing" error. When I look at the attributes of the FASTA file, the datatype is indeed set to FASTA. I have tried downloading the FASTA file and reuploading it as a FASTA file explicitly with the same result. I also tried changing the FASTA width to 79, and trimming the records to 70nt each – not the problem. If I make a file containing only the first FASTA record, I get the same error. Any suggestions? Thanks! Elaine

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A Query
by Eva Carolina Rueda 20 Feb '14

20 Feb '14

Dear users, My name is Eva, and Im researcher in FHUC-UNL Argentina. My work is in population genetics of freshwater fishes. I use microsatellite loci to test genpop data. I was wondering if Galaxy contains STRUCTURE software (Bayesian method to define number of clusters in a sample). If the answer is yes, ¿How should I use it? Thank you so much for your help, Dra. Eva Rueda Proffesor FHUC-UNL CIC-CONICET --- Este mensaje no contiene virus ni malware porque la protección de avast! Antivirus está activa. http://www.avast.com

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Disable seeding using Galaxy
by Thierry Grange 20 Feb '14

20 Feb '14

Hello I would like to disable seeding when doing a sequence mapping using bwa. Apparently, this is commonly performed using the aln -l option set at a value higher than the read length, and is often set at values above 1000. In Galaxy, the default option is -1 for this parameter, and it is indicated that -1 corresponds to infinity. Does that mean that seeding can be disabled using -1, and that it is disabled by default on Galaxy? I don't obtain exactly the same thing using -1 or 16000 for this parameter, even though the difference is marginal. Thanks for your insights Thierry Institut Jacques MONOD Paris

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confusion from "Extract Genomic DNA (version 2.2.3) "
by Lu, Mengmeng 19 Feb '14

19 Feb '14

Hi Galaxy team, I recently met two problems when I used " Fetch sequences> Extract Genomic DNA" in Galaxy Main instance. I wanted to extract the exons according to the coordinates in a GFF3 file from my reference sequences (from history, and I specified the genome build) which are in FASTA format. But after checking the output, I found: 1. The first base of each extracted exon was missing in the output, so each extracted exon sequence is one nucleotide shorter than the real length. 2. Some extracted exons are correct,but some extracted exons are wrong. The questionable exons could not be found in the corresponding reference. I can not figure out where they are from. I tried to read the manual/warnings in the page. But I have no idea with my strange output. Could anyone give me some clues,please? Thanks. Best, Miranda

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CummeRbund - biological replicates problem
by Dottorini, Tania 17 Feb '14

17 Feb '14

Dear all, I would like to visualise by CummeRbund the Cuffdiff results obtained using the cufflinks/cuffdiff workflow on the Galaxy server. My samples include replicates data and when I ask for analysis to be done by CummeRbund, to compare replicates, I get error messages. From past postings I red that the Galaxy Cuffdiff does not allows you to download all the required files to be used by CummeRbund for replicate comparisons. As far as I know, the only way to overcome this problem is to run local computer Cuffdiff. I would like to know if anything has changed so far concerning Galaxy Cuffdiff output files and if there are other options instead of running local computer Cuffdiff to solve this problem. Any help would be appreciated Thank you Tania

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Re: [galaxy-user] Galaxy job is waiting to run forever
by Martin Čech 17 Feb '14

17 Feb '14

Martina: it seems that the server you are downloading from has troubles communicating with Galaxy. This is probably FTP issue that we cannot control. The workaround is to download it yourself to your computer from the site and then upload it to Galaxy directly. Let me know how it goes regards Martin, Galaxy team On Mon, Feb 17, 2014 at 3:12 PM, Martina Kracikova < martina_kracikova(a)yahoo.co.uk> wrote: > Hi Martin, > > Unfortunately, this job also isn't running (I'm attaching a screen shot of > the job queue). I also got a new error message saying that Galaxy couldn't > be reached (I'm attaching that too), perhaps that's the problem? Thank you, > > Martina > > > On Monday, February 17, 2014 2:32 PM, Martin Čech <marten(a)bx.psu.edu> > wrote: > Hi Martina, > > this is the actual URL of the file: > ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052/SRR349685.fastq.bz2 > > The URL that you were using is the link to the folder, not the file (you > can tell e.g. by the suffix of the file - my link has it, yours does not). > > Please try the new link and let me know if you encounter any problems. > Goodluck. > > thank you for using Galaxy! > > Martin, Galaxy team > > > On Mon, Feb 17, 2014 at 2:23 PM, Martina Kracikova < > martina_kracikova(a)yahoo.co.uk> wrote: > > Hi Martin, > > Yes, I used usegalaxy.org. I uploaded the data from "Get Data", "Upload > File" and then pasted this link and selected FASTQ as file format: > ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052 It > should be 337MB. > > The job was running for over 20 hours and never finished, so I eventually > deleted it. Now I can't run any other jobs, not even a small job from the > Galaxy 101 tutorial (Sort on data 4 has been waiting to run for over 2 > hours now), which on my colleague's computer took less than a minute to > finish. This makes me think it's something specific to my account. Thanks > for your help! > > Martina > > > On Monday, February 17, 2014 1:36 PM, Martin Čech <marten(a)bx.psu.edu> > wrote: > Hello Martina, > > how did you try to upload it and on what server? I assume it was > usegalaxy.org but please confirm. DId you use the upload button on the > main page or *Get Data / Upload File* from the tool menu? How big is the > file? > > thanks > > Martin, Galaxy team > > > > On Mon, Feb 17, 2014 at 11:37 AM, Martina Kracikova < > martina_kracikova(a)yahoo.co.uk> wrote: > > Hello, > > I tried to upload some fasq data but the jobs never started running and I > waited over 20 hours. I deleted them but now even very small jobs in the > Galaxy 101 tutorial never start running. My colleague tried to execute the > same job in the tutorial and it finished in less than a minute, so is this > something to do with my account? I'm a registered user and am only using > 8.4MB and am only trying to run 1 job. I would appreciate any help. 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/ > > > > > > > >

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Re: [galaxy-user] Galaxy job is waiting to run forever
by Martin Čech 17 Feb '14

17 Feb '14

Hi Martina, this is the actual URL of the file: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052/SRR349685.fastq.bz2 The URL that you were using is the link to the folder, not the file (you can tell e.g. by the suffix of the file - my link has it, yours does not). Please try the new link and let me know if you encounter any problems. Goodluck. thank you for using Galaxy! Martin, Galaxy team On Mon, Feb 17, 2014 at 2:23 PM, Martina Kracikova < martina_kracikova(a)yahoo.co.uk> wrote: > Hi Martin, > > Yes, I used usegalaxy.org. I uploaded the data from "Get Data", "Upload > File" and then pasted this link and selected FASTQ as file format: > ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052 It > should be 337MB. > > The job was running for over 20 hours and never finished, so I eventually > deleted it. Now I can't run any other jobs, not even a small job from the > Galaxy 101 tutorial (Sort on data 4 has been waiting to run for over 2 > hours now), which on my colleague's computer took less than a minute to > finish. This makes me think it's something specific to my account. Thanks > for your help! > > Martina > > > On Monday, February 17, 2014 1:36 PM, Martin Čech <marten(a)bx.psu.edu> > wrote: > Hello Martina, > > how did you try to upload it and on what server? I assume it was > usegalaxy.org but please confirm. DId you use the upload button on the > main page or *Get Data / Upload File* from the tool menu? How big is the > file? > > thanks > > Martin, Galaxy team > > > > On Mon, Feb 17, 2014 at 11:37 AM, Martina Kracikova < > martina_kracikova(a)yahoo.co.uk> wrote: > > Hello, > > I tried to upload some fasq data but the jobs never started running and I > waited over 20 hours. I deleted them but now even very small jobs in the > Galaxy 101 tutorial never start running. My colleague tried to execute the > same job in the tutorial and it finished in less than a minute, so is this > something to do with my account? I'm a registered user and am only using > 8.4MB and am only trying to run 1 job. I would appreciate any help. 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/ > > > > >

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Galaxy job is waiting to run forever
by Martina Kracikova 17 Feb '14

17 Feb '14

Hello, I tried to upload some fasq data but the jobs never started running and I waited over 20 hours. I deleted them but now even very small jobs in the Galaxy 101 tutorial never start running. My colleague tried to execute the same job in the tutorial and it finished in less than a minute, so is this something to do with my account? I'm a registered user and am only using 8.4MB and am only trying to run 1 job. I would appreciate any help. Thank you!

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Same RNAseq samples give different FPKM values when run against different samples
by Elwood Linney 17 Feb '14

17 Feb '14

Hello, I am sure this has come up before and maybe I missed the answer. If in using cuffdiff I run a sample 1(3 repeats) vs a sample 2 and then run the same sample 1(3 repeats) against a sample 3 or a sample 4, I get different value for fpkm from sample 1 each time. Is there something going wrong here or is there something in the program that causes this difference? I have seen this with online Galaxy and with the instance I have on my Mac Pro el linney Duke University

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FTP Error
by Andres Lavore 14 Feb '14

14 Feb '14

Hello, I'm trying to upload a data set through FileZilla (url:usegalaxy.org, user........ and pass.........), but an error appear: Error: Failed to retrieve directory listing Error: Disconnected from serverr: ECONNABORTED - Connection aborted Could someone help me to send the data using the FileZilla program? thanks

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