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

where to submit galaxy error messgae
by Jennifer Jackson 10 Jan '13

10 Jan '13

Hi Kathryn, If you encounter an error while using the public Main Galaxy server at http://main.g2.bx.psu.edu (usegalaxy.org) the first thing to do is review the tool usage help (on tool form) and the input dataset formats. Often the error message or 'i' info page's standard out/error will have some details about the problem, or the info revealed when clicking on the 'bug' icon (this doesn't automatically send in a bug report, you can also just review it). Many problems can be solved with minor adjustments, some tips are in our wiki here: http://wiki.galaxyproject.org/Support#Help.21_Common_Solutions But if you are still stuck, then please submit the error as a bug report, being sure to leave the inputs and error itself undeleted in your history (this is important), following this method: http://wiki.galaxyproject.org/Support#Reporting_tool_errors When running your own instance, or a cloud instance, other factors can contribute to problems, including the instance administration options and set-up. It is best to send these types of questions, with clear descriptions of the issues and some description of the troubleshooting you have done (this tends to generate the most feedback) to the dedicated development mailing list at galaxy-dev(a)bx.psu.edu. This will give it the best exposure to the dev community. http://wiki.galaxyproject.org/Support#Mailing_Lists I see your other question now posted about MACS. At first glance this looks like a local install tool configuration problem, which would be a good fit for the galaxy-dev list, but we will respond to that question or move it over there and then respond. We do our best not to cross/double post to both lists. Hopefully this helps explain things a bit more! All list emails come to the same folks here on the core team - this org just helps us to track. But, the real benefit is for our community, so they can participate in their area of interest and more effectively search prior Q & A. Take care, Jen Galaxy team On Jan 10, 2013, at 2:31 PM, "Sun, Wenping [USA]" <Sun_Wenping(a)bah.com> wrote: > Hi Jennifer, > > I have few messages with the error that I had while running galaxy modules. Is galaxy-user is good email for sending and getting the responses? > > Thank you very much, > Kathryn Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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BWA and FASTQ Joiner issues
by Hilde Stawski 10 Jan '13

10 Jan '13

Hello, I hope someone might be able to help me with these issues, as I'm relatively new at Bioinformatics. When analyzing data on the main website of Galaxy (all samples from the same Illumina MiSeq run) some sets fail in the BWA alignment. I have tried rerunning my workflow again, reuploading the FastQ files (in case they were corrupted) but BWA fails every single time. I've pasted the error log below. Q1: Why are most of my datasets aligned by BWA without a problem, but some consistently fail? So, some people at SEQanswers suggested I install a local Galaxy client on my computer, and I'm now trying to rework my workflow so I can use BFAST as an aligner. BWA was giving us some trouble due to indels in our mtDNA sequence, so we are trying to find another aligning tool that is more capable of working with these indels, anyway. However, now I'm running into a second problem. I have PE data, and after grooming both FASTQ files, the FASTQ Joiner generates an empty file. I did try the workaround mentioned here ( http://lists.bx.psu.edu/pipermail/galaxy-user/2012-April/004519.html) but I'm not sure I understand the following instructions "NGS: QC and manipulation -> Tabular to FASTQ" run twice Recreate both FASTQ files from the same tabular file." I ran FASTQ to Tabular with two columns, and joined the files on the first column. Why/how should I recreate both FASTQ files if I wanted to create just one single file to use as input for alignment? FASTQ Groomer doesn't seem to be able to groom the data either "Based upon quality and sequence, the input data is valid for: None Input ASCII range: '0'(48) - 'N'(78) Input decimal range: 15 - 45" Q2: How do I create a single file as input for the aligner? Thanks in advance for any help, Hilde --- The alignment failed. Error generating alignments. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (2402, 5234, 8910) [infer_isize] low and high boundaries: 151 and 21926 for estimating avg and std [infer_isize] inferred external isize from 251269 pairs: 5940.068 +/- 4124.607 [infer_isize] skewness: 0.511; kurtosis: -0.744; ap_prior: 1.00e-05 [infer_isize] inferred maximum insert size: 23222 (4.19 sigma) [bwa_sai2sam_pe_core] time elapses: 1.37 sec [bwa_sai2sam_pe_core] changing coordinates of 0 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 3297 out of 10352 Q17 singletons are mated. [bwa_paired_sw] 0 out of 188377 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 2241.09 sec [bwa_sai2sam_pe_core] refine gapped alignments... 1.37 sec [bwa_sai2sam_pe_core] print alignments... 1.76 sec [bwa_sai2sam_pe_core] 262144 sequences have been processed. [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (2595, 7186, 11297) [infer_isize] low and high boundaries: 151 and 28701 for estimating avg and std [infer_isize] inferred external isize from 84557 pairs: 7236.733 +/- 4785.357 [infer_isize] skewness: 0.066; kurtosis: -1.262; ap_prior: 1.00e-05 [infer_isize] inferred maximum insert size: 27144 (4.16 sigma) [bwa_sai2sam_pe_core] time elapses: 0.38 sec [bwa_sai2sam_pe_core] changing coordinates of 0 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 482 out of 3212 Q17 singletons are mated. [bwa_paired_sw] 0 out of 40389 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 532.50 sec [bwa_sai2sam_pe_core] refine gapped alignments... /bin/sh: line 1: 28068 Segmentation fault bwa sampe /tmp/ 3030216.cyberstar.psu.edu/tmprNNXwj/tmpXybcjA /tmp/ 3030216.cyberstar.psu.edu/tmpq3YCcl/tmpKvAb8e /tmp/ 3030216.cyberstar.psu.edu/tmpq3YCcl/tmpvUAE3E/galaxy/main_pool/pool3/files/… /galaxy/main_pool/pool3/files/005/540/dataset_5540837.dat >> /galaxy/main_pool/pool2/tmp/job_working_directory/004/860/4860532/galaxy_dataset_5540842.dat

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Re: [galaxy-user] Download data using FTP-access?
by Jennifer Hillman-Jackson 09 Jan '13

09 Jan '13

Hi Karen, I don't run windows OS, but found this link that seems to describe the same situation with a solution. Maybe give it a try and see if it works? http://stackoverflow.com/questions/3562095/using-curl-to-get-a-https-webpag… This link also looked helpful, just from a set-up perspective and since your curl install is new, but I don't know if you are using a 64-bit machine or not: https://support.gradesfirst.com/forums/20230492-how-to-setup-curl-on-window… I found these with a google using "curl windows 7 https" - there are other hits, but these two looked the most promising as a first go for troubleshooting. Good luck! Jen Galaxy team On 1/9/13 1:46 AM, Karen Margrethe Jessen wrote: > Hi Jennifer, > > Thanks for your answer. I have downloaded the Curl program and I am trying to use it from commando promt in Windows 7. Hovewer, when typing the commando: > > ’C:\ curl https://xxxxxxxxxxxxxxxxxxx’ > > in commando promt, I get the following message: > > ’Protocol https not supported or disabled in libcurl’. > > How do I make Curl download from https? > > Karen > > > ________________________________________ > Fra: Jennifer Hillman-Jackson [jen(a)bx.psu.edu] > Sendt: 8. januar 2013 16:33 > Til: Karen Margrethe Jessen > Cc: galaxy-user(a)lists.bx.psu.edu > Emne: Re: [galaxy-user] Download data using FTP-access? > > Hello Karen, > > From a shell/unix/terminal window on your side, use "curl" to download > datasets. > > The link can be obtained by right clicking the floppy disk icon inside a > history item and choosing "Copy Link Address" (for most datasets) or > "Download Dataset/Download bam_index" (for BAM datasets there are two > downloads). Once you have the link: > > $ curl -O '<link>' > > Hopefully this helps! > > Jen > Galaxy team > > > On 1/8/13 2:27 AM, Karen Margrethe Jessen wrote: >> Is there any way of downloading processed files at galaxyproject.org by >> e.g. FTP, instead of “Save as” in the web browser? I have some large >> (~50Gb) BAM files to download, and downloading it via the browser is not >> stable. >> >> Thanks, Karen. >> >> >> ___________________________________________________________ >> 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 > -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Remove "unpaired" reads from quality-filtered pared-end fastq files.
by 柴田弘紀 09 Jan '13

09 Jan '13

Hi there, I obtained two fastq files from GA paired end run. I filtered each file by quality using fastq tool kit. Then some forward reads may be removed by low quality whereas the reverse counterparts are OK to be remained on the other file, or vice versa. I want to remove those "unpaired" reads from filtered fastq files so that the two new fastq files contain the identical sets of the reads. Is it possible to do it on galaxy? Thank you very much. Hiroki

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joining two FASTq files with overlap reads
by shamsher jagat 09 Jan '13

09 Jan '13

I have a data generated from Miseq 2X250 bp these reads are overlap, before aligning to a my custom bacterial genome, I have to join these two mate pair Fastq files and then use BWA alignment tool. I am aware of COPE/ FLASH can be used. I am looking for if there are similar tool or any way I can join two Fastq files which i can use for alignment. Just to clarify further with overlapping reads as such BWA is not aligning the reads. I have used both as mate pair or used only forward reads to align to genome. The idea is to find SNPs in different samples. Thanks Kanwar

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Download data using FTP-access?
by Karen Margrethe Jessen 08 Jan '13

08 Jan '13

Is there any way of downloading processed files at galaxyproject.org by e.g. FTP, instead of “Save as” in the web browser? I have some large (~50Gb) BAM files to download, and downloading it via the browser is not stable. Thanks, Karen.

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Trackster custom builds wrong
by Jennifer Hillman-Jackson 08 Jan '13

08 Jan '13

Repost to Galaxy-user ----------- When using Trackster on Galaxy( https://main.g2.bx.psu.edu/root ), as the Galaxy Wiki of Trackster (http://wiki.galaxyproject.org/Learn/Visualization) recommend , I need to build a track browsers for soybean because that it isn't installed for all users. But after I enter the all the request information on the webpage(new build name, key and definition) and submit, but I get an server error information, it says "an error occurred. see the error logs for more information.(Turn debug on to display exception reports here)" Since I find there is also someboby encounter this problem in the mail list, but did't find any useful solution. So, I want to know why it happend and how to fix it. Is there something wrong in my maniputation? Any replay will be appreciated. Thank you very much! Yours sincerely, Yanting Shen

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Re: [galaxy-user] [Ticket#2013010710000031] Installation de ChipMunk sur Genotoul
by Sarah Maman 08 Jan '13

08 Jan '13

Thanks Alban for your answer, Our admin system has tested to run ChIPMunk externally but didn't received the same error message. In fact, pretty.rb lib is found. It seems to be a difference between chiphorde version : we have run_chiphorde4.rb instead of run_chiphorde.rb Do you think that we have to install your version or thaht we just need to rename some files? Your error message when running ruby run_chiphorde4.rb is : LLIB 08 Jan 09:10:17 [ytilib] ytilib required, working directory /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts LLIB 08 Jan 09:10:17 [ytilib] use_chiphorde4.rb started, usage <motif_template> <ChIPHorde-engine-params> LLIB 08 Jan 09:10:17 [ytilib] run_chiphorde4.rb Thanks in advance, Sarah Support a écrit : > Bonjour, > > Voilà ce que j'obtiens quand je lance la commande qu'il demande: > > ruby run_chiphorde4.rb > LLIB 08 Jan 09:10:17 [ytilib] ytilib required, working directory > /usr/local/bioinfo/src/ChIPMunk/chipmunk_v41_scripts > LLIB 08 Jan 09:10:17 [ytilib] use_chiphorde4.rb started, usage <motif_template> > <ChIPHorde-engine-params> > LLIB 08 Jan 09:10:17 [ytilib] run_chiphorde4.rb > > Je n'obtiens donc pas l'erreur dont il parle. > Par ailleurs voici le chemin de la librairie: > /usr/lib/ruby/1.8/rexml/formatters/pretty.rb, mais il semble la trouver. > > Je continue à chercher avec ce que tu m'as envoyé. > Mais il est possible que ce soit un problème de version puisqu'il semble qu'ils > aient renommé les fichiers > > > Cordialement, > > Marie-Stephane Trotard > > Génopole - Plateforme bio-informatique > Centre INRA de Toulouse - Unité de BIA > Chemin de Borde-Rouge - AUZEVILLE > BP 52627 - 31326 CASTANET-TOLOSAN CEDEX > tél. : +33 (0)5 61 28 54 27 > Support : support.genopole(a)toulouse.inra.fr > 08.01.2013 09:05 - Sarah Maman a écrit: > > >> Bonjour Marie-Stephane, >> >> A priori, il manquerait une librairie : >> >> I think that there's some ruby libraries missing. >> >> Please try to run ChIPMunk externally this way: >> >> ruby /path/to/ChIPMunk/run_chiphorde.rb >> >> If you receive this kind of error message, it means that it missed one library >> > to work: > >> ChIPMunk/ytilib/hack1.rb:1:in `require': no such file to load -- >> > rexml/formatters/pretty (LoadError) > >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/hack1.rb:1 >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44:in >> > `require' > >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/ytilib/ytilib.rb:44 >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3:in >> > `require' > >> from /galaxy/galaxy-dist/tool-data/shared/jars/ChIPMunk/run_chiphorde.rb:3 >> >> I already had the problem and the missing library was this one: >> >> http://www.ruby-doc.org/stdlib-1.9.3/libdoc/rexml/rdoc/REXML/Formatters/Pre… >> >> >> Merci d'avance, >> Sarah >> >> >> Support a écrit : >> >>> Bonjour, >>> >>> Il me semble que je l'avais installé en même temps que FindPeaks: >>> >>> /usr/local/bioinfo/src/ChIPMunk/current >>> >>> Parles-tu d'un autre logiciel? D'un version? >>> >>> >>> Cordialement, >>> >>> Marie-Stephane Trotard >>> >>> Génopole - Plateforme bio-informatique >>> Centre INRA de Toulouse - Unité de BIA >>> Chemin de Borde-Rouge - AUZEVILLE >>> BP 52627 - 31326 CASTANET-TOLOSAN CEDEX >>> tél. : +33 (0)5 61 28 54 27 >>> Support : support.genopole(a)toulouse.inra.fr >>> 07.01.2013 14:35 - sarah.maman(a)toulouse.inra.fr a écrit: >>> >>> >>> >>>> A user filled out the contact form on bioinfo.genotoul.fr. >>>> >>>> >>>> ###master_email-line-plain_mailsubject## >>>> >>>> E-Mail: sarah.maman(a)toulouse.inra.fr >>>> >>>> >>>> Priority: Very low >>>> >>>> >>>> Your Message: Bonjour, >>>> >>>> Il me semble, sauf erreur de ma part, que ChipMunk n est pas installÃ© sur >>>> > Genotoul. > >>>> Est-il possible, s il vous plaÃ®t, de l installer. >>>> >>>> TrÃšs cordialement, >>>> Sarah Maman >>>> >>>> >>>> >>>> ---------------------------------- This message was created automatically. >>>> >>>> >>> -------------------------------- >>> >>> >>> >>> >>> >>> >>> >> > > > > > >

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gene names from cuffdiff data
by Elwood Linney 08 Jan '13

08 Jan '13

How does one get gene names when using cuffdiff when looking at "gene differential expression testing" results? I am doing some +/- exposure studies with zebrafish embryos and then processing the 50bp single-ended fastq files through Galaxy with particular interest in the cuffdiff readout of differential gene expression. It seems to be working well but my readout is only giving me gene ID's. It would by more efficient if I could get gene names from the output. I suspect I may be able to do this through selection of options from the UCSC TABLE BROWSER when I use its Zv9 danRer7 assembly as a reference genome. I see a place for selected genes but not for all the identified genes. Is this something that could be done directly or is there just a "beyond Galaxy" method of gene gene lists from a list of gene ID's. Thanks, el linney Duke University Medical Center

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Nominate topics for the 2013 Galaxy Community Conference (GCC2013) Training Day
by Dave Clements 08 Jan '13

08 Jan '13

Hello all, Nominations are now open <http://bit.ly/gcc2013nom> for Training Day topics<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay>at the 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013>. GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Any topic of interest to the Galaxy Community can be nominated<http://bit.ly/gcc2013nom>(see what was offered at GCC2012<http://wiki.galaxyproject.org/Events/GCC2012/TrainingDay>). Topics can be repeats from last year or brand new, and you are encouraged to nominate as many topics as you like. The 2013 Galaxy Community Conference (GCC2013) <http://wiki.galaxyproject.org/Events/GCC2013> will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Nominations will be compiled into a uniform list, and then topics will be voted on by the Galaxy Community starting in late January. Topic nomination closes 11 January. Thanks, Dave Clements, on behalf of the GCC2013 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Organizing_Committee> Links: http://bit.ly/gcc2013nom - nominate a topic http://bit.ly/gcc2013td - Training Day page http://galaxyproject.org/GCC2013 - Conference home page http://bit.ly/gcc2013prom - help get the word out -- <http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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