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

FASTQ quality stats & Bowtie
by Sharmistha Majumdar 26 Jun '13

26 Jun '13

Hi, I am a new Galaxy user and still navigating the platform. Can you explain the difference between these 2 operations that the instruction video asks us to perform before submitting to Bowtie? *NGS: QC and manipulation>Illumina data>FASTQ Summary Statistics by column *FASTX-Toolkit for FASTQ data> Compute quality statistics Also, does Galaxy use Bowtie 2.1.0 or earlier versions? Thanks SM

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Unable to start galaxy either via ami or https://main.g2.bx.psu.edu/cloudlaunch
by Brad Zeitner 25 Jun '13

25 Jun '13

I'm trying to get an instance launched and I'm not seeing an instance launch. When I start an ami directly : (ami-da58aab3) it never answers when I try and browser to it via the web (nor does it respond when I do curl localhost) When I use cloud launch, I can browse to it on the web but on the console it never shows galaxy or postgres as starting (when I try and start postgres it says Cannot find Postgres service – same with starting Galaxy) When I look at the cloud man log – I can see a couple of what appear to be errors in it : [INFO] sge:122 2013-06-25 22:15:08,979: Successfully setup SGE; configuring SGE [DEBUG] sge:123 2013-06-25 22:15:08,979: Adding parallel environments [DEBUG] misc:577 2013-06-25 22:15:08,993: 'cd /opt/sge; ./bin/lx24-amd64/qconf -Ap /tmp/SMP_PE' command OK [DEBUG] misc:577 2013-06-25 22:15:09,006: 'cd /opt/sge; ./bin/lx24-amd64/qconf -Ap /tmp/MPI_PE' command OK [DEBUG] sge:130 2013-06-25 22:15:09,006: Creating queue 'all.q' [DEBUG] sge:135 2013-06-25 22:15:09,006: Created SGE all.q template as file '/opt/sge/all.q.conf' [DEBUG] misc:577 2013-06-25 22:15:09,021: Successfully modified all.q [DEBUG] sge:137 2013-06-25 22:15:09,021: Configuring users' SGE profiles [DEBUG] master:1676 2013-06-25 22:15:09,022: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:09,022: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] misc:113 2013-06-25 22:15:10,054: Checking if bucket 'cm-81a2ec9d11e15570ea7136a31533170e' exists... it does not. [DEBUG] misc:124 2013-06-25 22:15:10,222: Created bucket 'cm-81a2ec9d11e15570ea7136a31533170e'. [INFO] misc:455 2013-06-25 22:15:10,637: Saved file 'persistent_data.yaml' to bucket 'cm-81a2ec9d11e15570ea7136a31533170e' [DEBUG] master:1601 2013-06-25 22:15:10,666: Saving current instance boot script (/tmp/cm/cm_boot.py) to cluster bucket 'cm-81a2ec9d11e15570ea7136a31533170e' as 'cm_boot.py' [INFO] misc:455 2013-06-25 22:15:10,713: Saved file 'cm_boot.py' to bucket 'cm-81a2ec9d11e15570ea7136a31533170e' [DEBUG] master:1605 2013-06-25 22:15:10,740: Saving CloudMan source (/mnt/cm/cm.tar.gz) to cluster bucket 'cm-81a2ec9d11e15570ea7136a31533170e' as 'cm.tar.gz' [INFO] misc:455 2013-06-25 22:15:11,120: Saved file 'cm.tar.gz' to bucket 'cm-81a2ec9d11e15570ea7136a31533170e' [DEBUG] misc:527 2013-06-25 22:15:11,120: Setting metadata 'revision' for file 'cm.tar.gz' in bucket 'cm-81a2ec9d11e15570ea7136a31533170e' [DEBUG] master:1619 2013-06-25 22:15:11,314: Saving '/mnt/cm/bz_test.clusterName' file to cluster bucket 'cm-81a2ec9d11e15570ea7136a31533170e' as 'bz_test.clusterName' [INFO] misc:455 2013-06-25 22:15:11,347: Saved file 'bz_test.clusterName' to bucket 'cm-81a2ec9d11e15570ea7136a31533170e' [DEBUG] sge:405 2013-06-25 22:15:15,747: qstat: ['all.q(a)ip-10-60-121-222.ec2.int BIP 0/0/2 0.64 lx24-amd64 '] [DEBUG] master:1650 2013-06-25 22:15:15,748: S&S: SGE..OK; post_start_script..Unstarted; [DEBUG] master:1676 2013-06-25 22:15:15,748: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:15,748: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:15:19,758: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:19,758: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:15:23,768: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:23,768: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] sge:405 2013-06-25 22:15:28,166: qstat: ['all.q(a)ip-10-60-121-222.ec2.int BIP 0/0/2 0.64 lx24-amd64 '] [DEBUG] master:1650 2013-06-25 22:15:28,167: S&S: SGE..OK; post_start_script..Unstarted; [DEBUG] master:1676 2013-06-25 22:15:28,167: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:28,167: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:15:32,178: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:32,178: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:15:36,188: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:36,188: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] sge:405 2013-06-25 22:15:40,584: qstat: ['all.q(a)ip-10-60-121-222.ec2.int BIP 0/0/2 0.64 lx24-amd64 '] [DEBUG] master:1650 2013-06-25 22:15:40,585: S&S: SGE..OK; post_start_script..Unstarted; [DEBUG] master:1676 2013-06-25 22:15:40,585: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:40,585: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:15:44,588: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:44,588: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:15:48,598: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:48,598: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] sge:405 2013-06-25 22:15:52,995: qstat: ['all.q(a)ip-10-60-121-222.ec2.int BIP 0/0/2 0.75 lx24-amd64 '] [DEBUG] master:1650 2013-06-25 22:15:52,996: S&S: SGE..OK; post_start_script..Unstarted; [DEBUG] master:1676 2013-06-25 22:15:52,996: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:52,996: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:15:56,998: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:15:56,998: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:16:01,008: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:16:01,008: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] sge:405 2013-06-25 22:16:05,406: qstat: ['all.q(a)ip-10-60-121-222.ec2.int BIP 0/0/2 0.75 lx24-amd64 '] [DEBUG] master:1650 2013-06-25 22:16:05,407: S&S: SGE..OK; post_start_script..Unstarted; [DEBUG] master:1676 2013-06-25 22:16:05,407: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:16:05,407: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:16:09,418: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:16:09,418: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:16:13,422: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:16:13,422: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] sge:405 2013-06-25 22:16:17,821: qstat: ['all.q(a)ip-10-60-121-222.ec2.int BIP 0/0/2 0.75 lx24-amd64 '] [DEBUG] master:1650 2013-06-25 22:16:17,821: S&S: SGE..OK; post_start_script..Unstarted; [DEBUG] master:1676 2013-06-25 22:16:17,821: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:16:17,822: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:16:21,832: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:16:21,832: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1676 2013-06-25 22:16:25,842: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:16:25,842: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] sge:405 2013-06-25 22:16:30,241: qstat: ['all.q(a)ip-10-60-121-222.ec2.int BIP 0/0/2 0.76 lx24-amd64 '] [DEBUG] master:1650 2013-06-25 22:16:30,242: S&S: SGE..OK; post_start_script..Unstarted; [DEBUG] master:1676 2013-06-25 22:16:30,242: Monitor adding service 'post_start_script' [DEBUG] pss:65 2013-06-25 22:16:30,242: Not adding post_start_script svc; it already ran (False) or the cluster was not yet initialized (None) [DEBUG] master:1247 2013-06-25 22:16:32,585: Checking for new version of CloudMan [DEBUG] misc:512 2013-06-25 22:16:32,585: Getting metadata 'revision' for file 'cm.tar.gz' from bucket 'cm-81a2ec9d11e15570ea7136a31533170e' [DEBUG] misc:512 2013-06-25 22:16:33,639: Getting metadata 'revision' for file 'cm.tar.gz' from bucket 'cloudman' [DEBUG] master:1251 2013-06-25 22:16:33,690: Revision number for user's CloudMan: '262'; revision number for default CloudMan: '262' [DEBUG] ec2:48 2013-06-25 22:16:33,690: Gathering instance type, attempt 0 … [DEBUG] pss:74 2013-06-25 22:18:00,864: post_start_script service prerequisites OK (i.e., all other services running), checking if post_start_script was provided... [DEBUG] pss:91 2013-06-25 22:18:00,899: Cluster bucket 'cm-81a2ec9d11e15570ea7136a31533170e' found; looking for post start script 'post_start_script' [DEBUG] misc:440 2013-06-25 22:18:00,960: Failed to get file 'post_start_script' from bucket 'cm-81a2ec9d11e15570ea7136a31533170e': S3ResponseError: 404 Not Found NoSuchKeyThe specified key does not exist.post_start_scriptC0097A621B19D07CJtBjACdzRU2Ko+A4xAe5hCPYd3p1EfXw6Hx0Y5DjXLPU7XS3CZyinJs6CMbxxXUS [DEBUG] pss:102 2013-06-25 22:18:00,960: post_start_script does not exist or could not be downloaded; continuing without running it. Any idea how I can get this started and running? Thanks! -Brad

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problem with GATK tools not accepting BAM file as input
by Politz, Samuel M. 24 Jun '13

24 Jun '13

I am using GATK tools on the useGalaxy main server to detect variants in a mutant C. elegans whole genome sequence obtained with an Illumina instrument (my own data). The first GATK tool I tried to use, Realigner Target Creator, gave me an error message. In the tool window, my input file (a BAM file previously run through Add or Replace Groups) did not generate an error, but the reference genome file (ce10) which I specified as found in History, produced the following reference list-specific error: "History does not include a dataset of the required format/build". I got the same error when I tried to use this input file to run the GATK Depth of Coverage tool. I have searched Galaxy mail archives for this error, and have found other examples, but none involving these tools. The ce10 database was listed in the History attributes of the BAM file I used, and this database has worked with all of the Galaxy tools I used up to this point. Something about the ce10 format is unacceptable to GATK, or it is not even picking it up from the History. I don't know how to access ce10 to check its format. I have only found the inbuilt reference genome files in Galaxy in drop-down menus for each tool. Searching the GATK site for solutions has not been helpful, because they suggest GATK-specific functions to fix the format such as Create Sequence Dictionary. I don't have access to these tools within the Galaxy main server. Can someone suggest a workaround or a direct solution?

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LOGIN PROBLEM
by Jennifer Jackson 24 Jun '13

24 Jun '13

Hello, You will need to register and log in with each of these public Galaxy servers separately. Each is maintained as a distinct instance. Best, Jen Galaxy team On 6/24/13 4:31 AM, nayaganviji(a)gmail.com wrote: > Dear mam, > actually i already had login id for Galaxy main server. but when i tried use same id for open south green or some other server its showing error message "User registration is disabled. Please contact your Galaxy administrator for an account or No such user (please note that login is case sensitive)". how i can access others galaxy server. please help me -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Problems when downloading a local galaxy tool (old version)
by xiong 23 Jun '13

23 Jun '13

Dear friends: As a locally installed Genomic-hyperbrowser need a rather old version of Galaxy, I runed the command "hg clone https://bitbucket.org/galaxy/galaxy-dist/ -u 26920e20157f galaxy-dist-hb" according to the website http://hyperbrowser.uio.no/hb/static/download.html. However, the hg did not download successfully, but reported "warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:6d:58:ff:e4:28:7d:2a:14:ae:3b not verified (check hostfingerprints or web.cacerts config setting) destination directory: galaxy-dist-hb requesting all changes adding changesets" and this information on the screen mainteined (at least half a day unless I hit "ctrl+Z" and kill the job) without any other errors (still in the destination directory it generated a nearly empty dir "galaxy-dist-hb" containing a filefold named ".hg”――one "store" filefold and several small files included). My mercurial version is 2.6, and I use Xshell to reach CentOS Server. Actually, even I downloaded the latest version of galaxy (hg clone https://bitbucket.org/galaxy/galaxy-dist/) it also reported the same information on the screen. On the other hand, I can get the latest tarballs of galaxy, but it can not be updated to an old version. Please give me some clues about problems above, and any ideas to get tarballs for an old version? Thanks in advance! Hsiong

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UCSC error
by YBao 22 Jun '13

22 Jun '13

Hi all, When I was trying to visualize MACS peaking calling results using UCSC browser, I encountered this error message: *Warning/Error(s):* - Error line 14252 of https://main.g2.bx.psu.edu/root/display_as?id=11074175&display_app=ucsc&aut…: chromStart after chromEnd (-94 > 335) Can someone help me to understand what this means? Thanks Yongde -- Yongde Bao DNA Sciences Core Dept. of Microbiology, Immunology, and Cancer Biology UVA

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Finding tools to annotate non-coding SNPs from GWAS
by sultana tahiri 21 Jun '13

21 Jun '13

Hello, We are starting a project in our laboratory which aims to annotate a given set of SNPs lying in non-coding DNA from GWAS studies. We would like to have the most comprehensive view of those non-coding SNPs putative and validated functions. We've already been through publications about Galaxy and GalaxyENCODE, we also been searching for similar request on the FAQ but found no similar request dated from 2013. We would like to know about the latest add to Galaxy, as we've seen that part of the BEDtools have been integrated to Galaxy for example. Our question is: -What Tools available in Galaxy would take as an input a list of non-coding SNPs (or DNA regions) identified in our GWAS studies and return annotations of those SNPs (annotations such as histones modification, transcription factor binding, and other non-coding DNA features around those SNP) ? We haven't found a searching option on Galaxy that would allows us to look for tools by keywords related to their function or purpose. We assumed that we might have missed something, thank you for letting us know if there were such searching options. Thanks you very much for your time, Kind regards, Sultana The Center for Neurogenomics and Cognitive Research De Boelelaan 1085 1081 HV Amsterdam The Netherlands

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How to trim sequences with low quality scores
by Hoang, Thanh 18 Jun '13

18 Jun '13

Hi guys, I did quality control on my RNA-seq data using FastQC. In the report for Per base sequence quality, there are some base positions with the quality scores less than 20 ( see attached picture) . I am just wondering if there is any way to remove these? I looked at the FASTQ Quality Trimmer<https://main.g2.bx.psu.edu/tool_runner?tool_id=fastq_quality_trimmer> but am not sure if this is the right tool to use and how to use the parameter settings? Best regards Thanh

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Re: [galaxy-user] Get Gene name from Cuffdiff's output?
by Jennifer Jackson 17 Jun '13

17 Jun '13

Hello, On 6/17/13 12:24 PM, Hoang, Thanh wrote: > Hi Jen, > Thank you very much for your quick response. > > I have just downloaded GTF file ( Mus musculus, UCSC, mm10) from > iGenome. > Correct me if I am wrong. I should start everything from the beginning > again by uploading the GTF file to Galaxy via FTP uploading. Then, > start mapping and assembly and analyzing the transcript using the GTF > file this time : TopHat>> Cufflink>> Cuffmerge -Cuffdiff ??? Yes, if not mapped against mm10, you will need to start from that step and work forward. > > Also, do you know any good software to assign genes into functional > groups ( Gene ontology) ? See the tool " Phenotype Association -> g:Profiler" for one option. The UCSC Table browser may also offer GO annotation in a mm10 track that you can intersect or join your results to. Biomart's Unigene annotation is another great resource. Best, Jen Galaxy team > Thank you so much for your help > Thanh > > > On Mon, Jun 17, 2013 at 2:30 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hello Thanh, > > These attributes would come from the reference GTF or GFF3 file > that you are using (not the reference genome). It looks like you > are not using one, or that it did not cover this particular gene > bound. > > The iGenomes GTF files are preferred as they contains all of the > attributes that will both populate these sorts of values, but also > allow the full compliment of statistics to be generated by the > tool package. This is explained in the tool's manual: > http://cufflinks.cbcb.umd.edu <http://cufflinks.cbcb.umd.edu/> > http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server > > That said, I don't think there is an iGenomes GTF for the > reference genome you have selected. I am not aware of a liftOver > file either (but I could be wrong, you can ask UCSC). You also > could try posting a question to the tophat.cufflinks(a)gmail.com > <mailto:tophat.cufflinks@gmail.com> google group to see what > others are using/what is available right now. > > It may come down to choosing which is more important for your > project - the most current genome or better annotation. > > Good luck! > > Jen > Galaxy team > > > On 6/17/13 11:13 AM, Hoang, Thanh wrote: >> Hi guys, >> I am trying to examine gene differential expression in my mouse >> samples using : >> Cufflink >> Cuffmerge>>Cuffdiff >> The output from Cuffdiff shows only gene id, but not gene name: >> test_id gene_id gene locus >> sample_1 sample_2 >> >> XLOC_000001 XLOC_000001 - 1:3200263-3200566 Epithelium Fiber >> >> Could anyone tell me how to make the gene name show up? >> I used Mus_musculus.GRCm38.71.dna.toplevel.fa as the reference >> sequence (not GRCm38/mm10 from UCSC table broswer because i think >> this may be old version). >> I have been trying to find a solution online but still very confused >> Thanks so much >> Thanh >> >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> atusegalaxy.org <http://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/ > > -- > Jennifer Hillman-Jackson > Galaxy Support and Training > http://galaxyproject.org > > -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Get Gene name from Cuffdiff's output?
by Hoang, Thanh 17 Jun '13

17 Jun '13

Hi guys, I am trying to examine gene differential expression in my mouse samples using : Cufflink >> Cuffmerge>>Cuffdiff The output from Cuffdiff shows only gene id, but not gene name: test_id gene_id genelocus sample_1 sample_2 XLOC_000001XLOC_000001- 1:3200263-3200566EpitheliumFiber Could anyone tell me how to make the gene name show up? I used Mus_musculus.GRCm38.71.dna.toplevel.fa as the reference sequence (not GRCm38/mm10 from UCSC table broswer because i think this may be old version). I have been trying to find a solution online but still very confused Thanks so much Thanh

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