- galaxy-user - lists.galaxyproject.org

FTP Upload Error
by Amanda Jones 01 Oct '12

01 Oct '12

I'm having trouble uploading via FTP to my Galaxy account. I've been receiving the following error message: 503 Sorry, the maximum number of clients(3) for this user are already connected. I've ensured that I'm only using a single connection to upload. Any clue what's going on? I still have available space in my Galaxy account for the upload and I've previously uploaded similarly sized files with no problems.

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October 2012 Galaxy Update
by Dave Clements 01 Oct '12

01 Oct '12

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igenome error
by Paul Brady 01 Oct '12

01 Oct '12

I try to download the human hg19 from igenomes in galaxy. I use 'shared data' > 'data libraries' > 'igenomes' > select hg19, but this persistently downloads the mm9 mouse genome not the human genome. Any suggestions? Paul Brady Afdeling CME-UZ, O&N I Herestraat 49 - bus 602, 3000 Leuven, Belgium. Tel: +32 16 345902 e-mail: Paul.Brady(a)med.kuleuven.be

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Errors during database migration after updating galaxy
by Joel Rosenberg 01 Oct '12

01 Oct '12

My cloud galaxy cluster can't boot up after attempting a bitbucket update due to a 502 HTTP error when trying to update the DB. Here's the log: /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility from csamtools import * python path is: /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg, /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loading references to tool sheds from tool_sheds_conf.xml galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,317 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-09-30 21:13:18,318 Loaded reference to tool shed: Galaxy test tool shed galaxy.model.migrate.check DEBUG 2012-09-30 21:13:18,344 psycopg2 egg successfully loaded for postgres dialect galaxy.model.migrate.check INFO 2012-09-30 21:13:18,610 At database version 107 galaxy.tool_shed.migrate.check DEBUG 2012-09-30 21:13:18,620 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 47, in __init__ verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/check.py", line 54, in verify_tools missing_tool_configs_dict = check_for_missing_tools( app, tool_panel_configs, latest_tool_migration_script_number ) File "/mnt/galaxyTools/galaxy-central/lib/galaxy/tool_shed/migrate/common.py", line 33, in check_for_missing_tools response = urllib2.urlopen( url ) File "/usr/lib/python2.6/urllib2.py", line 126, in urlopen return _opener.open(url, data, timeout) File "/usr/lib/python2.6/urllib2.py", line 397, in open response = meth(req, response) File "/usr/lib/python2.6/urllib2.py", line 510, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib/python2.6/urllib2.py", line 435, in error return self._call_chain(*args) File "/usr/lib/python2.6/urllib2.py", line 369, in _call_chain result = func(*args) File "/usr/lib/python2.6/urllib2.py", line 518, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 502: Bad Gateway Removing PID file paster.pid

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server down?
by DEDRICK＠pitt.edu 27 Sep '12

27 Sep '12

I am using Galaxy main and my jobs aren't running. They are still grey colored, indicating that they haven't started. I used Galaxy main yesterday just fine. Is something wrong with the server? I tried re-running the jobs, still no progress. -- Rebekah Dedrick, Ph.D. University of Pittsburgh Hatfull Laboratory 376 Crawford Hall 4249 Fifth Avenue Pittsburgh, PA 15260

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Training
by Ryan Peters 27 Sep '12

27 Sep '12

To whom it may concern, Can you tell me about how I can schedule a training for Galaxy and any Galaxy trainings that are coming up in the East Coast which I can attend. I would be willing to travel. Thanks

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FreeBayes repeated error
by Dalgard, Clifton 27 Sep '12

27 Sep '12

Dear Team and Galaxy Users, I have been running FreeBayes on BAM output generated from pooled sequencing of 30 haploid yeast genomes with a total of 90 million reads. I am observing an inconsistent but repeated error using FreeBayes which states: An error occurred running this job:*terminate called after throwing an instance of 'std::out_of_range' what(): vector<bool>::_M_range_check Aborted* * * Interestingly, I can view partial output of the tool run and after running the tool repeated with the same data and parameters, I have noticed that the partial output has different lengths (and thus suggests it is not data dependent). Is there any insight to why FreeBayes won't complete? Thank you, Clifton

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GFF not recognized in CUFFLINK
by Qian Dong 26 Sep '12

26 Sep '12

Dear Team, I've been having a problem with cufflink regarding GFF files. I tried searching the mailing list first and failed to find an answer. Could you help me look at this? I downloaded my genome annotation GFF file from NCBI (soon I realized NCBI format may be a problem) for my bacterial RNA-seq data analysis. My GFF file looks like the following: '##gff-version 3#!gff-spec-version 1.20#!processor NCBI annotwriter##sequence-region NC_011420.2 1 4355543##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=414684NC_011420.2 RefSeqregion14355543.+.ID=id0;Dbxref=taxon:414684;Is_circular=true;culture-collection=ATCC:51521;gb-synonym=Rhodocista centenaria SW;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=SW%3B ATCC 51521NC_011420.2RefSeqgene113343.+. ID=gene0;Name=RC1_0011;Dbxref=GeneID:7008893;gbkey=Gene;locus_tag=RC1_0011 NC_011420.2RefSeqCDS113343.+0ID=cds0;Name=YP_002296275.1;Parent=gene0;Note=Contains a type I secretion target ggxgxdxxx repeat %282 copies%29 domain%3B Contains a Cadherin domain%3B identified by match to protein family HMM PF02789;Dbxref=Genbank:YP_002296275.1,GeneID:7008893;gbkey=CDS;product=hypothetical protein;protein_id=YP_002296275.1;transl_table=11 I used this file for cufflink but all the FPKM values are 0. I checked out this link: http://cufflinks.cbcb.umd.edu/gff.html and thought that maybe the problem is because I don't have any mRNA feature in my gff file. Since I am dealing with a bacterial genome, there is no exon/intron or UTR info needed. Therefore I modified my GFF file into the following: ##gff-version 3#!gff-spec-version 1.20#!processor NCBI annotwriter##sequence-region NC_011420.2 1 4355543##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=414684NC_011420.2 RefSeqregion14355543.+.ID=id0;Dbxref=taxon:414684;Is_circular=true;culture-collection=ATCC:51521;gb-synonym=Rhodocista centenaria SW;gbkey=Src;genome=chromosome;mol_type=genomic DNA;strain=SW%3B ATCC 51521NC_011420.2RefSeqmRNA113343.+. ID=mRNA0;Name=RC1_0011;Dbxref=GeneID:7008893;gbkey=Gene;locus_tag=RC1_0011 NC_011420.2RefSeqCDS113343.+0ID=cds0;Name=YP_002296275.1;Parent=mRNA0;Note=Contains a type I secretion target ggxgxdxxx repeat %282 copies%29 domain%3B Contains a Cadherin domain%3B identified by match to protein family HMM PF02789;Dbxref=Genbank:YP_002296275.1,GeneID:7008893;gbkey=CDS;product=hypothetical protein;protein_id=YP_002296275.1;transl_table=11 I re-ran cufflink however this time there is error reported. I can only tell from the report that there is a segmentation fault but not further details. The report is as follows: Error running cufflinks. return code = 139 Command line: cufflinks -q --no-update-check -I 100 -F 0.100000 -j 0.150000 -p 4 -G /galaxy/test_pool/pool5/files/000/327/dataset_327777.dat /galaxy/test_database/files/000/325/dataset_325086.dat [19:41:41] Loading reference annotation. Segmentation fault cp: cannot stat `/galaxy/test_pool/pool3/tmp/job_working_directory/000/170/170197/global_model.txt': No such file or directory cp: cannot stat `/galaxy/test_pool/pool3/tmp/job_working_directory/000/170/170197/isoforms.fpkm_tracking': No such file or directory cp: cannot stat `/galaxy/test_pool/pool3/tmp/job_working_directory/000/170/170197/genes.fpkm_tracking': No such file or directory My questions will be: 1. Is there any way to modify a NCBI bacterial genome annotation GFF file to make it usable for cufflink? Our genome annotation is only available in NCBI, not ensemble or USDC so this is pretty much my only choice.. 2. Should I proceed with modifying the GFF file or should I convert it into GTF and use the GTF instead in cufflink? I am a biochemist and really new to the computer world so any advice will help! Thanks a lot, Qian -- Qian Dong Bauer Lab, MCBD Simon Hall: 313-317 212 S. Hawthorne Dr. Bloomington, IN 47405 Email:dong3@indiana.edu Lab Phone:812-855-8443

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adding D. yakuba reference genome
by Stern PhD, David L 26 Sep '12

26 Sep '12

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Galaxy for SAGESeq
by Sujoy Ghosh 26 Sep '12

26 Sep '12

Hello, I am interested in finding out anyone has any experience conducting SAGESeq analysis in Galaxy. Can the existing RNASeq tools be formatted easily for SAGESeq? Thanks. Sujoy

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