March 2012 - galaxy-user - lists.galaxyproject.org

error uploading from ftp site
by Keith E. Giles 02 Mar '12

02 Mar '12

All of a sudden I can not upload any files from the FTP server. The files upload into my ftp directory fine, but when I try to upload them into galaxy, I get the following error: "Error executing tool: normalize() argument 2 must be unicode, not str" any ideas?

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Error in DepthOfCoverage (GATK) tool
by Praveen Raj Somarajan 02 Mar '12

02 Mar '12

Hello, I'm facing an issue with "Depth Of Coverage" tool when it runs on refGene and target BED file. The error message is: File "cheetah_DynamicallyCompiledCheetahTemplate_1330588825_26_16118.py", line 402, in respond NotFound: cannot find 'omit_interval_statistics' while searching for 'gatk_param_type.omit_interval_statistics' I noticed that the issue is only when the "Advanced GATK options" is enabled to set target BED file. The commandline runs perfectly with the input files, but galaxy fails due to this error. Can anyone suggest what's the issue? Best, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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Re: [galaxy-user] [galaxy-bugs] GI errors in the megablast table of results ?
by Guru Ananda 01 Mar '12

01 Mar '12

Dear Sandrine, Thanks for pointing out this issue. The BLAST databases we have on Galaxy are from last year, while those on NCBI website are the latest (Jan 2012). As pointed out on NCBI website ( http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html) it appears that each time any change is made to a sequence/database, GI numbers change as well. This is perhaps why you're observing discrepancies in GI numbers and lengths between megablast outputs on Galaxy and NCBI. I'm currently in the process of downloading the latest BLAST databases from NCBI, and I'll let you know when they're available for use on Galaxy. Thanks for your patience, Guru Galaxy team. On Wed, Nov 9, 2011 at 8:03 AM, Sandrine Hughes <Sandrine.Hughes(a)ens-lyon.fr > wrote: > Dear all, > > I’m not sure where I need to send my email so I apologize if I’m wrong. > > I have a trouble with the Megablast program available in NGS Mapping and I > hope that you can help. Indeed, I think that there might be a problem with > the table given in output, and notably a shift between the GI numbers and > the parameters associated. > > Here are the details: > > I. First, what I have done : > I used the program to identify the species that I have in a mix of > sequences by using the following options: > Database nt 27-Jun-2011 > Word size 16 > Identity 90.0 > Cutoff 0.001 > Filter out low complexity regions Yes > I run the analyses twice and obtained exactly the same results (I used > the online version of Galaxy, not a local one). > > II. Second, I analysed the data obtained for one of my sequence (1-202). > The following lines are the beginning of the table that I obtained after > the megablast and two lines with troubles: > > 1-202 312182292 484 99.33 150 1 0 1 > 150 1 150 2e-75 289.0 > 1-202 312182201 476 99.33 150 1 0 1 > 150 1 150 2e-75 289.0 > 1-202 308228725 928 99.33 150 1 0 1 > 150 19 168 2e-75 289.0 > 1-202 308228711 938 99.33 150 1 0 1 > 150 22 171 2e-75 289.0 > 1-202 308197083 459 99.33 150 1 0 1 > 150 10 159 2e-75 289.0 > 1-202 300392378 920 99.33 150 1 0 1 > 150 10 159 2e-75 289.0 > 1-202 300392376 918 99.33 150 1 0 1 > 150 9 158 2e-75 289.0 > 1-202 300392375 922 99.33 150 1 0 1 > 150 11 160 2e-75 289.0 > 1-202 300392374 931 99.33 150 1 0 1 > 150 21 170 2e-75 289.0 > 1-202 300392373 909 99.33 150 1 0 1 > 150 21 170 2e-75 289.0 > 1-202 300392371 1172 99.33 150 1 0 1 > 150 9 158 2e-75 289.0 > ... > 1-202 179366399 151762 98.67 150 2 0 1 > 150 46880 47029 6e-73 281.0 > 1-202 58617849 511 98.67 150 2 0 1 > 150 21 170 6e-73 281.0 > > > III. Third, what I’ve noticed: > My first trouble was that among all the species identified, two were > very different from the expected ones (2 last lines). So I decided to > search if that could be possible for that sequence and performed > independently a megablast on the NCBI with similar options. I was not able > to find these two species in the results. > So, I decided to check the hits identified in the table above and > identified a second trouble. In the table, the second column give the GI of > the database hit and the third column give the length of the database hit. > However, when I manually checked in NCBI the length of the GI, this one was > incorrect. Indeed, for the GI 312182292, the length should be 580 and not > 484. > By checking different lines, I noticed that the length that is given > for a GI corresponds to the length of the GI-1. As you can see in the above > table, some GI are consecutive (300392376, 300392375,...). When checking > the length of 300392376 in NCBI, I should have 920. But when I checked > 300392375, I found 918. And this was true for the following lines : > 300392374 give normally 922 and 300392373 give 931... My conclusion at that > point was that there was a shift of –1 between the GI and the other > parameters of the line (indeed the parameters for the remaining columns are > in agreement with the length of the GI-1). However, that’s not always > true.... For some GI given in the table (for example, the two last lines), > if we check the parameters of the GI-1, the parameters are completely > different... So, I suppose that there is a trouble in the GI sorting during > the megablast but I’m not able to clearly define the problem. > > IV. Fourth, confirmed with an other dataset > In order to be sure that the problem was not linked to my data or my > process, I asked a colleague to do a megablast on independent data. The > conclusions were similar to mine : a shift in the GI given in the table > and the parameters associated, that most of the time but not always, > correspond to GI-1. > > Can you confirm that there is a problem with the output of the megablast > available in Galaxy ? If yes, do you think you can fix it ? > > Many thanks for your help, > > Best regards, > > Sandrine > -- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team Penn State University 505 Wartik lab University Park PA 16802 guru(a)psu.edu

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Getting errors trying to enable samtools_mpileup
by Waldron, Michael H 01 Mar '12

01 Mar '12

I am running a local copy of Galaxy, last ran 'hg pull -u' on 2/20/12. I am trying to enable use of Mpileup for SAM Tools, and have added the entry for the samtools_mpileup.xml file in tool_conf.xml. However, when I startup Galaxy, the link for Mpileup does not appear in the Tools pane, and I see the following errors from the Galaxy startup: galaxy.tools ERROR 2012-02-29 16:28:51,919 error reading tool from path: samtools/samtools_mpileup.xml Traceback (most recent call last): File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 212, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 305, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 531, in __init__ self.parse( root, guid=guid ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 641, in parse self.parse_inputs( root ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 723, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 922, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 989, in parse_input_elem case.inputs = self.parse_input_elem( case_elem, enctypes, context ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 945, in parse_input_elem group.inputs = self.parse_input_elem( elem, enctypes, context ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1015, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/__init__.py", line 1027, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 1330, in __init__ ToolParameter.__init__( self, tool, elem ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 43, in __init__ self.validators.append( validation.Validator.from_element( self, elem ) ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 23, in from_element return validator_types[type].from_element( param, elem ) File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/parameters/validation.py", line 279, in from_element tool_data_table = param.tool.app.tool_data_tables[ table_name ] File "/nas02/apps/galaxy-prod/galaxy-dist/lib/galaxy/tools/data/__init__.py", line 21, in __getitem__ return self.data_tables.__getitem__( key ) KeyError: 'sam_fa_indexes' Can someone tell me what is wrong here? Am I missing something in the database? Thanks, Mike Waldron

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Filtering reads on wrong strand before FPKM scoring on cufflinks
by Noa Sher 01 Mar '12

01 Mar '12

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Quality trimming of sequences before RNA-Seq
by Noa Sher 01 Mar '12

01 Mar '12

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