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Could Not Calculate Ungapped Karlin Altschul Parameters

There is a problem with this specific query. converting a fasta database to blastp database hello im runnnig a wwwblast software on my server i do have a fasta database and i would like to ... I am having trouble getting blast to give me "correct" results. Running A Standalone Batch Blast With Fasta File Using Perl, Can'T Get Results For All Sequences. have a peek at this web-site

blast error invalid query/ sequence/ filtering options. Please don't refer me to the similar thread on biostar, I see it, but not useful for me. empyrean Bioinformatics 3 03-10-2011 08:13 PM Thread Tools 01-12-2015, 03:02 PM #1 morning latte Member Location: MI Join Date: Jun 2013 Posts: 86 blastall error Hello experts, I I can't get the staxids with my blastn.

Given that your sequences are highly repetitive, this is likely if you have some filtering turned on, which I seem to remember blastall does by default. Please verify the query sequence(s) and/or filtering options Owner lmrodriguezr commented Apr 20, 2011 Solved in branch issue13, to be merged with master soon. Terms Privacy Security Status Help You can't perform that action at this time. blast two DNA sequence which were repeat-masked How to blast two DNA sequence that were repeat-masked using blastn.

Find More Posts by maubp « Previous Thread | Next Thread » Thread Tools Show Printable Version Email this Page Posting Rules You may not post new threads You may not Help For Blastx, No Output Untill The Program Finished I have run blastx program agaist NR with about 50,000 sequences locally. Powered by Biostar version 2.3.0 Traffic: 418 users visited in the last hour [protocols] blastall error "Could not calculate ungapped Karlin-Altschul parameters" Michael R. Similar posts • Search » Some Questions About Using Orthomcl To Find Orthologs Within Many Species When I follow the OrthoMCL User to do my work, I use orthomclAdjustFasta to produce

Blastp -outfmt Problem With Format Specifiers Hi, I'm using the 2.2.31+ version of the blast+ executable in a bash command line to execute a b... Below - the command ... Personal Open source Business Explore Sign up Sign in Pricing Blog Support Search GitHub This repository Watch 2 Star 10 Fork 0 chenying2016/queries Code Issues 1 Pull requests 0 Projects read this article Powered by Biostar version 2.3.0 Traffic: 418 users visited in the last hour Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » View Posts Latest Open

Aborted (core dumped)` HS-BLASTN ran to completion when I changed just one N to an A. Shortlisting Genes From Various Gene Prediction Methods Based On Blast Results. Thanks, ┬á blast • 3.5k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 17 months ago by Ginsea Chen • 70 BLAST options error: tried to set option (130) and value (1), line (537) I'm running local blast/2.2.30+ (on a server), command blastx (-task blastx-fast) against the nr ...

However, remember that an empty result file without any fatal error message could also mean that there are no results to be had. have a peek at this web-site Is the following error from blastall normal? [blastall] WARNING: gi|9256636|ref|NP_061348.1|: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. ADD REPLY • link written 2.6 years ago by Pierre Lindenbaum ♦ 87k Guessing from your file naming, the query is nucl and the DB is protein. I have run blastn on two sequ...

Already have an account? Check This Out How to use maximum identity > 95%, length > 200 bp as search parameters for tblastn standalone version hallo guys, Could someone please suggest to me how to use following search I wrote ... In your case, my guess is that it's because your peptide sequences are highly repetitive.

Tango Icons ę Tango Desktop Project. URL: Next message: [protocols] blastall error "Could not calculate ungapped Karlin-Altschul parameters" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about Crusoe mcrusoe at msu.edu Tue Aug 5 12:05:07 PDT 2014 Next message: [protocols] blastall error "Could not calculate ungapped Karlin-Altschul parameters" Messages sorted by: [ date ] [ thread ] [ Source Biopython Ncbistandalone Blastall Gives Different Result Than Calling Blastall Directly From Cmd So, first I tested what results I should get from the blastall program using the command line, wi...

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For example this test sequence: >test NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Produced this error: hs-blastn: sources/commandline_options/parameters.cpp:182: BlastInitialWordParameters::BlastInitialWordParameters(const BlastInitialWordOptions*, const BlastHitSavingParameters*, const BlastScoreBlk*, QueryInfo*, Int8): Assertions_BlastKarlinBlkIsValid(kbp)' failed.

You signed out in another tab or window. Blast+ Nucleotide "-Matrix" Command HI, I've been trying to run a nucleotide blast (blastn) using BLAST+ here is what it should lo... I'm trying to use InParanoid (v4.1) to detect orthologs in two de novo transcriptomes I assembled... vBulletin ę2000 - 2016, Jelsoft Enterprises Ltd.

Trouble obtaining chromosome number using standalone blastn Hello, I'm having trouble obtaining the exact chromosome number, when using standalone BLAST. What is the problem? 0 13 months ago by john • 0 European Union john • 0 wrote: Hello people I'm trying to run blast (blast-2.2.26) on a fasta file. Moreover, as above Ram RS stated, your query should be protein and subject should be nucleotide sequences. have a peek here We recommend upgrading to the latest Safari, Google Chrome, or Firefox.

Single Sign On provided by vBSSO FAQ Forum Quick Links Unanswered Posts New Posts View Forum Leaders FAQ Contact an Admin Forum Community Forum Council FC Agenda Forum Governance Forum Staff Warning message in findOverlap function in R I am trying to find overlap between chicken (galGal4) repeat masker file (.rmsk), and promoter re... Tblastx Exception Error Hi, I am having some problems running tblastx locally on my HPC. about • faq • rss Community Log In Sign Up Add New Post Question: getting error in runing tblastn 0 2.6 years ago by inayat45shaikh • 30 India inayat45shaikh • 30

ADD REPLY • link modified 13 months ago • written 13 months ago by genomax2 ♦ 19k 0 13 months ago by Jean-Karim Heriche ♦ 7.2k EMBL Heidelberg, Germany Jean-Karim Heriche Augustus scipio error Hi, I am trying to use Augustus. Have anyone been experienced Socrates ? I think the option to turn this off is -F F. ┬á ADD REPLY • link written 12 months ago by Jean-Karim Heriche ♦ 7.2k Please log in to add an

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