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Could Not Calculate Ungapped Karlin

It seems to parse th... I first make a compatible dat... This took a... The time now is 06:39 PM. have a peek at this web-site

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 It can happen that for some choices of blast parameters and some sequences, the statistics can't be calculated. But I get this error message: [blastall] WARNING: MaulwurfLeber_H21F7XH01DFTZ0_rank=0133853_x=1293_: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. The following sequence could be used as test sequence with BLAST/Rfam9.1 and comparative analysis with blast. >test NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN For information, here is the output obtained in vm-rnaspace /usr/local/bioinfo/bin/bl2seq -p blastn -S https://www.biostars.org/p/167725/

i used dustmasker also for filtering and masking and then run with masked genome, but still got the same error. https://github.com/simroux/VirSorter I'm running the script on a cluster. Ncbi Legacy Blast Usage With Tblastn/Pssm I'm trying to get a webservice for protein discovery running. 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 Ubuntu Forums Code of Conduct Forum

If it is not a fatale error, than something else is wrong with the call or my db. Can'T Exec "Blastall":No Such File Or Directory... tBLASTn at standalone I am using tBLASTn for ~370 MB size genome as database and around 3000 proteins sequences as quer... All Rights Reserved.

However I keep getting the error: Possibly "scipio" is not ins... Reload to refresh your session. I think the option to turn this off is -F F.   ADD REPLY • link written 12 months ago by Jean-Karim Heriche ♦ 7.2k Please log in to add an https://www.biostars.org/p/146471/ Bowtie Results Not Matching The Expected Error Qualities I stumbled upon this problem when playing with different flags of bowtie.

I would like to perform a tblastn w... 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. Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Blast Error: Tax database file not found Hello, I am running this command for a blast search.

Reload to refresh your session. Similar Threads Thread Thread Starter Forum Replies Last Post tblastx in blast+ gives an error regareding a DB alias but blastall works fine rangel Bioinformatics 2 08-19-2014 01:42 AM couldn't find I am having trouble getting blast to give me "correct" results. No, thanks

Skip to content Ignore Learn more Please note that GitHub no longer supports old versions of Firefox. http://awendigital.com/could-not/could-not-calculate-ungapped-karlin-altschul-parameters.html Please let me know how to... You might wanna try swapping the query and subject if that's the case, or use BLASTX/ explore other options. 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

Password Register FAQ Community Calendar Today's Posts Search You are currently viewing the SEQanswers forums as a guest, which limits your access. Hello people I'm trying to run blast (blast-2.2.26) on a fasta file. 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 Source Hey Folks, Background: I am trying to shortlist the list of genes predicted by different gene pr...

Output blastx top hits as fasta of the original sequences I have performed a blastx of 1,000,000,000 short sequences against a small database. Different output in tblastn web-command line I've starting to use tblastn tool to align protein sequences against a genomic reference. can't get staxids with blastn megablast against nt Hi everyone, Please I really need help.

Below - the command ...

For details and our forum data attribution, retention and privacy policy, see here Google Grupları Tartışma Forumları'nı kullanmak için lütfen tarayıcı ayarlarınızda JavaScript'i etkinleştirin ve sonra bu sayfayı yenileyin. . 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 ... 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. You signed out in another tab or window.

Please verify the query sequence(s) and/or filtering options. Duplicated terminal-version BLAST results Hi there! thanx Adv Reply Quick Navigation General Help Top Site Areas Settings Private Messages Subscriptions Who's Online Search Forums Forums Home Forums The Ubuntu Forum Community Ubuntu Official Flavours Support New have a peek here 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

Have anyone been experienced Socrates ? Extracting Fasta Alignments From Parsed Blastxml File Hello, I have cobbled together a small script that parses a BLASTxml file. myposts blastp blast fasta • 1.0k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 13 months ago • written 13 months 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

URL: Next message: [protocols] blastall error "Could not calculate ungapped Karlin-Altschul parameters" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about In contrast, BLAST reports the following warning for the seqeuence consisting of all Ns: Warning: lcl|Query_1 test: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or 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.