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Could Not Calculate Ungapped Karlin Altschul Parameters Due

about • faq • rss Community Log In Sign Up Add New Post Question: blast error invalid query/ sequence/ filtering options. Old Blastall Vs New Blastall I've been using blast 2.2.15 for a while, and I recently downloaded blast 2.2.25 on my new comput... 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... 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 have a peek at this web-site

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. Trinity : average transcript size check + quality assessment Hello all   I have performed trinity assembly , now i want assess the quality of the the assemb... 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 blastall -i query.fa -d database -p blastx -e 1e-5 -a 8 -o output.txt And all of sudden, I am getting the same warning message as below.

I would like to perform a tblastn w... Augustus scipio error Hi, I am trying to use Augustus. Ubuntu Ubuntu Insights Planet Ubuntu Activity Page Please read before SSO login Advanced Search Forum The Ubuntu Forum Community Ubuntu Official Flavours Support General Help blastall query Results 1 to 1 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 ] [

Shortlisting Genes From Various Gene Prediction Methods Based On Blast Results. Running A Standalone Batch Blast With Fasta File Using Perl, Can'T Get Results For All Sequences. 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 Any help would be greatly appreciated.

Obtaining A Maximum Number Of Blast Hits: Problem... Thanks for your help in advance.   sequencing blast alignment genome • 600 views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified Psiblast Warning: Composition-Based Score Adjustment Warning: lcl|Query_1 1DCH:A|PDBID|CHAIN|SEQUENCE: Warning: Composition-based score adjustment ... i thought about this However, remember that an empty result file without any fatal error message could also mean that there are no results to be had.

ADD COMMENT • link written 17 months ago by Ginsea Chen • 70 Please log in to add an answer. I'm trying to run a script that BLASTs against the per-formated BLAST databases. I first make a compatible dat... Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » View Posts Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » Home

User contributions on this site are licensed under the Creative Commons Attribution Share Alike 4.0 International License. http://seqanswers.com/forums/showthread.php?t=49493 Mothur_chimera.uchime running error Please any body help me. BLASTp query/options error Hello everyone, I am performing standalone blastp, I already used these commands on windows but ... 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.

lmrodriguezr closed this Apr 20, 2011 lmrodriguezr pushed a commit that referenced this issue Apr 20, 2011 RODRIGUEZ Luis-M Issues Check This Out 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. I am trying to retrieve as many h... Unable To Install 'Pasilla' On R I am trying to install or load on R.

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 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 Similar posts • Search » getting error in runing tblastn Hello group, i am trying to run tblastn of version 2.2.26+ for mapping peptides on eukaryotic ge... Source ADD REPLY • link written 2.6 years ago by Ram ♦ 10k 3 2.6 years ago by Prakki Rama • 1.9k Singapore Prakki Rama • 1.9k wrote: The option "-F"  for masking

Warning in Genemark and maker Thanks everyone After my training with Genemark, there are two kinds of warning in the "log" 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 Get the line number using grep -n "Query_18905 AT1G56045.1" arapr.fasta Remove the line to see if blast succeeds , eg if 10th line sed 10d arapr.fasta | ./tblastn -i -db database1

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What is the problem? Below - the command ... blast error invalid query/ sequence/ filtering options. The following warning is now reported for each sequence that consists of all Ns: [ScoreBlkKbpUngappedCalc] Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence.

snayfach closed this Sep 8, 2015 Sign up for free to join this conversation on GitHub. need help about blast2 Hello everyone, there is a warning after i ran blast2: [email protected]:~/Desktop$ blast... RSeQC (infer_experiment) problem HI everyone I am using RSeQC to determine strandness.  When running the command infer_experiment... http://awendigital.com/could-not/could-not-calculate-ungapped-karlin-altschul-parameters.html I built my own database and I a...

Blast+ Nucleotide "-Matrix" Command HI, I've been trying to run a nucleotide blast (blastn) using BLAST+ here is what it should lo... I even tried the same query file that was run fine without problem last time but it wasn't run fine this time generating the warning message. [blastall] WARNING: contig-100_131270: Could not i ahve also run by keeping filtering turn off with the following command tblastn -query sequence.fa -out output.txt -F T -subject ref_protein.fa -evalue 1e-5 -outfmt 7 -max_target_seqs 5 -best_hit_score_edge 0.05 -best_hit_overhang Single Sign On provided by vBSSO Skip to content Ignore Learn more Please note that GitHub no longer supports old versions of Firefox.

Ncbi Legacy Blast Usage With Tblastn/Pssm I'm trying to get a webservice for protein discovery running. 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 ... 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. If it is not a fatale error, than something else is wrong with the call or my db.