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Error Cannot Initialize Readdb

I have a simple parser script that looks something like: #!/usr/bin/perl -w use strict; use Bio::SearchIO; my $in = Bio::SearchIO -> new (-format => 'blastxml', -file => "consensusSeqs.BLASTp.xml"); open (OUT, ">consensusSeqs.parse.OUT"); Thanks in advance.

0 0 03/29/11--19:41: Downloading And Maintaining A Local, Blast-Able Nr Database Contact us about this article I am planning to set up and maintain a local version I understand that I can withdraw my consent at any time. ADD REPLY • link written 4.6 years ago by Sakti • 280 we all make silly mistakes all the time - in fact the simpler the problem the more stupefying it his comment is here

very much appreciated Neilws!!!! Blast Results Wont Return This isnt my usual way if doing things but because im using Plone it has to be done this way. Or is there any other way of retrieving sequences from blast db?

0 0 05/24/13--07:59: How To Merge Contiguous Blast Hsps! (-M 8 Tab) Contact us about this article Hi, Create a text file in the same directory as formatdb that contains the following lines: [NCBI] Data="path/data/" Where "path/data/" is the path to the location of the Standalone BLAST "data" subdirectory.

This is the version of RMBlast modified for use with RepeatMasker from their site. I tried to map them to the reference genome/transcritpome, but almost nothing mapped using BWA or Bowtie. Thanks!

0 0 11/14/12--13:08: Almost Nothing Mapped Using Bwa Or Bowtie. thanks!

There is a huge difference between the two output formats, using the same data and bank. David

0 0 05/10/13--12:32: Are Alignment Lengths Reported In Ncbi Blast+ Results Counting Nucleotides Or Amino Acids? Please don't fill out this field. A few of my queries are actually full length BAC end sequences running to around 150,000 bases.

In that case you may use the '-n' option to specify a path to the real database in the production environment. In the example below the -n option is used to Afterwards I try to obtain sequence from defined positions of the db. The first section introduces the proposed ANSI standard features, tips and techniques about C programming style, working with the C preprocessor, and tips for using pointers and managing memory allocation tasks. All BLAST database source files must be in FASTA format.

Powered by Biostar version 2.3.0 Traffic: 1387 users visited in the last hour SourceForge Browse Enterprise Blog Deals Help Create Log In or Join Solution Centers Go Parallel Resources Newsletters Cloud yeah. The Latest Version: Make sure you are using the latest version of the formatdb executable. I have a metagenome like a db, and i need to blast a genome with this metagenome, the results are...

  1. Query sequence or subject sequence?
  2. The 32-bit Solaris formatdb binary on the NCBI FTP site is now compiled large file aware.
  3. No error messages in case you were wondering. ...so any ideas on where the heck the results are?

I want to run over local Blast but getting some error, I would greatly appreciate some suggestions. '''from Bio.Blast.Applications import NcbiblastxCommandline help(NcbiblastxCommandline)''' from Bio.Blast.Applications import NcbiblastpCommandline from StringIO import StringIO from http://biostar9.rssing.com/chan-9878198/all_p295.html Información bibliográficaTítuloAdvanced Programming with Microsoft QuickCAutorKeith WeiskampEditorElsevier Science, 2014ISBN1483265579, 9781483265575N.º de páginas564 páginas  Exportar citaBiBTeXEndNoteRefManAcerca de Google Libros - Política de privacidad - Condicionesdeservicio - Información para editores - Notificar un error Minor fixes to Int4List functions. 519 * 520 * Revision 6.405 2003/04/24 15:44:42 camacho 521 * Fixes for windows build 522 * 523 * Revision 6.404 2003/04/24 13:16:25 camacho 524 * Should it not recognize that I'm using DNA and not proteins?

How can I ask about the "winner" of an ongoing match? this content Is it ethical for a journal to cancel an accepted review request when they have obtained sufficient number of reviews to make a decision? My accountSearchMapsYouTubePlayNewsGmailDriveCalendarGoogle+TranslatePhotosMoreShoppingWalletFinanceDocsBooksBloggerContactsHangoutsEven more from GoogleSign inHidden fieldsSearch for groups or messages current community chat Stack Overflow Meta Stack Overflow your communities Sign up or log in to customize your list. Fixed readdb_gi2seq to look into subsequent rdfps if no isam indices are 508 * found in the first rdfp 509 * 510 * Revision 6.408 2003/04/28 19:50:10 camacho 511 * Fixes

The option is ignored in case of FASTA input database. -e Input is a Seq-entry [T/F] Optional default = F A source ASN.1 database I use the commands: formatdb -p F -i 12.fa -o T -t C57Bl6_chr12 -n C57Bl6_chr12 fastacmd -d C57Bl6_chr12 -p T -L 1000000,10001000 -o test.txt [fastacmd] ERROR: ERROR: Cannot initialize readdb for yes no add cancel older | 1 | .... | 147 | 148 | 149 | (Page 150) | 151 | 152 | 153 | .... | 759 | newer HOME weblink I downloaded the fasta from NCBI.

Mutecies shared same ISAM structures, so I had to put additional mutex. 1492 * 1493 * Revision 6.104 1999/11/24 18:01:38 egorov 1494 * Bug fixed: it truncated full database name to ADD COMMENT • link written 4.6 years ago by Neilfws ♦ 46k Please log in to add an answer. Any help as to this problem?

These are ISAM indices for mapping a sequence identifier to a particular sequence in the BLAST database If gi's are not use there will be only two additional files created (.nsd,

Browse other questions tagged python flash syntax-error or ask your own question. A sorry, didn't read that far. For that I have Installed NCBI-BLAST p... The Blast code uses BioPython's blast wrapper so we cannot use the normal Biskit mechanism to set environment variables at run time... > > Is there any parameter I must set?

A sample "nal" file, resulting from formatting the datafile "hugefasta" into three volumes, is given below. I am using CentOS 6.5. This issue, I am convinced is most definitely due to some very very long query sequences - I'd highly appreciate any help in this regard! http://haywirerobotics.com/error-cannot/error-cannot-initialize-ole-wxwidgets.html Modified fdfilter/genmask refseq_protein callback function 835 * 3.