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Error Cannot Initialize Readdb

There is a huge difference between the two output formats, using the same data and bank. This is the version of RMBlast modified for use with RepeatMasker from their site. The NLM and the U.S. 21 * Government disclaim all warranties, express or implied, including 22 * warranties of performance, merchantability or fitness for any particular 23 * purpose. 24 * Use -input_type to specify the input type being used. this contact form

How can I ask about the "winner" of an ongoing match? This function seems syntactically correct to me: def init_db(): """Initializes the database.""" with app.app_context(): db = get_db() with app.open_resource('schema.sql', mode='r') as f: db.cursor().executescript(f.read()) db.commit() But I am getting this error: --------------------------------------------------------------------------- For that I have Installed NCBI-BLAST p... Please help

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Raik > > thanks in advance, > Thomas > -- ________________________________ Dr. This is caused when the formatdb program can not find the /data subdirectory. I am using a sequence length of 80% and a fraction identical measure of 80% relative to the query as cut-offs. The bar ("|") separates different fields as listed in the above table.

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  3. In the latter case the "-e" switch should be set to TRUE. -n Base name for BLAST files [String] Optional This options allows one to produce


0 0 11/14/12--13:08: Almost Nothing Mapped Using Bwa Or Bowtie. Change to CommonIndex to support using of mask databases. 1440 * 5. Please don't fill out this field. I tried searching online and I saw some posts that suggests using -K, but I realized this does not work with the new version that I am using.

How did you know the syntax error was within the schema? –meepl May 21 '14 at 21:25 2 By the exception type - it is OperationalError (not a built-in one), The exact blastall command used is as follows: blastall -p blastn -d /Users/anjan/blastdb/nt -i -o RPMBBP10.fasta.blast.out -m 8 -b 10000. how i can??

0 0 07/20/11--12:54: Is Makeblastdb Creat 3 Files Like Formatdb + Blast Error Contact us about this article Hi everyone, I have a big problem! C.) Note on formatting large (4 Gig and larger) FASTA files: A single BLAST database can contain up to 4 billion letters. If one wishes to formatdb a FASTA file containing

Are there alternative solutions? NCBI suggests using the update_blastdb.pl (http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl) to download the latest versions of all the pre-formatted databases. Count trailing truths Locker Service: How to get the event target? Initialize OffsetAllocated=1024 1151 * 2.

Error in run blastpgp Hi, I am trying to have the command line blast work, however, I did not manage to execute it pro... The user manual says that makeblastdb is supposed to recognise the data type automatically. If gi's are present in the FASTA definition lines of the source file, there will be four additional files created (.nsd, nsi, nni, nnd). Added readdb_merge_gifiles to deal with Microbial blast database issues. 518 * 2.

If you are having problems formatting a BLAST databases please scroll down to the "Formatdb Notes/Troubleshooting" section below. weblink alias file 1384 * 1385 * Revision 6.134 2000/02/11 19:59:29 shavirin 1386 * Increased nthreads when attaching to the rdfp structure. 1387 * 1388 * Revision 6.133 2000/02/09 19:35:51 madden 1389 Fixed readdb_merge_gifiles to properly sort the rdfp linked list (rdfp_chain) 507 * 3. The -o option is really not important for BLAST searching unless you are going to use the results to parse out the identifiers for searching Entrez and downloading the sequences.

Rearrange order of functions to have Fastacmd, ID1, and CommonIndex stuff separate. 1418 * 1419 * Revision 6.123 2000/01/12 20:28:31 dondosha 1420 * Fixed readdb_new_ex2 behavior with multiple volume database 1421 I am trying to iterate over the list of sequences in the fasta file and do a sequence alignment of each sequence in one file with each sequence in the other. The volumes will have names consisting of the root database name, "hugefasta" followed by a two-digit volume extension, followed by the usual BLAST database extensions. navigate here Extension Content Format --------------------------------------------- Nucleotide database formatted without "-o T" nhr deflines binary nin ISAM binary

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 Please don't fill out this field. Section 2 presents data structures, discussing techniques for constructing useful and reliable data structures from linked lists to binary trees.

Modified FDReadDeflineAsn to return the correct 945 * BlastDefLine structure when dealing with subset 946 * (mask) databases. 947 * 2.

For this, I first have to generate a BLASTx output of my metagenomic sequences against a huge data base such as nr or pfam. I downloaded the fasta from NCBI. I did a 'ulimit -s unlimited' to set the stack size to unlimited, but to no avail. All BLAST database source files must be in FASTA format.

I had earlier run a smaller query dataset against the same genome which worked fine, the BLAST completed in half a day. So, what is the option in blast+ to turn off filtering?  

0 0 04/03/12--10:25: Blast Database Sequences Length Contact us about this article Hi all I am doing blast 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. http://optimisersonpc.com/error-cannot/error-cannot-initialize-wordperfect.html Help with custom database of a genera and count of hits (NGS, 454) Hello biologists and bioinformaticians around the world!

I am using CentOS 6.5. I am, however, unsuccessful up to now as I end up creating a PROTEIN database, although my file obviously contains DNA sequences. Other small changes 1442 * 1443 * Revision 6.117 1999/12/29 13:46:42 madden 1444 * Fix for moving virtual rdfp to end, remove bad fix for infinite recursion 1445 * 1446 * My next steps for refining the results include GC content analysis, RepeatMasker etc.

I tried to map them to the reference genome/transcritpome, but almost nothing mapped using BWA or Bowtie. Does anyone have experiences to share on using this script? Made genmask show progress if SHOW_PROGRESS is defined. 893 * 894 * Revision 6.286 2001/12/04 21:21:19 camacho 895 * Eliminated unnecessary condition in readdb_gi2seq 896 * 897 * Revision 6.285 2001/11/28 mydata=read.table("C:/Users/du0/Desktop/Downloads/CDPKbeta_BLAST_results.csv", header=TRUE,sep=",") mydata=as.matrix(mydata) AAs=c() BLAST_AA_seqs=c() for(i in 1:nrow(mydata)){  print(i)  BLAST_AA_seqs[i]=mydata[i,8]  AAs[i]=table(strsplit(BLAST_AA_seqs[i],"", useBytes=TRUE))  pie(AAs, col=rainbow(length(AAs)), main="Residue abundance") }

0 0 02/01/14--10:59: Protein Sequence Alignment Using Blast Contact us about this article

It is expected that the proper alias file and oidlist for searching such subsets will be made available on the NCBI FTP site in mid January. When I try to create the database specifying in the input_type the 'asn1_bin', 'asn1_txt' and 'xml' respectively, I get the following error: Error: NCBI C++ Exception: "/am/ncbiapdata/release/blast/src/2.2.25/Linux64-Suse-icc/c++/ICC1010-ReleaseMT64--Linux64-Suse-icc/../src/serial/objistr.cpp", line 838: Error: ncbi::CObjectIStream::SkipFileHeader() Contact us about this article Possible Duplicate:make a custom BLAST library using the output of another blast result Hello, I would like to create a BLAST database using as input a 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

Refactored code to create multiple volumes. 452 * 2. Problems Running The Ncbi-Blast Tools I want to find core genome of around 30 bacterial genomes. Contact us about this article I am interested in getting ungapped sequence hits (hspsnogap) from blast output, I tried using this: result_handle = NCBIWWW.qblast("blastp", "nr", record.format("fasta"),expect=10,"hsps_no_gap") blast_records=NCBIXML.read(result_handle) but there are still Two billion is the current limitation on the NCBI toolkit command-line parser.

Troubleshooting "SeqIdParse Failure" errors The most frequent cause of SeqIdParse Failure errors come from the syntax of the FASTA definition lines in the source database file. Thanks!

0 0 07/26/10--14:10: Creating A Dna Sequence Database Locally For Blastplus Contact us about this article Hi, I have a fasta file containing cDNA sequences and I would like D.) Note on running formatdb on a database without uncompressing it: Under UNIX it is possible to uncompress a database on the fly and pipe it to formatdb. In some cases a field is left empty, even though the original specification called for including this field. To make these identifiers backwards-compatiable for older parsers the empty field is denoted

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