formatdb error Quogue New York

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formatdb error Quogue, New York

This can reduce the amount of disk-space and memory needed by half in this case. Thanks I just hit what is probably the same issue, and believe this is a new bug in BLAST+ 2.2.29 (the older versions I tested were fine) when FASTA query files Also, the input sequences were obtained after using the extract program in glimmer3. 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.

It is necessary to use parseable identifiers for the following cases: 1.) ASN.1 is to be produced from blastall or blastpgp, then "-o" must be TRUE. 2.) query-anchored alignments are desired I tried the following script that I found in... What does it actually mean by specified time? Hello BLAST1.1 What Is BLAST?1.2 Using NCBI-BLAST1.3 Alternate Output Formats1.4 Alternate Alignment Views1.5 The Next Step1.6 Further ReadingPart II: TheoryChapter 2.

ID's must fit into the framework described above to ensure that they can be reliably parsed and indices built for them. This means that it is not possible for users to For two of my input databases, the program runs fine. My command is: ./interpros... Make sure you download all the nr* files.

How to reliably reload package after change? Problems With Blast And Nr Database I'm familiar with the BLAST family of software: I've used both the old interface (blastall, forma... ADD REPLY • link written 4.5 years ago by Neilfws ♦ 46k 3 4.5 years ago by Neilfws ♦ 46k Sydney, Australia Neilfws ♦ 46k wrote: The error has a simple This can reduce the disk-space needed for running formatdb on a large database. In addition, some operating systems cannot write files larger than 2 Gig to disk. To circumvent this on

Security Patch SUPEE-8788 - Possible Problems? These smaller databases can be searched as if they were a single entity using: blastall -i infile -d hugefasta -p blastn -o out In this case, BLAST recognizes that the database I am seemingly stuck with something that should be very simple and I hope I haven't overlooked so... [Ncbi-Blast-2.2.28+] Thrownullpointerexception() When Running Blastn Hello, I'm still rather new to blast+ and If GI numbers are included and more than one sequence has the same GI number, formatdb terminates with an error.

ADD REPLY • link written 5.2 years ago by Dan Gaston ♦ 6.3k can i change the permission of a directory and to write there? The Latest Version: Make sure you are using the latest version of the formatdb executable. BLAST Protocols9.1 BLASTN Protocols9.2 BLASTP Protocols9.3 BLASTX Protocols9.4 TBLASTN Protocols9.5 TBLASTX ProtocolsPart IV: Industrial-Strength BLASTChapter 10. blast2table.plGlossaryNumbersA-GH-UColophon Remember the name: Copyright 2008-2016.

Interproscan nucleotide sequence scanning Hi, Dear All, have fasta file of nucleotide sequences (~ 30,000). That doesn't require to download any databases as well as i can do it on my sloppy machine. :-) Best, Christian Hi, just a question, how many transcripts did you search If this is the case for you, do not be surprised when fastacmd generates an empty output file. The error message will contain more information about the nature of the problem.

BLAST Databases11.1 FASTA Files11.2 BLAST Databases11.3 Sequence Databases11.4 Sequence Database Management StrategiesChapter 12. I first make a compatible dat... I'm hoping this doesn't come off as a lazy question, but I am wondering if anyone is aware of a t... Chapter 11 covers this process in more detail. -n [string]Default: Optional, required with -i stdin Sets the base name for the BLAST database.

I install blast+ for windows. 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 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, Easiest way would be to supply the the full path to a directory you have writing permissions.

If accession numbers aren't unique, an error won't be issued (see -V). -p [T/F]Default: T Specifies the type of type of file being formatted. You can find more information about ASN.1 at Um Google Groups Discussions nutzen zu können, aktivieren Sie JavaScript in Ihren Browsereinstellungen und aktualisieren Sie dann diese Seite. . I'm trying to figure out how to create a local BLAST database from a fasta file with 2000+ sequen...

If not specified, the name of the FASTA file will be used. Ncbi Legacy Blast Usage With Tblastn/Pssm I'm trying to get a webservice for protein discovery running. For Example: Data=/root/blast/data For PC's this would be [NCBI] Data="C:\path\data\" Where "C:path\data\" is the path to the location of the Standalone BLAST "data" subdirectory. GenoMax05-26-2014, 03:53 AMHello, GenoMax, I have a question, there are 16 nr files in the ftp, can I use cat to concatenate the files with the same extension in those 16

Do not create indexes. [T/F] Optional default = F If the "-o" option is TRUE (and the source database is in FASTA format), then the database identifiers This is caused when the formatdb program can not find the /data subdirectory. ForwardPrefaceAudience for This BookStructure of This BookA Little Math, a Little PerlConventions Used in This BookURLs Referenced in This BookComments and QuestionsAcknowledgmentsPart I: IntroductionChapter 1. Thanks!

Also I find it interesting that your input file 'nr' does not have an extension -- are you sure this is correct? ADD COMMENT • link written 5.2 years ago by Dan Gaston ♦ 6.3k Thanks DAN for your answer . All BLAST database source files must be in FASTA format. How to tell why macOS thinks that a certificate is revoked?

Formatdb problem in Unus package I´m using Unus, which is Perl package for phylogenomic analyses.