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formatdb error could not open Port Gibson, New York

DZhang View Public Profile Send a private message to DZhang Find More Posts by DZhang Tags bioinformatics, blast, formatdb « Previous Thread | Next Thread » Thread Tools Show Printable Version Users with a current NCBI toolkit will not be able to use the blast assignment. H. Same input files with chimera.slayer in the previous version of Mothur works fine.formatdb.log looks like this:========================[ May 20, 2011 9:03 AM ]========================Version 2.2.16 [Mar-25-2007]Started database file "STR_6743seqs_200511_core_blast_min700bp.align.29317463.template.unaligned.fasta"NOTE: CoreLib [002.003] FileOpen(".formatdbrc","r") failedNOTE:

Top westcott Posts: 1579 Joined: Thu Sep 03, 2009 7:47 am Re: chimera.slayer: could not open file Quote Postby westcott » Tue May 24, 2011 8:45 am Could you send the Finally - there are easier ways to extract sub-sequences from larger sequences (using the original FASTA file) than dumping from a BLAST database. Thanks!! But as far as I can see the program I use expects plain-text blast output, and not the tab-delimited format.

The procedure to produce an alias file for searching (protein) nr limiting it to a list of zebrafish GI's would be: 1.) obtain the list of zebrafish GI's from Entrez or Thus gi identifiers provide a mechanism for identifying the exact sequence that was used or retrieved in a given search. And about retrieving sequences with fastacmd, well, it is at least fastest than my previous experiences with SeqIO when managing huge data volumes, but once again, it might be just the F.

Formatdb must be able to open files larger than 2 Gig in order to work on very large files. This is not a problem on a 64-bit OS and on certain 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. Hi all, in the legacy BLAST, the command formatdb is used for formating fasta files into BLAST da... Blast Gives Cryptic Errors I have a list of proteins in fasta format (say goodProteins.fasta).

The bar ("|") separates different fields as listed in the above table. IgnoringNOTE: [000.000] No number of membership bits used found in config file. Formatdb problem in Unus package I´m using Unus, which is Perl package for phylogenomic analyses. Top tmchughie Posts: 1 Joined: Tue Jul 12, 2011 8:42 pm Re: chimera.slayer: could not open file Quote Postby tmchughie » Tue Jul 12, 2011 9:26 pm I started preprocessing my

Although this could get fixed entirely within the /cogent/app/formatdb.py, I thought i would file the bug here since it will primarily affect Qiime users. — Reply to this email directly or G. We uploaded a new version of mothur that has a warning message it this occurs. 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

Top rockx Posts: 4 Joined: Wed May 18, 2011 2:26 am Re: chimera.slayer: could not open file Quote Postby rockx » Thu May 26, 2011 8:27 pm Thanks for the quick Now, when I rerun the new commands on the same dataset, there are problems. I have downloaded and successfully compiled mothur from the source code. Unfortunately, they don't work.

Can you double check the file? Error in run blastpgp Hi, I am trying to have the command line blast work, however, I did not manage to execute it pro... When I run formatdb on a chromosome 12 sequence downloaded from NCBI and I look at formatdb.log, I see that 7 sequences were formatted, corresponding to 7 contigs. I am having an extremely difficult time with formatdb and fastcmd from NCBI blast.

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. I changed the ClassName and references to the class but since only the functions from this file seem to be called directly this change should work fine as a fix. I'm running mothur last version in Ubuntu. I first make a compatible dat...

What'S The Different Between Formatdb (In The Legacy Blast) And Makeblastdb (In Blast+)? Edit Blast Not Finding Locally Downloaded Database (Nr) Local Blastn Stopping Early I downloaded nr locally and am trying to BLAST my fasta files against the nr database. This is a quick first-pass at addressing: biocore/qiime#1225 467d2f9 zachcp referenced this issue in pycogent/pycogent Nov 26, 2013 Open Updates Cogent to use Makeblastdb instead of the deprecated formatdb about • faq • rss Community Log In Sign Up Add New Post Question: Problems Using Formatdb And Fastacmd 2 4.5 years ago by Sakti • 280 United States Sakti •

When I try other options, this is what I get:> chimera.slayer(fasta=McHughB.trim.unique.good.filter.unique.precluster.fasta, name=McHughB.trim.unique.good.filter.unique.precluster.names)Only reporting sequence supported by 90% of bootstrapped results.[NULL_Caption] ERROR: Could not open self243671296683758.template.unaligned.fasta> chimera.slayer(fasta=McHughB.trim.unique.good.filter.unique.precluster.fasta, reference=silva.gold.filter.fasta, processors=2)[NULL_Caption] FATAL ERROR: Database Powered by Biostar version 2.3.0 Traffic: 583 users visited in the last hour The mothur forum The community-supported forum for the mothur software package Skip to content Search Advanced search Quick 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. If you need to use the -o T option then your best option is to examine the definition lines of the database sequences and attempt to make them conform the FASTA

Please note that if you are going to apply periodic updates to your BLAST databases using fmerge (ftp://ftp.ncbi.nih.gov/blast/fmerge/README), you will need to keep the source database file. Do you know why. For that I have Installed NCBI-BLAST p... It looks like your sequence names contain ::.

blast • 2.4k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 4.5 years ago • written 4.5 years ago by Sakti DZhang View Public Profile Send a private message to DZhang Find More Posts by DZhang 08-07-2011, 07:22 AM #3 sammy07 Member Location: austria Join Date: Nov 2010 Posts: 20 Although this could get fixed entirely within the /cogent/app/formatdb.py, I thought i would file the bug here since it will primarily affect Qiime users. Is it in your path?``` the problem here is that formatdb has been deprecated in favor of `makeblastdb` and it is called form this script.

The problem looks like this: Quote: [emailprotected]:/tmp/blast/bin$ ls . Or contact the BLAST Desk at [email protected] Command Line Options -------------------- A list of the command line options for formatdb may be obtained by executing formatdb without options, as in: Want to give it a try? Is it installed?

General troubleshooting tips. 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 This can reduce the amount of disk-space and memory needed by half in this case. Bookmark the permalink. 发表评论 取消回复 电子邮件地址不会被公开。 必填项已用*标注评论 姓名 * 电子邮件 * 站点 请启用Javascript,以完成验证! 版权协议 本站采用创作共用版权协议, 要求署名、非商业用途和保持一致. 转载本站内容必须也遵循“署名-非商业用途-保持一致”的创作共用协议.

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 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. sammy07 View Public Profile Send a private message to sammy07 Find More Posts by sammy07 08-07-2011, 07:01 AM #2 DZhang Senior Member Location: East Coast, US Join Date: Jun If you are having problems formatting a BLAST databases please scroll down to the "Formatdb Notes/Troubleshooting" section below.

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 We recommend upgrading to the latest Safari, Google Chrome, or Firefox. in a future version of BLAST. 3.) membership bits. These specify that a given gi in a database also belongs to a subset database. An example of this relationship is the Chimera.slayer reports no errors, however no chimeras are detected in an alignment with known chimeras (Linux Mothur detected 30 chimeras).