fatal error when adding sequence to blast database Kings Bay Georgia

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fatal error when adding sequence to blast database Kings Bay, Georgia

Shavirin 32 33 Version Creation Date: 10/01/96 34 35 $Revision: 6.104 $ 36 37 File Description: formats FASTA databases for use by BLAST 38 39 $Log: formatdb.c,v $ 40 Revision 6.104 Regards, Rolf Previous message: pdb-l: Problem with formatdb Next message: pdb-l: Problem with blastpgp Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information We have used MS/MS data from Jacek et al, a representative spectra from mutationDB is shown below 19. By default this is named pgtools_scratch and is placed in your current working directory.

Even though the fasta file appears fine on the surface, formatdb is saying that it's not happy with it. For example any of the standard known protein database such as ENSEMBL, RefSeq and UniProt should run fine while one cannot run six frame translated database. 13. asked 2 years ago viewed 392 times active 2 years ago Related 0Loading Big files into Hashes in Perl (BLAST tables)430Why is this program valid? more stack exchange communities company blog Stack Exchange Inbox Reputation and Badges sign up log in tour help Tour Start here for a quick overview of the site Help Center Detailed

Check the Percolator installations. NoDatabase CategorySourceSize 1PseudogeneDBENSEMBL135MB 2SpliceDBENSEMBL30MB 3NONCODEDBNONCODE417MB 4UTRDBENSEMBL156MB 5Six-frameDBENSEMBL12GB 6MutationDBCOSMIC119MB 7FusionDBCOSMIC10MB 14. If the annotation does not exist in the resources, they can’t be annotated. Some Questions About Using Orthomcl To Find Orthologs Within Many Species When I follow the OrthoMCL User to do my work, I use orthomclAdjustFasta to produce a compliant ...

The procedure was successful in local disk, but FAIL in PVFS2. Yes, PGTools proteome_run and genome_run commands represent the complete pipeline. I want to use annotate module for a set of proteins that was generated using other tools. Error in run blastpgp Hi, I am trying to have the command line blast work, however, I did not manage to execute it pro...

Also, the input sequences were obtained after using the extract program in glimmer3. Books for chess traps Appease Your Google Overlords: Draw the "G" Logo What does かぎのあるヱ mean? Notepad++ is helpful for revealing otherwise-invisible special characters. I inspected the sequences, and they don´t have zero-length.

blast FATAL ERROR: BlastFormattingInfoNew returned non-z Hi, I'm running blast commands from a cluster of nodes and sometimes if succeeding and sometimes... A module called as generatedb within PGTools is used to build custom databases. PGTools accepts .MGF and .mzML formats. This is the log file of FORMATDB in local disk with successful messages: ========================[ Dec 6, 2007 9:07 PM ]======================== Version 2.2.17 [Aug-26-2007] Started database file "nr" Closing volume nr with

Some of my proteins could not be annotated, why? MSG: Muscle call crashed: 512 Hi all, I'm having trouble with the same error while running MUSCLE in Unus that is a Perl packa... The processing time of PGTools modules depends on the following hardware in which PGTools is running version of the MS search engine used (X-tandem versus Parallel Tandem) the size of the Hardware sources of entropy on an FPGA What does a well diversified self-managed investment portfolio look like?

In the United States is racial, ethnic, or national preference an acceptable hiring practice for departments or companies in some situations? However, PGTools provides a list of un-annotated protein IDs in annotate.error.log file within pgtools_scratch dir. MSGF+ have an upper limit of 1GB for the database size unlike Tandem and OMSSA. Powered by Biostar version 2.3.0 Traffic: 596 users visited in the last hour Um Google Groups Discussions nutzen zu können, aktivieren Sie JavaScript in Ihren Browsereinstellungen und aktualisieren Sie dann diese

Is it possible run multiple modules within PGTools as a pipeline? There are two ways to configure this path, and they are picked in chosen in the following order of priority. I see multiple entries with same ID why? xx.fa(-i 后的输入文件) 文件中有无效的序列,比如仅有>xxxx 换行后没有有效的序列,会告诉你是第几条序列发生了错误。 [NULL_Caption] ERROR: No database name was specified 不输入任何参数时,报告的错误。 [NULL_Caption] ERROR: Invalid argument: -h 参数错误,查看帮助应该是-help 新书推荐 Amazon.cn Widgets  » 转载文章请注明,转载自:博耘生物 » 《本地Blast常见错误及其处理》 » 原文链接:http://boyun.sh.cn/bio/?p=1600 This entry was posted

Hey guys, I've been trying to figure out why this script has been running painfully slowly. perl blast share|improve this question edited Jul 9 '14 at 16:38 Miller 31k42446 asked Jul 9 '14 at 15:56 user3275981 164 add a comment| 1 Answer 1 active oldest votes up I'm brand new to mothur (and to command line anything actually) and am having some issues. A example of a input sequence is: > orf00002 3568 4905 len=1338 GTGATTGTTTTTAAAGGAAATTTAGGGGCCGAAACCCTGTGTTTACCGCCCTGTTTTCTC ACAAACAAGCTGTGGATAAGCGAAAGCACCTCCACAGGCCCTATTTTTATCCACATGTTA TCCCCTGCCTGTCCGGTCATTCCTGGCGGCCATGTCTGCACGGTTTCATGCCGATCCCGT ATCCTTCGAACCGACCGGCATGCCGGATTACAGCCCAGAGCACACCGATCGATGCATGTA GTGCGGTTGTCCATTCATCGGCTTCGTCGGTTTCAAACCGTCGAGCTTCATCCCTCCAGT GCCTTGAATCTGCTGACCGGCGACAACGGCGCGGGCAAGACCAGCGTGCTCGAAGCGCTA CACCTGATGGCTTACGGCCGCAGCTTCCGCGGGCGCGTCCGCGACGGCCTGATCCAACAA GGCGCCAACGACCTCGAAGTGTTCGTGGAGTGGAAAGAAGGCGGCGGCGCTGCGGTCGAG CGGACGCGTCGGGCTGGCTTGCGTCATAGCGGGCAGGAATGGACAGGGCGCCTGGACGGG GAAGACGTGGCGCAGCTTGGCTCTCTTTGCGCTGCGCTGGCAGTGGTGACGTTCGAGCCC GGCAGCCACGTATTGATCAGTGGCGGTGGTGAACCCCGCCGCCGTTTTCTGGATTGGGGC CTGTTCCACGTGGAACCCGATTTTCTAACCTTGTGGCGCCGCTATGCGCGAGCCCTCAAA >orf00004 5020 7464 len=2445 ATGACCGACGAACAAAACACCCCGCCAACACCCAACGGCACCTACGACTCCAGCAAGATC ACCGTGCTGCGTGGCCTGGAAGCCGTCCGCAAGCGTCCCGGCATGTATATCGGCGACGTC CATGACGGCACCGGCCTGCATCACATGGTGTTCGAGGTGGTCGACAACTCGGTCGACGAA

Similar posts • Search » Error In Using Viralfusionseq With The Test Data On Centos 5 System hi there, I am also getting this error while running VFS (http://sourceforge.net/projects/viralfu... Satagopam Schneider Group Structural and Computational Biology EMBL Meyerhofstr. 1 69117 Heidelberg phone: +49-(0)-6221-387-140 fax: +49-(0)-6221-387-517 venkata.satagopam at embl.de http://www.embl-heidelberg.de/~satagopa/ -------------- next part -------------- An HTML attachment was scrubbed... Not the answer you're looking for? Annotate modules relies on protein annotations from two resources: HPRD and The Human Protein Atlas.

How do investigators always know the logged flight time of the pilots? Removed single-volume database nr FATAL ERROR: [001.000] Fatal error when adding sequence to BLAST database. I guess other people might also having problem to run the blast with these sequences, it may be worth fixing fasta files on ftp site. We will update the custom databases regularly and host it on our web site.

SeqEntryLoad()) 925 ErrShow(); 926 927 /* get pointer to all loaded ASN.1 modules */ 928 amp = AsnAllModPtr(); 929 930 if (amp == NULL) { 931 ErrLogPrintf("Could not load ASN.1 modules.\n"); Is accuracy binary? The NLM and the U.S. 21 Government disclaim all warranties, express or implied, including 22 warranties of performance, merchantability or fitness for any 23 particular purpose. 24 25 Please cite the In this package, the blast-2.2.25 is used because the package uses the formatdb program, as follows: if ( ( grep { $self->{'program'} eq $_ } qw(blastn tblastx tblastn) ) && !(

Building custom genome databases not only involves multiple steps, files and scripts, but also require access to computing power (to process large database files such as sixframeDB). MSGF+ failed in my PGTools run, why ? Help with custom database of a genera and count of hits (NGS, 454) Hello biologists and bioinformaticians around the world! It ta...

x $pgtools protome_run hela.mgf x command does not exist: protome_run x Use of uninitialized value within %commands in concatenation (.) or string at /panfs/home/snagaraj/bio/src/../lib/PGTools.pm line 114. 17. We convert output file to Genomic... New tech, old clothes Is intelligence the "natural" product of evolution?