Error Entry Not Found In Blast Database
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faq • rss Community Log In Sign Up Add New Post Question: Strange "Error: OID not found" in NCBI's blastdbcmd oid not found blast+ 0 22 months ago by juanma_lace • 10 Argentina juanma_lace •
Blastdbcmd Oid Not Found
10 wrote: I'm getting a OID not found when executin blastdbcmd. My file is as follows: >cat blastdbcmd example data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted | grep scaffold00001_37_1_21 >scaffold00001_37_1_21 And I run >makeblastdb -dbtype 'nucl' -in data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted -out data/4D/blastdb-parseqid/4ds_splitted -parse_seqids Building a new DB, current time: 12/18/2014 14:12:08 New DB name: data/4D/blastdb-parseqid/4ds_splitted blastdbcmd entry_batch New DB title: data/4D/4ds_newbler2.6_shotgun_lmp_scaffolds.fasta.splitted Sequence type: Nucleotide Deleted existing BLAST database with identical name. Keep Linkouts: T Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 307 sequences in 0.021672 seconds. And then >blastdbcmd -db data/4D/blastdb-parseqid/4ds_splitted -entry scaffold00001_37_1_21 -outfmt %f -out 1_scaffold00001_37_1_21.fsa Error: scaffold00001_37_1_21: OID not found BLAST query/options error: Entry not found
Makeblastdb Parse_seqids
in BLAST database Please refer to the BLAST+ user manual. Any ideas? thank you in advance EDIT: if I take a look to the output of blastdbcmd with entry "all" I cannot find the original sequence, why is it missing? >blastdbcmd -db data/4D/blastdb-parseqid/4ds_splitted -entry all -outfmt %f -out 1_scaffold00001_37_1_21.fsa >cat 1_scaffold00001_37_1_21.fsa | grep 0001_ nothing. blastdbcmd makeblastdb blast blastcmd fasta • 2.5k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 22 months ago by Siva • 1.4k • written 22 months ago by juanma_lace • 10 are you sure about "-parse_seqids" ? ADD REPLY • link written 22 months ago by Pierre Lindenbaum ♦ 86k 1 22 months ago by juanma_lace • 10 Argentina juanma_lace • 10 wrote: Deleting previous generated databases with makeblastdb solve the issue. I was getting no error, but the database was not being generated again. ADD COMMENT • link written 22 months ago by juanma_lace • 10 1 22 mo
the C 'legacy' BLAST suite) lets you do a lot of clever things with a BLAST database. As long as you follow the baroque NCBI FASTA naming blastdbcmd outfmt scheme you can do this with local BLAST databases too. However, if blastdbcmd extract sequences you don't want to bow down to the NCBI naming (e.g. use FASTA files directly from your favourite assembler),
Blast+ User Manual
then blastdbcmd seems needlessly crippled. Update (2 April 2013): Some changes in BLAST 2.2.28+ (released yesterday) seem to be intended to address these issues, but there remain problems with this https://www.biostars.org/p/124292/ which I intend to expand on later. Update (20 April 2013):I found a quiet moment this weekend to update this post with the BLAST 2.2.28+ problems I was alluding to. There has been some progress on this issue with the new release, but it is flawed. See below. To demonstrate the problem (tested using BLAST 2.2.27+), consider this small silly protein http://blastedbio.blogspot.com/2012/10/my-ids-not-good-enough-for-ncbi-blast.html FASTA file example: $ more silly.faa>example1 Here is an example with a simple nameMVKLRLKRCGRKQRAVYRILAIDVRYRREGRDLSKVGFYDPITNQTFLNLSAILDFLKKGAQPTRTAHDISKKAGIFTE>example2MVKLRLKRCGRKQRAVYRILAIDVRYRREGRDLSKVGFYDPITNQTFLNLSAILDFLKKGAQPTRTAHDISKKAGIFTE>example3|truncated Note pipe characters but this isn't using NCBI style!MLNIFNLICIFFNSTLFSSTFLVAKLPEAYAFLNPIVDVMPVIPLFFLLLAFVWQAA First, here's what happens if I tell BLAST+ that I'm using the NCBI style naming and it can parse the sequence identifiers: $ ~/downloads/ncbi-blast-2.2.27+/bin/makeblastdb -dbtype prot -in silly.faa -out silly -parse_seqids...Error: NCBI C++ Exception: "/am/ncbiapdata/release/blast/src/2.2.27/Linux64-Centos-icc/c++/ICC1010-ReleaseMT64--Linux64-Centos-icc/../src/objects/seq/../seqloc/Seq_id.cpp", line 1689: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type example3 Here BLAST+ has quite rightly rejected my FASTA file when I told it to try and parse the sequence identifiers as if they were using the NCBI style. (Update: Error handling improved in BLAST 2.2.29+, see end of post). Clearly we shouldn't try to do that, so: $ ~/downloads/ncbi-blast-2.2.27+/bin/makeblastdb -dbtype prot -in silly.faa -out sillyBuilding a new DB, current time: 10/30/2012 16:59:24New DB name: sillyNew DB title: silly.faaSequence type: ProteinKeep Linkouts: TKeep MBits: TMaximum file size: 1000000000BAdding sequences from FASTA; added 3 sequences in 0.00222683 seconds. Now, what does blastdbcmd make of this? For this we can call blastdbcmd with the special argument 'all' as the entry name: $ blastdbcmd -db silly -entry all >gnl|B
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here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this site About Us Learn more about Stack Overflow the company Business Learn more about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 4.7 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up Blast+: blastdbcmd - error message up vote -1 down vote favorite I want to convert 16S Microbial database format in fasta format. I use Blast+ program (2.2.27+ version Window). I could install this program and I know that I must to use blastdbcmd command. The problems are that I don´t know how I have to write right the commannd and also, I have an error message: No alias or index file found nucleotide database 16SMicrobial in search path C:users\Debora\blast-2.2.27+; C:users\Debora\blast-2.2.27+\db\16SMicrobial The 16S Microbial file is in db file. The 16S Microbial is ungzipped and untarzipped. I tried to edit the environment variable, I intented to edit the User and System variable but I don´t really understand what I must write. So, I suspect that the database is in the wrong place, but I don´t know how to correct. I´ll hope someone can help me!!!!! Thanks for all!!! database windows blast share|improve this question asked Dec 10 '12 at 18:00 user1892205 11 add a comment| 1 Answer 1 active oldest votes up vote 0 down vote What's happening is your blastdbcmd program cannot find your 16s database. You need to have the database set up as .phr/.pin/.psq or .nhr/.nin/.nsq files first. Then you have to make sure your program knows where to look. The easiest way is to use a .ncbirc file, and this file should be in the same directory as your actual blastdbcmd executable. On Windows the file would be .ncbi.ini I think, but I'm not sure. I also don't know the format, but you should be able to google that. To give you an idea on my mac the file contains the line BLASTDB=/Users/myName/blast/db, where that directory is where I'm storing my databases. share|improve this answer answered Jan 2 '13 at 23:18 DaveTheScientist 1,252913 add a comment| Your Answer draft saved draft discarded Sign up or log in Sign up using Google Sign up u