Blast database error no alias or index file

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August undefined, 2024

WebDec 17, 2024 · The problem was in the way I decompressed the nr file. Previously I used the following command: $ formatdb -i nr.fa -p T. Now I used: $ makeblastdb -in nr.fa …

BLAST Database error: No alias or index file found for nucleotide ...

Webblast needs a file from the tools repository and can't find it. When you downloaded Rosetta, did you get the tools repo with it (it's in the bundle version)? Is it at the location specified? WebDec 17, 2024 · BLAST Database error: No alias or index file found for nucleotide database. 1. BLAST: can't find reference file in db. Hot Network Questions Is -ist a … heal our planet

Timeout when downloading the ncbi nr blast database

WebBLAST Database error: No alias or index file found for nucleotide database. I need all possible hacks or tricks around this situation since it is pretty perplexing. All answers welcome! Heads up: Changing blastdb variable didn't work. fasta file blast database standalone • 291 views WebJan 23, 2014 · 1) I suggest using full path names instead of '~'. 2) To help troubleshoot cases of 'no file found' it is handy for us to see an 'ls' of the directory in question just to … BLAST Database error: No alias or index file found for nucleotide database. Ask Question Asked 8 years, 5 months ago. Modified 2 years, 4 months ago. Viewed 19k times 4 I am trying to run blastn, and then also SIFT standalone. I am having database configuration issues however as I am getting the following: healov ear drops

ERROR: Too many erroneous kmers, the estimates might be

Use blastdb_aliastool to manage the BLAST databases

WebMar 13, 2024 · @mike I will check with the researcher if they are running any special config files. I was not able to find any in the Tracer base install directory located in site-packages of Python 2.7.13. @krzysztof, We can support Docker but due to the nature of the applications and research, it would be a short term solution.We have a CPU and GPU … WebMar 16, 2024 · Created nucleotide BLAST (alias) database testdb with 12692 sequences ## Test testdb.nal... BLAST Database error: No alias or index file found for nucleotide … golf courses with hotels ukWebMay 17, 2024 · TBLASTN search translated nucleotide databases using a protein query, but in your case I can see that you have prepared protein database using -dbtype 'prot' … golf courses within 10 miles of 85283

"WebJul 26, 2024 · BLAST Database error: No alias or index file found for nucleotide database 在本地使用blast确实比较麻烦，需要两个步骤建库比对这里，根据官网提供的信息，建库又需要两个步骤；产生masking data 产生真正的BLAST数据库 1. " - Blast database error no alias or index file

Blast database error no alias or index file

WebApr 3, 2024 · 2024/04/03 15:15:24 Creating tab files for R 2024/04/03 15:15:25 Create EMBL files 2024/04/03 15:15:26 Creating files with the nucleotide sequences for every cluster 2024/04/03 15:15:34 Cleaning up files Aligning each cluster Use of uninitialized value in require at (eval 2091) line 1. 2024/04/03 15:15:34 Running command: … WebJan 24, 2024 · I inquired with the NCBI BLAST help desk today, and within an hour they provided a very helpful response. To summarize, when redundant records in the database are collapsed, the deflines (accessions + descriptions) of the original entries are placed on a single line separated by an invisible control character (Ctrl-A or \x01).The makeblastdb …

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WebOct 31, 2024 · Teams. Q&A for work. Connect and share knowledge within a single location that is structured and easy to search. Learn more about Teams WebJun 23, 2008 · Locally available BLAST database name to search when resolving protein sequences using BLAST databases. Ignored if DATA_LOADERS does not include the blastdb keyword. ... If defined, no …

WebMar 18, 2014 · BLAST Database error: No alias or index file found for protein database [Arabido psis_thaliana.fas] in search path [C:\blast-2.2.25+;C:\blast-2.2.25+\db;] makeblastdb -in swissprot.fas -dbtype prot -out Thaliana Error: Unable to open input swissprot.fas as either FASTA file or BLAST db makeblastdb -in swissprot.fas -dbtype … WebOct 18, 2014 · No volumes were created because no sequences were found. BLAST Database creation error: Defline lacks a proper ID around line 1. When I try it without '-parse_seqids', it works fine and it generated the three files with pin, psq and phr. I put these 3 files with my database.fa fasta file in one folder called DB and then I try to run blastp …

WebMay 24, 2015 · BLAST Database error: No alias or index file found for protein database. Collapse. Announcement. Collapse. No announcement yet. X. Collapse. Posts; Latest Activity; Photos . Search. Page of 1. Filter. Time. All Time Today Last Week Last Month. Show. All Discussions only Photos only Videos only Links only Polls only Events only. WebJan 29, 2024 · Hello, nr is a multi-volume database, so you need to download all the tar files starting with nr (e.g., nr.01.tar.gz, nr.02.tar.gz). The BLAST+ packages have a perl script called update_blastdb.pl that will download all the volumes.

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WebJun 25, 2024 · BLAST Database error: No alias or index file found for nucleotide database Author: Zoila Kingston Date: 2024-06-25 Solution 2: You could try running protein blast, because swissprot is a protein database, and blastn is for nucleotide sequences Question: I am trying to find sequence homology between viral sequences and my … heal over kt tunstall chordsWebIndex a BLAST database Database name: blastsw Database directory [.]: database base filename [blastsw]: Release number [0.0]: Index date [00/00/00]: N : nucleic P : protein ? : unknown Sequence type [unknown]: p 1 : wublast and setdb/pressdb 2 : formatdb 0 : unknown Blast index version [unknown]: 2 ... To avoid overwriting of index files you ... heal overWebI have contig sequences of S.pneumoniae. since you are working with bacterial sequences, predict ORF, translate into protein and use blastp. That would be the easiest for you. @Vishal is ur ... golf courses with home rentals near sarasotaWebMar 24, 2024 · That should be all you need to do (haven’t worked with NT in a while now). Just download and decompress; the folder everything is now in is your complete index. … golf courses within 10WebApr 28, 2024 · from the look of it it seems your DB is called swissprot.fasta (it's the basename for all the other files makeblastdb has created). So that is the name you have to use in your blast cmdline. Indeed, any of the files with extensions as .phr. pin ... are files internally used by blast and should thus not be used to call/access the DB heal over kt tunstall lyricsWebJan 7, 2024 · Use blastdb_aliastool to manage the BLAST databases - BLAST® Command ... golf courses within 3 hours of peoriaWebThat said, this problem is clear -- the database needs to be indexed before using it as a -db input. The utility that indexes is called makeblastdb and comes in the BLAST package. Also, double check both that the query and target are both nucleotide, not protein, when using Blastn. See the BLAST help for details, or do a google search for the ... heal over nyt crossword