2024 Blast database error no alias or index file

Blast database error no alias or index file

Author: kymo

August undefined, 2024

WebHave a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 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 …

Indexing and configuring BLAST databases - SourceForge

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 … free online degree courses+methods

BLAST Database error: No alias or index file found for protein

WebThat 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. … 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: WebJan 7, 2024 · Use blastdb_aliastool to manage the BLAST databases - BLAST® Command ... free online degree courses+means

BLAST Database error: No alias or index file found for protein database …

WebMay 13, 2024 · BLAST Database error: No alias or index file found for nucleotide database [nr] in search path. Hi, I'm a newbie in bioinformatics. I've tried using blast. … 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 … farm building definition irsWebApr 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: … free online degree in theology

"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. " - Blast database error no alias or index file

Blast database error no alias or index file

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 … 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 …

Did you know?

WebQuestion: BLAST Database error: No alias or index file found for protein database. 0. 2.9 years ago by. christophe.habib • 340. France. christophe.habib • 340 wrote: Hi everyone, … WebIndex 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 ...

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 WebMay 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' …

WebApr 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 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 …

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 …

WebMay 25, 2024 · Hi. I've updated NanoCLUST. The behaviour of --db and --taxdb parameter has changed. Now it is assumed that databases are downloaded inside the NanoCLUST … farm building concrete panelsWebmakeblastdb -in nr -dbtype prot. This is the minimum required information to create the DB, you might want to check additional optional parameters. Running this command will create index files in the directory of your nr db. You don't have to change the blast command you've tried to use, just create the database index before running blast. 0 ... free online degree courses with creditWebDec 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 … farm building conversion ideasWebMar 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. … free online degrees chemistryWebApr 14, 2024 · The timeout happens after ~35 minutes and a file that is approximately 18GB big is being downloaded, which matches the expected filesize. The checksum file (nr.00.tar.gz.md5) is not downloaded. So I'm not sure which of the two files is actually the problem. I tested downloading the nt database and everything seems to work fine, so I … farm building erectors near meWebBLAST 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 free online degrees for military free online degree courses+possibilities