Blast database error no alias or index file

Author: ccoy

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 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 …

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

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. 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. othello frantic assembly music

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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: 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 … WebI 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 ... othello fredericia

Use blastdb_aliastool to manage the BLAST databases

Cannot blast database created with blastdb_aliastool: …

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: … 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 … rocket ship birthday partyWebJan 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 … rocket ship bed plans

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

Blast database error no alias or index file

BLAST Database error · Issue #321 · sanger-pathogens/Roary

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. …

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WebApr 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 … 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 …

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' … 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

Webmakeblastdb -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 ... 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.

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 …

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 … rocket ship birthdayWebIndex 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 ... rocketship bell scheduleWebJun 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 … othello frantic assembly trailerWebblast 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? othello free bookWebQuestion: 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, … rocket ship black and white imageWebJan 7, 2024 · Use blastdb_aliastool to manage the BLAST databases - BLAST® Command ... othello free online board gameWebMar 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 … rocketship big rock candy mountain