Command makeblastdb not found

Author: dsyd

August undefined, 2024

WebTeams. Q&A for work. Connect and share knowledge within a single location that is structured and easy to search. Learn more about Teams WebI have a couple of .fasta files which I want to turn into databases using the makeblastdb program stored in Blast+ 2.4.0 for OS X 10.11. ... thank you for posting. Would I be …

Could not run command: cat, parallel, blastp #252 - GitHub

WebThere are other options for makeblastdb. Here, we are using a yeast reference, in the file Scerevisiae_reference_GCF_000146045_2.fasta. Creating a database is a simple file operation and does not use significant memory or computation, therefore it can be done on a login node; however, do not use a script to create multiple databases simultaneously. WebJun 22, 2024 · Makeblastdb for tblastn; In this step, command line will be written as below to make nucleotide database of all artificially assembled genome. makeblastdb -in input.fas -dbtype nucl -parse_seqids -out input.fas ... Potential pseudogenes will be found in pseudo_target_use_query files. choosing golf clubs for men

makeblastdb -max_file_sz · Issue #63 · …

WebJun 23, 2008 · For example, we can use the following command line to apply the masking information, created above, to the existing BLAST database generated in Obtaining sample data for this cookbook entry: $ … WebApr 11, 2024 · This stuff is tricky. I tried to make Bandage just call which makeblastdb to see where it is, but I fear that Bandage doesn't have access to the same PATH variable as your shell or something. That would be why you can see it with which but Bandage can't.. I'll have to look into this more to come up with a good solution. WebCreate Local BLAST Database. The basic way to create a local BLAST database is to use the makeblastdb command: $ makeblastdb -in input_reads.fasta -dbtype [nucl prot] -out input_reads_db. where input_reads.fasta is the input file containing all sequences that need to be made into a database, and dbtype can be either nucl or prot depending on ... choosing golf clubs

No alias or index file found for nucleotide database BLASTn HELP

makeblastdb: Create BLAST Databases in …

WebNov 27, 2014 · 2 Answers Sorted by: 5 You've listed the folder that the database file is in, not the database itself. Try: blastn -query test/lacI.fasta -db db/swissprot/swissprot.fa (of … WebMay 23, 2024 · Dear @mjcoynejr - sorry for these frustrations. Some thoughts already: can you try running makeblastdb outside of sequenceserver to format the fasta file into a blast database? If it fails, just try running your fasta file through seqtk seq which may clean up some weird characters....; @yeban - i think that we should display the makeblastdb … choosing good or evilWebBy default Magic-BLAST reports unaligned reads, with unmapped bit (4) set in SAM flags or ‘*’ in the second column of the tabular output. If you do not want unmapped reads reported, use -no_unaligned option: magicblast -query reads -db reference … choosing granite

"WebMar 17, 2024 · makeblastdb; or ask your own ... Merging / Concatentating BLAST Databases. Related. 4. What command/invocation is used to generate NCBI 16SMicrobial blastdb. 9. BLAST(n): No hits found. 2. Hits in Primer-BLAST not found with programmatic blastn query. 4. How is BLAST's nr database created? 1. Primer-Blast Custom Database … " - Command makeblastdb not found

Command makeblastdb not found

makeblastdb - Cannot blast database created with …

WebSep 8, 2024 · sh: 1: makeblastdb: not found Database ncbi has not been indexed; formatting now. sh: 1: makeblastdb: not found Database ncbibetalactamase has not been indexed; formatting now. sh: 1: makeblastdb: not found Database plasmidfinder has not been indexed; formatting now. sh: 1: makeblastdb: not found Database resfinder has … WebJan 18, 2024 · Every time I run a script using bash scriptname.sh from the command line in Debian, I get Command Not found and then the result of the script.. The script works …

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WebJun 23, 2008 · For example, we can use the following command line to apply the masking information, created above, to the existing BLAST database generated in Obtaining sample data for this cookbook entry: $ … 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. 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 ...

WebSo by my understanding BLAST should find the local alignment of B in A easily? But the program returns 'No hits found'? Maybe I am doing something wrong here? I executed the following: makeblastdb -in A.fna -dbtype 'nucl' makeblastdb -in B.fna -dbtype 'nucl' blastn -db A.fna -query B.fna output of blastn: WebThe objective of this lab is to get accustomed with performing BLAST searches from the command line (called BLAST+). ... we will say the path (found with pwd) is ~/tools/ncbi …

WebJul 26, 2024 · Kind regards, Natacha From: Ryan Wick [mailto:[email protected]] Sent: donderdag 14 september 2024 3:27 To: rrwick/Unicycler Cc: Monge Gomes do Couto, N (mmb); Author … WebOct 3, 2012 · Building a BLAST database with local sequences has never been this easy. Follow the instructions below and create your own searchable BLAST db in seconds. This is for creating custom database …

WebWhy is this makeblastdb command not working? 2. Hits in Primer-BLAST not found with programmatic blastn query. 2. What kind of BLAST do I need to do to accomplish this task? 2. Timeout when downloading the ncbi nr blast database. 1. How to retrieve fasta sequence after local blast? 1.

WebJul 29, 2024 · Looking at the internal implementation, I ran the command executed by run_command() for makeblastdb: makeblastdb -dbtype prot -in hgtectordb/db.faa -out a -title db -parse_seqids -taxid_map hgtectordb/taxon.map.gz great american nightmareWebThe -parse_seqids option is required to keep the original sequence identifiers. Otherwise makeblastdb will generate its own identifiers, -title is optional. For more information on … choosing golf ironsWebUse the full path and the makeblastdb command: makeblastdb -in human.1.protein.faa -dbtype prot ls. Note that this makes a lot of extra files, with the same name as the … choosing graphics cardWebAug 4, 2024 · Hi Torsten. My apologies for not replying to you earlier. I upgraded my version of parallel to 20240822, and that fixed the problem. Prokka now runs on my system with no issues. Thank you very much for the suggestions regarding annnotation of viral genomes. choosing graphics cardsWebMar 16, 2024 · makeblastdb; or ask your own ... Merging / Concatentating BLAST Databases. Related. 4. What command/invocation is used to generate NCBI … great american northern garageWebJun 9, 2015 · Quoting the command line help: $ makeblastdb -help ... -max_file_sz Maximum file size for BLAST database files Default = `1GB' ... Given the discussion above, it sounds like using a larger value … choosing grass seedWebDec 28, 2024 · So, the command line might be something like this: blastp -db refseq_protein -query amino_acid_100.fa There are a ton more options you may want to use (try blastp -help) , but the above should work. Use the -remote option in blastp to run from the command line against the NCBI server. The below line should perform the BLAST … choosing granite slab