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Error message in Standalone BLAST

I was trying to make a nucleotide database for standalone blast. but this message keeps coming. Any suggestion to overcome this problem?

BLAST Database error: No alias or index file found for nucleotide database [C:\Program] in search path [C:\Program Files\NCBI\blast-BLAST_VERSION+\bin;;]
windows commandprompt standaloneblast ncbi blast
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updated by xiaoleiusc xiaoleiusc • written by noobiestar • noobiestar

This was my command

makeblastdb -in ABCScaffolds.fasta -dbtype nucl -out ABCScaffolds

After the below runtime command, I got the mentioned error message

Building a new DB, current time: 04/05/2022 15:38:56
New DB name:   C:\Program Files\NCBI\blast-BLAST_VERSION+\bin\ABCScaffolds
New DB title:  ABCScaffolds.fasta
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 604 sequences in 0.254797 seconds.
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updated by lieven.sterck lieven.sterck • written by noobiestar • noobiestar

1 answer

Few things :

it's good practise to not put your blastDBs in the binary folder of blast , so specify an output path as well in the -out parameter (or don't call the makeblastdb command from within your binary folder)

the no alias found error can only appear when you actually run the blast search, what is the command you used for that? (the cmdline you provided is to format a fasta file as blast database)

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written by lieven.sterck lieven.sterck

I have the same problem, I did not actually run the blast search, I just run "makeblastdb" makeblastdb -in test3.fasta -input_type fasta -dbtype nucl -out Data_test3 and got the error BLAST Database error: No alias or index file found for nucleotide database [/Users/xiaolei/Downloads/Peng] in search path [/Users/xiaolei/Downloads/Peng Zhang/BPHunter_fastq2BP_test::]

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written by xiaoleiusc xiaoleiusc

are the data input files accessible from the path where you execute the blast cmd? (and the fasta file is a nucleotide sequences one?)

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written by lieven.sterck lieven.sterck

Yes. I downloaded the most recent version of blastn, deleted the old output files generated with the previous version of makeblastdb (from another person), and tried again, it worked. Thanks.

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written by xiaoleiusc xiaoleiusc

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