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Error with makeblastdb from UniProt fasta file: no sequences were found

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  • Error with makeblastdb from UniProt fasta file: no sequences were found

    Hello there

    I am trying to create a custom database for BLAST to run a local BLAST with some of my own proetin sequences.

    First, I searched for sequences from IDs in UniProt Retrieve/ID mapping tool. Then, I downloaded the output in FASTA (canonical) format.

    With this file, I tried to run 'makblastdb' on BLAST 2.8.1+ standalone executable through command line in Windows 10 (ftp version I downloaded is named after 'Windows 7'):

    Code:
     makeblastdb -in prots.fasta -parse_seqids -blastdb_version 5 -dbtype prot -out prots
    and I always get the same error:

    Code:
    No volumes were created because no sequences were found
    I have tried several modifications on the command line, such as not using '-parse_seqids' or including/excluding '-out' option. Similarly, I have tried several modifications on my FASTA file, such as changing '|' to a lower bar or eliminating spaces (entering a lower bar instead, again) or reducing ID length... and I always got the same error.

    What is intriguing me is that the command worked if I only used as input a FASTA file with only one sequence, although I only got two output files, i.e. '.pdb' and '.pdb-lock' files.

    Any idea on what is going wrong? How can it be possible to have the problem with more than one sequences in the file but not with only one?

    I have searched many different forums and I did not find anything similar...

    Thanks a lot
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