ReadStdioFile failed fatal error when run -udb2fasta

[hdschwe...@gmail.com]

I am trying to convert my .udb files to fasta files and I keep getting a ReadStdioFile fatal error when I try using usearch -udb2fasta

I run this command: >$ usearch -udb2fasta nmsA_NT.udb -output nmsA_NT.fasta

usearch v10.0.240_i86linux32, 4.0Gb RAM (264Gb total), 48 cores

(C) Copyright 2013-17 Robert C. Edgar, all rights reserved.

http://drive5.com/usearch

License: xxxxxxxx

00:00 3.8Mb   100.0% Rows

00:00 3.8Mb  Reading pointers...done.

00:00 3.8Mb  Reading db seqs...

usearch -udb2fasta nmsA_NT.udb -output nmsA_NT.fasta

---Fatal error---

ReadStdioFile failed, attempted 3294624 bytes, read 7465 bytes, errno=0

[toro...@gmail.com]

Hi!

I am sorry, but this is a forum for vsearch, not usearch. Please see http://www.drive5.com/usearch/ or contact Robert Edgar regarding support for usearch.

It looks like the udb file is smaller than expected, perhaps it is corrupted.

You could always try vsearch instead! :-) It supports the udb2fasta command. You'll find it at https://github.com/torognes/vsearch

- Torbjørn