Usearch error - "Sequence too long"

[kga1978]

Hi All,

I am trying to create a usearch udb database of hg19 using the following:

usearch -makeudb hg19.fasta --output hg19.udb -slots 400000009 -w 16 -id 0.90

However, I keep getting this error:

---Fatal error---
Sequence too long (pos=0, bytes=16777216)

Any idea what is going on here? I have tried a couple of other fasta files (bigger than hg19) and also get this error.

[maubp]

Which version of USEARCH are you using? In v5.1 the documentation says:

Splitting large UDB databases no longer required
In version 5.0 of usearch, there was a limit on the maximum size of a UDB index, which required splitting large databases. This restriction is removed in v5.1.

Perhaps you are still using v5.0 and hitting this limit?

[kga1978]

Ya, I though about that as well, but I have version 5.2.32 (64bit), so I don't think that is the problem?

K

[GenoMax]

Are the input files in the "unix" format? Something to check.

[kga1978]

Hi GenoMax,

I am a little unsure what you mean by that? The files are in standard fasta format.

[maubp]

I guess he was saying to check you had Unix new lines rather than DOS/Windows new lines. Worth trying.

The error message itself suggests it is the length of an individual sequence in the FASTA file that is the problem, not the total file size. Have you looked at how long your sequences are - does truncating them make the error go away? That would be a big clue as to the problem.

[kga1978]

Hi maubp,

I'll try out your suggestions - this happened to me using several different fasta files though, so I'm wondering whether something else is going on. Thanks for the suggestions - much appreciated.

[hepcat72]

Same problem

I too am trying to compile an hg19 ublast database and have encountered the same error. I just checked for carriage returns in the hg19.fa file and there are none. Yet I get the error:

---Fatal error---
Sequence too long (pos=0, bytes=16777216, -sfasta_buff_bytes 16777216)

usearch -version
usearch v7.0.1090_i86osx32

I also was getting an error when I used the -alpha parameter that is in the documentation (and is used in an example):

usearch -makeudb_ublast hg19.fa -output hg19.udb -alpha nt 

Invalid command line
Unknown option alpha

Any idea how to make this work?

Thanks,
Rob