lastdb: bad symbol error

[shearn...@gmail.com]

Hello,

I'd like to align some Lemur scaffolds using the human X chromosome as a reference:
http://www.ncbi.nlm.nih.gov/nuccore/NC_000023.11

So I tried preparing the reference with:
lastdb -m1111110 humandb humanChrX.fasta

which failed (no output files) and the following error was returned:
lastdb: bad symbol: -

However, there are no '-' in the fasta file. I haven't been able to find any explanation of this error in the documentation or on google. lastdb works fine on the example files/tutorials.

Any help would be much appreciated,

Ry

[shearn...@gmail.com]

Edit: I just tried downloading the chromosome again, now it seems to work so perhaps there was something wrong with the file I previously downloaded.

Still curious about this error since there weren't any '-' in the file...

[FrithMartin]

Hello Ry,

I'm glad it's working for you now, but I fear I can't answer why it didn't work the first time. It works for me. That error message should only appear if there is a '-' in the sequence. If you can give me an input file that triggers the problem, I'll investigate.

Have a nice day,
Martin Frith

________________________________________
From: last-...@googlegroups.com <last-...@googlegroups.com> on behalf of shearn...@gmail.com <shearn...@gmail.com>
Sent: Thursday, July 23, 2015 10:48 PM
To: last-align
Cc: shearn...@gmail.com
Subject: [last-align] Re: lastdb: bad symbol error

Edit: I just tried downloading the chromosome again, now it seems to work so perhaps there was something wrong with the file I previously downloaded.

Still curious about this error since there weren't any '-' in the file...

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[shearn...@gmail.com]

Hi Martin,

It seems this has been a problem with both the sequence file, and the software I'm using to search it. I've been looking at the problematic file with seaview, and using the search dialogue with query '-' but it does not return with anything. However I did manually scroll through to the end and saw a single '-' at the very end of the sequence file. Not really sure why this wasn't found in the search... but the problem definitely isn't with lastdb

The file can be downloaded here for a few days if you are interested in having a look:
https://www.dropbox.com/s/eswe7opi4w7o7ib/humanChrX.fasta?dl=0

Maybe you could suggest another way of searching for the '-' for next time?

Cheers,
Ry