sff file size limit in Newbler?

[lmilne]

I have tried using runAssembly on the sff files I received from the sequencing guys, but for one file I get an error message:

$ runAssembly -o newbler_191009 -ace -m -large ./WRM.sff
newbler_191009 is now ready for assembly
Error: Read file/run not found: ./WRM.sff
Error in runAssembly: Unable to launch addRun, or error running addRun.

It accepts the other files. The problematic sff file is much larger than the others (2.3Gb). Is there a file size limit with this version of the Newbler software (v 1.1.03.23) ?

I could run it with the fasta/qual file, but sff would be nicer.

[maubp]

I don't know that it matters, but isn't Newbler already on 2.00.01.xx by now?

Are you sure (from the error message) that this isn't just a path issue?

[lmilne]

Yes, I've been trying to get the latest version, but no reply from the 454 support guys as yet.

There shouldn't be a path issue as all four files are in the cwd, but only this file creates this error message.

[maubp]

Can you make sure the other Roche tools can read your big SFF file? e.g. sffinfo and sfffile should be able to read it. If they can't, it suggests a corrupt SFF file (or a Roche bug). If they can, it narrows things down to a problem in runAssembly.

[flxlex]

Is your WRM.sff file from a titanium run? I am not certain newbler 1.1.03 will be able to use Titanium reads...

[lmilne]

Ah, I tried using sffinfo and it does:

$ sffinfo WRM.sff
Error: Unable to open SFF file: WRM.sff

The other 3 files were ok for sffinfo. It must be corrupt. I will contact the lab.

Thanks for all your help guys!

[lmilne]

I wanted to add that using a newer version of Newbler (v2.0.01.14), runAssembly can read this problem file ok.

[maubp]

Cool - good guess flxlex