flow order


we’ve done an exploratory IonTorrent run, with several mock communities and controls.
I originally got FASTQ data, but now I’m trying to improve (if possible …) the data by starting from .sff.

When setting flow order to =I, mothur crashes, probably due to a lack of memory. It’s a 22 core server with 64 GB RAM.
This even happens when selecting only 1 sample, and using only 1 processor. (as the latter is suggested in the error message). This does not happen when using order=A (TACG).

Now, looking up the flow order ‘I’, this is a string TACGTACGTCTGAGCATCGATCGATGTACAGC repeated 21 times*.

Why is order=A a single TACG, and order=I a repetition of TACGTACGTCTGAGCATCGATCGATGTACAGC and not just once?
Could this be the cause of the error? Or do I effectively lack RAM?

Thanks in advance

Where is it crashing - trim.flows or shhh.flows? If it’s in shhh.flows then it’s because IonTorrent data are really bad and have a high error rate. This results in a lot of unique sequences and sucks up tons of RAM.


No, trim.flows(), sorry, should have mentioned.

Hmmm… Can you post the sff and oligos files for me somewhere to take a look?