Sff.multiple - problem with oligos file in the last file

mothur bugs
1

Hi,

I tried Sff.multiple command using a list of 25 files, in Mothur v.1.28.0, Linux 64 bit version.

I had a problem with only the last file of the 25, with trim flows:

Running command: trim.flows(flow=H57KI5M03.MID153.flow, oligos=MID_oligos.txtÿ, maxhomop=8, maxflows=450, minflows=300, pdiffs=2, bdiffs=1, ldiffs=0, sdiffs=0, tdiffs=3, signal=0.5, noise=0.7, order=TACG, processors=1)
Unable to open MID_oligos.txtÿ
20000
22418

I figured the ÿ character is an end-of-file indicator, but did I do something wrong, or is it a bug?

2

I think your oligos file needs to be renamed to MID.oligos . Remove the txt extension completely. Then .oligos becomes the extension which is the required format.

Cheers.

3

Mothur was reading the end of file character as part of the oligos file name if there was not a blank line at the end of the file. This issue was fixed in version 1.30.0. You can upgrade to 1.30.0 or add a blank line to correct the issue.

4

Yes, in the meantime I added an extra line and it worked. I did not see it being fixed in the new version, but, then I upgrade! Thank you!

5

Nope, it always worked like this as well. But thank you!

6

Thanks for the heads up. I forgot to add it to the release notes for 1.30.0.