I am using metastats to look at whether there are any OTUs differentially represented between my samples.
However, when using metastats the analysis appears to start fine, but it does not stop regardless of my grouping design (even if I leave it for 1 week, it is still running…). In my study I have 75 samples total, and these are divided into three groups.
Does anyone know what is wrong? Should I instead use an alternative analysis?
Many thanks for any help or suggestions.
thanks for the reply Pat! (although not sure why I can’t see your reply here any longer).
Updating the version of Mothur to 1.35.1 did help somewhat. Thanks! Using metastats, two out of three comparisons have been made successfully.
However, it does still appear to get stuck and keep running, and does not make the third comparison (I have three types of samples I would like to compare in this group design).
Is there anything else that might be wrong?
Sorry - we had another server glitch that lost the post
Can you send a copy of your shared and design files to firstname.lastname@example.org? Be sure to include a link to this thread.
Ok many thanks, I have sent through the files.
Did anything get resolved for this issue? I am having a similar problem, metastats runs, sometimes it spits out comparison files for 2 of my 3 groups in my design file, sometimes it doesn’t produce anything. I am running it with a .shared file and a .design file (18 samples, 6 samples per ‘group’).
Thanks for reporting this bug. It is an infinite loop that occurs in the fisher exact test included in metastats. I have fixed the bug and the change will be part of our next release coming soon. Feel free to send me an email at email@example.com if you need help processing your files immediately.
I am getting a similar error. I am using mothur v 1.35.1 for using metastats to look what OTUs are differentially represented between my samples.
First it starts running, and then appears this error: segmentation fault (core dumped).
My shared file is about 18,500 Kb, and I used a computer with 8 processors. Is it a problem due to metastats or maybe to a insufficient capacity of the computer?
Many thanks for any help,