I got lots of OTUs just having 1 tag only after using cluster.split, which impact my subsequent analysis seriously. I want to use filter.shared command to remove these size 1 OTUs from my shared file. However, I got Segmentation fault (core dumped) error when I deal with my data, which will not appear with 454SOP data.
mothur > filter.shared(shared=fileList.paired.trim.contigs.good.unique.good.good.filter.unique.precluster.pick.pick.an.unique_list.shared, mintotal=2, makerare=F)
Segmentation fault (core dumped)
I have tried this work in the last version of mothur, the problem still existed.
My shared file is big (151071518) compared with shared file in 454SOP. I don’t know if this situation is correlated with my problem.
And I also want to know any other way to deal with my shared file.
All suggestions are welcomed! I need your help!