Problem with chimera.uchime command

Hi, everyone
When I use chimera.uchime command as mothur > chimera.uchime (fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta,count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t), there was a warning, which said "Ignoring gaps in FASTA file ’
stability.trim.contigs.good.unique.good.filter.unique.precluster.temp’ . The output file names:stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.count_table
This command often cause my mothur (V 1.36.1, win7-64) crash.
Any suggetions? Thanks!

What does the “crash” message say? The warning about the alignment is nothing to worry about.


Thank you for your reply.
Chimera.uchime command always cause mothur(V 1.36.1 for win7 64bit) shut down by some unknown reason. Even if it done, the output file names are: stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.pick.count_table; stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.chimeras; stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.uchime.accnos. Containg denovo in file names,I think this is not correct. Using those files in classify.seqs and remove.seqs commands, many sequences are classified as unknown sequences. How can I handle it?
Thank you very much!

Are you running out of memory? How big are the files? How much memory do you have? Are you running the command with multiple processors?

Hi Sarah,
Thank you for your reply. When I running through the MiSeq SOP using your sample data, the chimera.uchime command also cause mothur(v 1.36.1–win_64) shunt down with unknown reason in my computer (win7 64bit–RAM 10G). The linux version of mothur (v 1.36.1-cen_64) seems not has this problem.