classify.seqs problem

Hi, I have two questions:

  1. when I run following command with ksize=10, two files missing ‘10’ is created in the same folder that Silva files are:
    classify.seqs(fasta=s_ecoli.trim.contigs.pick.fasta, reference=/db/bio/bmd/ngs/fan/ref_data/mothur_silva/silva.nr_v123.filter.fasta, taxonomy=/db/bio/bmd/ngs/fan/ref_data/mothur_silva/silva.nr_v123.tax, cutoff=90, ksize=10, processors=10)

silva.nr_v123.silva.nr_v123.filter.:mer.numNonZero, silva.nr_v123.silva.nr_v123.filter.:mer.prob.
They should be like “xxxx.10mer.xxxx”.

  1. If I run several classify.seqs jobs simultaneously, and if they all use the same Silva files, will the .prob and .numNonZeor files be overwritten since each classify.seqs job try to write its one files and the file names are the same?
    Thanks.
  1. when I run following command with ksize=10, two files missing ‘10’ is created in the same folder that Silva files are:
    classify.seqs(fasta=s_ecoli.trim.contigs.pick.fasta, reference=/db/bio/bmd/ngs/fan/ref_data/mothur_silva/silva.nr_v123.filter.fasta, taxonomy=/db/bio/bmd/ngs/fan/ref_data/mothur_silva/silva.nr_v123.tax, cutoff=90, ksize=10, processors=10)
    silva.nr_v123.silva.nr_v123.filter.:mer.numNonZero, silva.nr_v123.silva.nr_v123.filter.:mer.prob.
    They should be like “xxxx.10mer.xxxx”.

Why are you using ksize=10? I suspect we never foresaw anyone wanting to use such a kmer size. We normally find that 7 or 8 provide the best classification and that larger kmer sizes suck up more RAM and are considerably slower.

  1. If I run several classify.seqs jobs simultaneously, and if they all use the same Silva files, will the .prob and .numNonZeor files be overwritten since each classify.seqs job try to write its one files and the file names are the same?

That’s correct. You would have to run the commands in series or in separate folders.

Also, you seem to frequently post the same questions in multiple posts. Please stop doing this and only put up a single post with related questions. What you are doing makes it very hard for us to manage the forum.