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filter.seqs(fasta=Samples.makecontigsfile.trim.contigs.good.unique.good.align, vertical=T, trump=.) Theyve tried with both 80G and 160G memory and after some time it crashes with the following error:
By default, dist.seqs will only count a string of gaps as a single gap and will penalize for terminal gaps Options calc. mothur has several ways of calculating a distance based on how gaps are treated. First, the default option - onegap - only counts a string of gaps as a single gap.
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I made a blastdb using the makeblastdb command using 901 sequences. and I did not notice this at first but the file size for the .ntf and .ndb files was HUGE. Both of these were 300gb size each and it was taking the majority of the remaining space of my poor hard drive. I deleted them and remade the database using -max_file_sz option set to 1GB.
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dist.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.fasta, cutoff=0.20) I omitted some steps (chimera search, undesirables remove) consciously because they are not important for me now. But I am having problems with dist.seqs command - it is just producing several files with size > 40 Gb, until I am out of my hard drive space
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