Missing denovo.vsearch.fasta file

Hello, I put in the command for the chimera to get the denovo.vsearch output file but I am missing the denovo.vsearch fasta file

Hi - you don’t have the denovo.vsearch.fasta file because no sequences were flagged as being chimeras. I find this hard to believe. What do you get for output to the screen when you run summary.seqs on the input fasta and count_table files?


hello Pat, sorry for the late reply. But the data that you saw I have already scraped it and started a new one. But I still have the same issue. I’ll shared the summary.seqs

but my fasta is still missing

  • Iqmal

Hi -

Again, no chimeras are being found and so an updated fasta file is not being returned. The likely no chimeras are being returned is because your sequences at this stage in the pipeline are very short 12-43 nt in length. I suspect the start and end positions you selected earlier for screen.seqs were not the best choice. Can you post the output of running summary.seqs on the input to screen.seqs along with the arguments you used for screen.seqs?


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